From 730cb6b7b6c0eedf8857f2c154afad1862fb4985 Mon Sep 17 00:00:00 2001 From: Tim Sears Date: Mon, 16 Mar 2020 13:26:35 -0700 Subject: [PATCH] bioconductor packages: 3.8 -> 3.10, update R packages, other fixes --- .../development/libraries/bwidget/default.nix | 2 +- .../r-modules/bioc-annotation-packages.nix | 358 +- .../r-modules/bioc-experiment-packages.nix | 744 ++-- pkgs/development/r-modules/bioc-packages.nix | 3447 +++++++++-------- .../r-modules/bioc-workflows-packages.nix | 36 + pkgs/development/r-modules/build_packages.sh | 27 + pkgs/development/r-modules/default.nix | 1001 ++--- .../r-modules/generate-r-packages.R | 14 +- .../development/r-modules/generic-builder.nix | 1 + pkgs/development/r-modules/get_names.sh | 4 + .../r-modules/patches/EMCluster.patch | 6 - .../r-modules/patches/RAppArmor.patch | 20 - .../r-modules/patches/Rhdf5lib.patch | 15 +- pkgs/development/r-modules/patches/spMC.patch | 8 - .../r-modules/sample-devenv-shell.nix | 517 +++ .../development/r-modules/test-evaluation.nix | 437 ++- pkgs/tools/misc/xvfb-run/default.nix | 3 +- .../misc/xvfb-run/patches/xvfb-run.patch | 30 + 18 files changed, 3965 insertions(+), 2705 deletions(-) create mode 100644 pkgs/development/r-modules/bioc-workflows-packages.nix create mode 100755 pkgs/development/r-modules/build_packages.sh create mode 100755 pkgs/development/r-modules/get_names.sh delete mode 100644 pkgs/development/r-modules/patches/EMCluster.patch delete mode 100644 pkgs/development/r-modules/patches/RAppArmor.patch delete mode 100644 pkgs/development/r-modules/patches/spMC.patch create mode 100644 pkgs/development/r-modules/sample-devenv-shell.nix create mode 100644 pkgs/tools/misc/xvfb-run/patches/xvfb-run.patch diff --git a/pkgs/development/libraries/bwidget/default.nix b/pkgs/development/libraries/bwidget/default.nix index 154b8634551b3..ff9e6aa038f51 100644 --- a/pkgs/development/libraries/bwidget/default.nix +++ b/pkgs/development/libraries/bwidget/default.nix @@ -6,7 +6,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "mirror://sourceforge/tcllib/bwidget-${version}.tar.gz"; - sha256 = "0knlnpmwam74v0qa1h9gg4f32vzzz7ays2wbslflf51ilg7nw6jk"; + sha256 = "0wm6hk3rnqhnn2cyw24drqwbfnysp6jyfi8lc1vih5k704a955lf"; }; dontBuild = true; diff --git a/pkgs/development/r-modules/bioc-annotation-packages.nix b/pkgs/development/r-modules/bioc-annotation-packages.nix index 863d7c9fcfe04..62acd746f801d 100644 --- a/pkgs/development/r-modules/bioc-annotation-packages.nix +++ b/pkgs/development/r-modules/bioc-annotation-packages.nix @@ -4,10 +4,10 @@ # Rscript generate-r-packages.R bioc-annotation >new && mv new bioc-annotation-packages.nix { self, derive }: -let derive2 = derive { biocVersion = "3.8"; }; +let derive2 = derive { biocVersion = "3.10"; }; in with self; { AHCytoBands = derive2 { name="AHCytoBands"; version="0.99.0"; sha256="0g92nz33rx14zl5can7s701bipdgz7rxqygvvc22c4a0qj52ijnq"; depends=[]; }; - AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.0.8"; sha256="1v1177l4y0l546mzp8ybhvhnjwrsck5bkic8w6n6n2xq07d6aahz"; depends=[AnnotationHubData ensembldb]; }; + AHEnsDbs = derive2 { name="AHEnsDbs"; version="1.0.13"; sha256="0nfjhzji6v5kvg5qafffr5xbd9qc8gyyzc91c0hkgvrvw3784q4y"; depends=[AnnotationHubData ensembldb]; }; BSgenome_Alyrata_JGI_v1 = derive2 { name="BSgenome.Alyrata.JGI.v1"; version="1.0.0"; sha256="06549kkzy36n378zb61lrf9zardncp7i20r73rmmiq1pnfjp3gww"; depends=[BSgenome]; }; BSgenome_Amellifera_BeeBase_assembly4 = derive2 { name="BSgenome.Amellifera.BeeBase.assembly4"; version="1.4.0"; sha256="02zs16q441zcbfp7xvv1gny5nn02ivfr8md1wh5s5rpnj6sdl6kj"; depends=[BSgenome]; }; BSgenome_Amellifera_UCSC_apiMel2 = derive2 { name="BSgenome.Amellifera.UCSC.apiMel2"; version="1.4.0"; sha256="1967w7aly7qydykk7rar712kvgsav3zjr4kirybkj17nwiynd74g"; depends=[BSgenome]; }; @@ -22,6 +22,7 @@ in with self; { BSgenome_Btaurus_UCSC_bosTau6 = derive2 { name="BSgenome.Btaurus.UCSC.bosTau6"; version="1.4.0"; sha256="0waaf9wfmdl5jbi3la64vsiqb83lyw9fqg3sn90bf1q7k3k617p3"; depends=[BSgenome]; }; BSgenome_Btaurus_UCSC_bosTau6_masked = derive2 { name="BSgenome.Btaurus.UCSC.bosTau6.masked"; version="1.3.99"; sha256="07isv0lcvlsl0aha1p474l0pps0j7bsh455m33vfxwahivqsfy27"; depends=[BSgenome BSgenome_Btaurus_UCSC_bosTau6]; }; BSgenome_Btaurus_UCSC_bosTau8 = derive2 { name="BSgenome.Btaurus.UCSC.bosTau8"; version="1.4.2"; sha256="16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"; depends=[BSgenome]; }; + BSgenome_Btaurus_UCSC_bosTau9 = derive2 { name="BSgenome.Btaurus.UCSC.bosTau9"; version="1.4.3"; sha256="108s504l8bcifi544wnvfn2x0za367k04dx8xhc4rjkdmwdj1yfj"; depends=[BSgenome]; }; BSgenome_Carietinum_NCBI_v1 = derive2 { name="BSgenome.Carietinum.NCBI.v1"; version="1.0.0"; sha256="1asyyb1p1bzc7dv9s2igjxrf9f144vvz2xbv9qxg15w9qzzx7r33"; depends=[BSgenome]; }; BSgenome_Celegans_UCSC_ce10 = derive2 { name="BSgenome.Celegans.UCSC.ce10"; version="1.4.0"; sha256="1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"; depends=[BSgenome]; }; BSgenome_Celegans_UCSC_ce11 = derive2 { name="BSgenome.Celegans.UCSC.ce11"; version="1.4.2"; sha256="0d4bxfglpqiv1f0n6imdgz101g9383hfj3ra91268wryzlm0yk5w"; depends=[BSgenome]; }; @@ -31,12 +32,14 @@ in with self; { BSgenome_Cfamiliaris_UCSC_canFam2_masked = derive2 { name="BSgenome.Cfamiliaris.UCSC.canFam2.masked"; version="1.3.99"; sha256="14108j73z7959d070xiqar5s14pac18cs8a22lcggbmp5x93hmqz"; depends=[BSgenome BSgenome_Cfamiliaris_UCSC_canFam2]; }; BSgenome_Cfamiliaris_UCSC_canFam3 = derive2 { name="BSgenome.Cfamiliaris.UCSC.canFam3"; version="1.4.0"; sha256="1ir092yh1h03ag1lnj2rh5hjp2mqrw7fcyb6mqyjm0h8g1pmpicr"; depends=[BSgenome]; }; BSgenome_Cfamiliaris_UCSC_canFam3_masked = derive2 { name="BSgenome.Cfamiliaris.UCSC.canFam3.masked"; version="1.3.99"; sha256="07y28g6b4sbp38yg5rwldda7s1cwcpil6rzsb4csskvs0xi5286l"; depends=[BSgenome BSgenome_Cfamiliaris_UCSC_canFam3]; }; + BSgenome_Cjacchus_UCSC_calJac3 = derive2 { name="BSgenome.Cjacchus.UCSC.calJac3"; version="1.4.2"; sha256="1s1srg6lr3dndbpv83bqlxz5lhyhxh431yrd919yl4fwmr5rvx0z"; depends=[BSgenome]; }; BSgenome_Dmelanogaster_UCSC_dm2 = derive2 { name="BSgenome.Dmelanogaster.UCSC.dm2"; version="1.4.0"; sha256="1vnqbm1123zmpn1iwyygr1p4js0j6vifyz7iwzgkiw543yb1mwnl"; depends=[BSgenome]; }; BSgenome_Dmelanogaster_UCSC_dm2_masked = derive2 { name="BSgenome.Dmelanogaster.UCSC.dm2.masked"; version="1.3.99"; sha256="1qclf62c3qrdhnrb6p4rhj7wrarlsbm716d37k0gbdzkfm2vhyr7"; depends=[BSgenome BSgenome_Dmelanogaster_UCSC_dm2]; }; BSgenome_Dmelanogaster_UCSC_dm3 = derive2 { name="BSgenome.Dmelanogaster.UCSC.dm3"; version="1.4.0"; sha256="19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"; depends=[BSgenome]; }; BSgenome_Dmelanogaster_UCSC_dm3_masked = derive2 { name="BSgenome.Dmelanogaster.UCSC.dm3.masked"; version="1.3.99"; sha256="1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"; depends=[BSgenome BSgenome_Dmelanogaster_UCSC_dm3]; }; BSgenome_Dmelanogaster_UCSC_dm6 = derive2 { name="BSgenome.Dmelanogaster.UCSC.dm6"; version="1.4.1"; sha256="1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"; depends=[BSgenome]; }; BSgenome_Drerio_UCSC_danRer10 = derive2 { name="BSgenome.Drerio.UCSC.danRer10"; version="1.4.2"; sha256="1grlxihdx65fwgb9gbp1jibbqan9a5667w4jgswhg0qsia608lzs"; depends=[BSgenome]; }; + BSgenome_Drerio_UCSC_danRer11 = derive2 { name="BSgenome.Drerio.UCSC.danRer11"; version="1.4.3"; sha256="0gam2ffjqins14z8asyxg2zhwqasp3gklrwl7n73x9d3x5i46896"; depends=[BSgenome]; }; BSgenome_Drerio_UCSC_danRer5 = derive2 { name="BSgenome.Drerio.UCSC.danRer5"; version="1.4.0"; sha256="1mxmy4ika192xvlrsynyvnb7kvcvbsl89g39q53vrkibhml1q0v5"; depends=[BSgenome]; }; BSgenome_Drerio_UCSC_danRer5_masked = derive2 { name="BSgenome.Drerio.UCSC.danRer5.masked"; version="1.3.99"; sha256="03y08jlknb52x37wg95xaf62n5fbsfpmx57bjyxz2gj0n8zhcdgv"; depends=[BSgenome BSgenome_Drerio_UCSC_danRer5]; }; BSgenome_Drerio_UCSC_danRer6 = derive2 { name="BSgenome.Drerio.UCSC.danRer6"; version="1.4.0"; sha256="0h2chcpdi2vy29fg43r6q37vvb7p4d4cpnszlsmiy7ax358sd5ji"; depends=[BSgenome]; }; @@ -51,6 +54,7 @@ in with self; { BSgenome_Ggallus_UCSC_galGal4 = derive2 { name="BSgenome.Ggallus.UCSC.galGal4"; version="1.4.0"; sha256="1qfl046akdf43azigprc13sssgbmxdz9dmlrvy13ag8fgfkjxign"; depends=[BSgenome]; }; BSgenome_Ggallus_UCSC_galGal4_masked = derive2 { name="BSgenome.Ggallus.UCSC.galGal4.masked"; version="1.3.99"; sha256="0fvqimjf1xvgka4nw66nd0rbyb7r93v8cyw33776lhfv68ny058v"; depends=[BSgenome BSgenome_Ggallus_UCSC_galGal4]; }; BSgenome_Ggallus_UCSC_galGal5 = derive2 { name="BSgenome.Ggallus.UCSC.galGal5"; version="1.4.2"; sha256="0gi82xr2b3fn3wi608nmqp3cgjx63rm82wy24p9l0s1qqh2z3jdb"; depends=[BSgenome]; }; + BSgenome_Ggallus_UCSC_galGal6 = derive2 { name="BSgenome.Ggallus.UCSC.galGal6"; version="1.4.3"; sha256="13da9fprwhi0aknrl41s7j48b2ipj8r6n110k3rywswmbwz090n5"; depends=[BSgenome]; }; BSgenome_Hsapiens_1000genomes_hs37d5 = derive2 { name="BSgenome.Hsapiens.1000genomes.hs37d5"; version="0.99.1"; sha256="1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"; depends=[BSgenome]; }; BSgenome_Hsapiens_NCBI_GRCh38 = derive2 { name="BSgenome.Hsapiens.NCBI.GRCh38"; version="1.3.1000"; sha256="0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"; depends=[BSgenome]; }; BSgenome_Hsapiens_UCSC_hg17 = derive2 { name="BSgenome.Hsapiens.UCSC.hg17"; version="1.3.1000"; sha256="1q8p0zp5xpp22znwnygl3jhc159db4q3kkpj5wfij5a6z19zs1w3"; depends=[BSgenome]; }; @@ -61,8 +65,10 @@ in with self; { BSgenome_Hsapiens_UCSC_hg19_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg19.masked"; version="1.3.99"; sha256="0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg19]; }; BSgenome_Hsapiens_UCSC_hg38 = derive2 { name="BSgenome.Hsapiens.UCSC.hg38"; version="1.4.1"; sha256="1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"; depends=[BSgenome]; }; BSgenome_Hsapiens_UCSC_hg38_masked = derive2 { name="BSgenome.Hsapiens.UCSC.hg38.masked"; version="1.3.99"; sha256="0plfrhkwgpgp22mj5n704k4ml0vl6hs5wb5vzqnw3vr8qwv0bli1"; depends=[BSgenome BSgenome_Hsapiens_UCSC_hg38]; }; + BSgenome_Mdomestica_UCSC_monDom5 = derive2 { name="BSgenome.Mdomestica.UCSC.monDom5"; version="1.4.2"; sha256="16kzb66kjpmf9j92pwh98ah5rhrnfyzdpr0rk659zham6dzga9ck"; depends=[BSgenome]; }; BSgenome_Mfascicularis_NCBI_5_0 = derive2 { name="BSgenome.Mfascicularis.NCBI.5.0"; version="1.4.2"; sha256="1lrdj7aibx4i60hpbaqgk3qir9zjs67mxdgp5jmgmw7gf2nwyn3x"; depends=[BSgenome]; }; BSgenome_Mfuro_UCSC_musFur1 = derive2 { name="BSgenome.Mfuro.UCSC.musFur1"; version="1.4.1"; sha256="0c0569a1k36sk0vzf7afhnfm0n2nwcdp3dc88s1hghpg7lwi9g9j"; depends=[BSgenome]; }; + BSgenome_Mmulatta_UCSC_rheMac10 = derive2 { name="BSgenome.Mmulatta.UCSC.rheMac10"; version="1.4.3"; sha256="0y5khxwf8wzvfwpdv1dvd799v820jxxyhrryi79la66gm7dsd9s4"; depends=[BSgenome]; }; BSgenome_Mmulatta_UCSC_rheMac2 = derive2 { name="BSgenome.Mmulatta.UCSC.rheMac2"; version="1.4.0"; sha256="15vswd1fq7a7g1dkm0wzkmclih8z373nfzjyc3zrn9l0nawdv9jj"; depends=[BSgenome]; }; BSgenome_Mmulatta_UCSC_rheMac2_masked = derive2 { name="BSgenome.Mmulatta.UCSC.rheMac2.masked"; version="1.3.99"; sha256="1j4z4iy13n4qbi9a50qw1hn8z14xz0z8hbiwhy2bb9znykkf4chd"; depends=[BSgenome BSgenome_Mmulatta_UCSC_rheMac2]; }; BSgenome_Mmulatta_UCSC_rheMac3 = derive2 { name="BSgenome.Mmulatta.UCSC.rheMac3"; version="1.4.0"; sha256="0r3v4p567rxcczwqi7zdz7pmdiffgrq83j488libdb4s0hdg5jmi"; depends=[BSgenome]; }; @@ -99,8 +105,9 @@ in with self; { BSgenome_Vvinifera_URGI_IGGP12Xv0 = derive2 { name="BSgenome.Vvinifera.URGI.IGGP12Xv0"; version="0.1"; sha256="1m8mqkiqs7291hccb8pfyf2yxpky45qr6j3d9wkvp9x3ra3h0yxf"; depends=[BSgenome]; }; BSgenome_Vvinifera_URGI_IGGP12Xv2 = derive2 { name="BSgenome.Vvinifera.URGI.IGGP12Xv2"; version="0.1"; sha256="1saavsi75gw33jphhm3qb5psyfrv850ss4cmqr4i7aw1kc0fvs1j"; depends=[BSgenome]; }; BSgenome_Vvinifera_URGI_IGGP8X = derive2 { name="BSgenome.Vvinifera.URGI.IGGP8X"; version="0.1"; sha256="0v0hi2pbbi5ynd92bvbv4bzr7bgv48kvyz62hdv7k9gh7s5pg0id"; depends=[BSgenome]; }; - ChemmineDrugs = derive2 { name="ChemmineDrugs"; version="1.0.0"; sha256="0h4jxcb6vkf9ijljas7yvcx6vmrd5rpjgj202cf2jb9hx8h9497i"; depends=[BiocGenerics ChemmineR RSQLite]; }; + ChemmineDrugs = derive2 { name="ChemmineDrugs"; version="1.0.2"; sha256="0l47ac6lkycmghra2cbcdcxcv47ari8xg6lxpzilvkf4n6ld6064"; depends=[BiocGenerics ChemmineR RSQLite]; }; DO_db = derive2 { name="DO.db"; version="2.9"; sha256="10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"; depends=[AnnotationDbi]; }; + ENCODExplorerData = derive2 { name="ENCODExplorerData"; version="0.99.4"; sha256="05fyb1ya21hip7bsb4h99ghbk5i7m58998n151p17kl6vrjhcksw"; depends=[data_table jsonlite RCurl tidyr]; }; EnsDb_Hsapiens_v75 = derive2 { name="EnsDb.Hsapiens.v75"; version="2.99.0"; sha256="0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"; depends=[ensembldb]; }; EnsDb_Hsapiens_v79 = derive2 { name="EnsDb.Hsapiens.v79"; version="2.99.0"; sha256="0k94iml0417m3k086d0bzd83fndyb2kn7pimsfzcdmafgy6sxwgg"; depends=[ensembldb]; }; EnsDb_Hsapiens_v86 = derive2 { name="EnsDb.Hsapiens.v86"; version="2.99.0"; sha256="1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"; depends=[ensembldb]; }; @@ -108,7 +115,7 @@ in with self; { EnsDb_Mmusculus_v79 = derive2 { name="EnsDb.Mmusculus.v79"; version="2.99.0"; sha256="1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7"; depends=[ensembldb]; }; EnsDb_Rnorvegicus_v75 = derive2 { name="EnsDb.Rnorvegicus.v75"; version="2.99.0"; sha256="02sx9l1p67ihkn0dfzbi08cpp8x4k2mjdqn7hvzfiaibsbqp70bb"; depends=[ensembldb]; }; EnsDb_Rnorvegicus_v79 = derive2 { name="EnsDb.Rnorvegicus.v79"; version="2.99.0"; sha256="1ki2hrn0a55f3ipxny0hpgl5ld9pjkhcwmvvqwwd99f3sqbxf3br"; depends=[ensembldb]; }; - EuPathDB = derive2 { name="EuPathDB"; version="1.0.0"; sha256="08yl7zx5j6ywnrdcrrsvfkkxnvhrhrcddxw0g5sv90gy55zgv86n"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDbData GenomicRanges]; }; + EuPathDB = derive2 { name="EuPathDB"; version="1.0.1"; sha256="0k23f34hnvcf2ig9sic7gf7pypc2jmwymg605qym7x32bjhi6rlm"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDbData GenomicRanges]; }; FDb_FANTOM4_promoters_hg19 = derive2 { name="FDb.FANTOM4.promoters.hg19"; version="1.0.0"; sha256="04sn5x1r5fcbghzw6n1bvy0z8zyhrbk86wsqz1p5gk665vicz8rw"; depends=[AnnotationDbi Biostrings GenomicFeatures]; }; FDb_InfiniumMethylation_hg18 = derive2 { name="FDb.InfiniumMethylation.hg18"; version="2.2.0"; sha256="0vwzqzj49imjdsn8ssiwqi7qic7rqw5pbsiinyxgy7y10fn2i42a"; depends=[AnnotationDbi Biostrings GenomicFeatures org_Hs_eg_db TxDb_Hsapiens_UCSC_hg18_knownGene]; }; FDb_InfiniumMethylation_hg19 = derive2 { name="FDb.InfiniumMethylation.hg19"; version="2.2.0"; sha256="0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"; depends=[AnnotationDbi Biostrings GenomicFeatures org_Hs_eg_db TxDb_Hsapiens_UCSC_hg19_knownGene]; }; @@ -116,8 +123,9 @@ in with self; { FDb_UCSC_snp137common_hg19 = derive2 { name="FDb.UCSC.snp137common.hg19"; version="1.0.0"; sha256="1q1r7rk29q0zlzxz6fvfy1kjfli6wxzvhvhhfnf3z4ksy5332q63"; depends=[AnnotationDbi GenomicFeatures]; }; FDb_UCSC_tRNAs = derive2 { name="FDb.UCSC.tRNAs"; version="1.0.1"; sha256="1dymdalx9fzrplxyc0fd9faa4r5jimi7zyry9k65lyz1pabpkwqz"; depends=[AnnotationDbi GenomicFeatures]; }; GGHumanMethCancerPanelv1_db = derive2 { name="GGHumanMethCancerPanelv1.db"; version="1.4.1"; sha256="0ag1pkbh4mx4aplfrrz1q4f4cl05mczq9pcsfkd1071qk51dcwvx"; depends=[AnnotationDbi AnnotationForge org_Hs_eg_db]; }; - GO_db = derive2 { name="GO.db"; version="3.7.0"; sha256="0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"; depends=[AnnotationDbi]; }; - GenomeInfoDbData = derive2 { name="GenomeInfoDbData"; version="1.2.0"; sha256="0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"; depends=[]; }; + GO_db = derive2 { name="GO.db"; version="3.10.0"; sha256="17vwn9hibb6qb78sy8r3b9ngkj0nxzxkzi61ffa9mwp1f2nv5vr4"; depends=[AnnotationDbi]; }; + GenomeInfoDbData = derive2 { name="GenomeInfoDbData"; version="1.2.2"; sha256="04gp9a1yf55xqg5cwcc0s896a7j91hvydbnjlr8300wzsxlcjlv8"; depends=[]; }; + GenomicState = derive2 { name="GenomicState"; version="0.99.9"; sha256="0qpa77bsycm3y82jrxq7r27gsygb1qbhkakz3cln3jv3sfkf0aj7"; depends=[AnnotationDbi AnnotationHub bumphunter derfinder GenomeInfoDb GenomicFeatures IRanges org_Hs_eg_db rtracklayer]; }; Homo_sapiens = derive2 { name="Homo.sapiens"; version="1.3.1"; sha256="151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"; depends=[AnnotationDbi GenomicFeatures GO_db org_Hs_eg_db OrganismDbi TxDb_Hsapiens_UCSC_hg19_knownGene]; }; Hs6UG171_db = derive2 { name="Hs6UG171.db"; version="3.2.3"; sha256="034aady3hy8j9bm7pbl8l8h0gcfnzmpyxg9l9s1ky0pj7ryzr93a"; depends=[AnnotationDbi org_Hs_eg_db]; }; HsAgilentDesign026652_db = derive2 { name="HsAgilentDesign026652.db"; version="3.2.3"; sha256="0x6nxvzmc8k4qp382ca32y58awkxpg0b3kc7m1mz9iag6sq7c5vx"; depends=[AnnotationDbi org_Hs_eg_db]; }; @@ -140,115 +148,114 @@ in with self; { JazaeriMetaData_db = derive2 { name="JazaeriMetaData.db"; version="3.2.3"; sha256="04lvcmm4ybxkfwgbiwcnpyj6kpbd0gd7jz6ijlbbvv6zdgdmvykb"; depends=[AnnotationDbi org_Hs_eg_db]; }; KEGG_db = derive2 { name="KEGG.db"; version="3.2.3"; sha256="0qv9in1nmnqcbjxh0y45x33xyw9zdp4jf5hmlvcsh1pclcq4dsh2"; depends=[AnnotationDbi]; }; LAPOINTE_db = derive2 { name="LAPOINTE.db"; version="3.2.3"; sha256="0960gy5p4ybs5zs6251cgc3nk5a9gsh1nh23gkbkr3gc8jddinfm"; depends=[AnnotationDbi org_Hs_eg_db]; }; - LRBase_Ath_eg_db = derive2 { name="LRBase.Ath.eg.db"; version="0.99.1"; sha256="0v7zyp6mngdfrqgx0fb6lj0ara7q4ch2dahnwqjk5y9psmvi8m16"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Bta_eg_db = derive2 { name="LRBase.Bta.eg.db"; version="0.99.1"; sha256="14yl5d4vmm2hjrlxsflwvkw18j0kcz364b3mc3fnxzbk8phisy3l"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Cel_eg_db = derive2 { name="LRBase.Cel.eg.db"; version="0.99.1"; sha256="18w8ay874qjs4qgb3g1j77k2fspvvvbyy3p85wgzy1yl839ngy3b"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Dme_eg_db = derive2 { name="LRBase.Dme.eg.db"; version="0.99.1"; sha256="0qbc5942g57mjdlhqpnapwq58bmi5xbc0mrqbqkfbxpx881ka2v6"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Dre_eg_db = derive2 { name="LRBase.Dre.eg.db"; version="0.99.1"; sha256="0wpx9dg2nhw20f3vvmaqy5yip8xwg1niswspxs4jv9krd0z6h5d8"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Gga_eg_db = derive2 { name="LRBase.Gga.eg.db"; version="0.99.1"; sha256="0nycj3h69ca2gxxmc08zvf0jv5zylfayhd6sgzrmqz0zsr0n5fxk"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Hsa_eg_db = derive2 { name="LRBase.Hsa.eg.db"; version="0.99.1"; sha256="0g690d63sp5pb0i28zvi80y41n6b31mzza46invjvq9c1j2rijzd"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Mmu_eg_db = derive2 { name="LRBase.Mmu.eg.db"; version="0.99.1"; sha256="0kmd69a31hw8i2p8qg64m074ypa102cfa7qpyz2m7nr6gwb3ik3z"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Pab_eg_db = derive2 { name="LRBase.Pab.eg.db"; version="0.99.1"; sha256="0scycwpdmr6yvfyqsani1372pmyqxzvv30wsvy8hx3km7dcd4ypz"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Rno_eg_db = derive2 { name="LRBase.Rno.eg.db"; version="0.99.1"; sha256="1b5rzb9kpnak90fb55y380qmspd8gah3wxvsliv1lddab65m5ch3"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Ssc_eg_db = derive2 { name="LRBase.Ssc.eg.db"; version="0.99.1"; sha256="1p1crrh3wkinvhqmy9b1h4j9yfvwbsykhm6b0xlhn0kzdqxlizjf"; depends=[LRBaseDbi RSQLite]; }; - LRBase_Xtr_eg_db = derive2 { name="LRBase.Xtr.eg.db"; version="0.99.1"; sha256="0aqzcll2ylzbbq42ns0hp7l9p6343l2qlsv5zkglla1bxdxl6m4h"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Ath_eg_db = derive2 { name="LRBase.Ath.eg.db"; version="1.2.0"; sha256="1y2dgmqhv0x4ydvxq6dcg5m0gzcvlzb9jq4hs3axdyy8d62i8flh"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Bta_eg_db = derive2 { name="LRBase.Bta.eg.db"; version="1.2.0"; sha256="04z4fmfyl1k6m3paab6ip9h015q90xpxxn5lccm03k3pcv7wf5mh"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Cel_eg_db = derive2 { name="LRBase.Cel.eg.db"; version="1.2.0"; sha256="1kdcm469qkvncw92c5wjlgnfc9fnqpn15nc124zv0ykpx34fd922"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Dme_eg_db = derive2 { name="LRBase.Dme.eg.db"; version="1.2.0"; sha256="1amsik0g0pl72jfi8v9jnqpfs8rdsrq1ybly79lyhq1rpdjicayk"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Dre_eg_db = derive2 { name="LRBase.Dre.eg.db"; version="1.2.0"; sha256="16c0fcw6y4nqgvwzx3v8h822dbw3cbmb8h4sd7g9zwmylibbl35g"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Gga_eg_db = derive2 { name="LRBase.Gga.eg.db"; version="1.2.0"; sha256="1rdamsg3gikh22sfkafacl0b8507z5hk28j1vcaxdscrwwyrc6bz"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Hsa_eg_db = derive2 { name="LRBase.Hsa.eg.db"; version="1.2.0"; sha256="1qdyh4i016i40zn72h1x7194x1wi8pddl6cyln658k334p60x86l"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Mmu_eg_db = derive2 { name="LRBase.Mmu.eg.db"; version="1.2.0"; sha256="1viw7vhy3m7b7fwkm38y7f26bzywl1n2i1cff7mp91czss26bq9s"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Pab_eg_db = derive2 { name="LRBase.Pab.eg.db"; version="1.2.0"; sha256="1s5i4167ygwq35j60ns4f1yf6llasxx6wad61xng5p8lgq3186nr"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Rno_eg_db = derive2 { name="LRBase.Rno.eg.db"; version="1.2.0"; sha256="08xnr1wlg3lkjdmjdvy2i12ki3ym7z4gr3zvyj2ghkyn0gyd73gp"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Ssc_eg_db = derive2 { name="LRBase.Ssc.eg.db"; version="1.2.0"; sha256="0hqns1c4xgay7aagbhl46b9zwf5hp1p33jf9f28l5mxvvc96zrbn"; depends=[LRBaseDbi RSQLite]; }; + LRBase_Xtr_eg_db = derive2 { name="LRBase.Xtr.eg.db"; version="1.2.0"; sha256="0kl6f7a1fxxrchz8s5dsh2vqsa8ckigi4clpnr76qvhlcfn77hk7"; depends=[LRBaseDbi RSQLite]; }; LowMACAAnnotation = derive2 { name="LowMACAAnnotation"; version="0.99.3"; sha256="0ri301ci54s8wwkah1jccy5h44xg8yjk08j5b15qmdsm25hli4wm"; depends=[]; }; LymphoSeqDB = derive2 { name="LymphoSeqDB"; version="0.99.2"; sha256="1cdyn2imjh4zr23szndc4vwyiacxs1jsp14gil2dyq9aifa25qr7"; depends=[]; }; - MafDb_1Kgenomes_phase1_GRCh38 = derive2 { name="MafDb.1Kgenomes.phase1.GRCh38"; version="3.7.0"; sha256="160whyhwjspqji6ys19qgi4y3k7z1qqzr75nhpw0yl8h1rc6rfg0"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_1Kgenomes_phase1_hs37d5 = derive2 { name="MafDb.1Kgenomes.phase1.hs37d5"; version="3.7.1"; sha256="1yxhb3kysgj95wdp7v5kq3bvn9xj09ywkfm2fdrkqxmzpan7q9q5"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_1Kgenomes_phase3_GRCh38 = derive2 { name="MafDb.1Kgenomes.phase3.GRCh38"; version="3.7.0"; sha256="0z0v2kld7xqk2plrwb594q3al2kxi64k5phyknnpb0hhgddl688z"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_1Kgenomes_phase3_hs37d5 = derive2 { name="MafDb.1Kgenomes.phase3.hs37d5"; version="3.7.0"; sha256="0rg4vzk3ik2ikdr57fp1za37kfpci6ha0qn8wpnyf8qyc3h9q5xf"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_ESP6500SI_V2_SSA137_GRCh38 = derive2 { name="MafDb.ESP6500SI.V2.SSA137.GRCh38"; version="3.7.0"; sha256="1iybhk64lqar1b8qv1rjxzf53mci9bq684m4l7zqrz8g91jx7myq"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_ESP6500SI_V2_SSA137_hs37d5 = derive2 { name="MafDb.ESP6500SI.V2.SSA137.hs37d5"; version="3.7.0"; sha256="1nfcnlwcx1sr2z4icg893zv3j9c9gnhd0nbgnjrl1fh2nrl25wsd"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_ExAC_r1_0_GRCh38 = derive2 { name="MafDb.ExAC.r1.0.GRCh38"; version="3.7.0"; sha256="1xs52xivxjzg14d0fr3ifb29shysxvw062c3wzb1nfmnydixcqmf"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_ExAC_r1_0_hs37d5 = derive2 { name="MafDb.ExAC.r1.0.hs37d5"; version="3.7.0"; sha256="00b022hzwr0l6m9wzw76iirdq5szvi5z8a9yi2i44sydhwqsb4cy"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_ExAC_r1_0_nonTCGA_GRCh38 = derive2 { name="MafDb.ExAC.r1.0.nonTCGA.GRCh38"; version="3.7.0"; sha256="1dvzzwj9dhrls8caabdcgddsk64a6q9jqcya424h8n48fkx6fpjn"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_ExAC_r1_0_nonTCGA_hs37d5 = derive2 { name="MafDb.ExAC.r1.0.nonTCGA.hs37d5"; version="3.7.0"; sha256="10rn7nqrnhmhdqcygi8l3cwf1385jyy56qzqjgqyhvmi4g8dnjsn"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_TOPMed_freeze5_hg19 = derive2 { name="MafDb.TOPMed.freeze5.hg19"; version="3.7.1"; sha256="0a8rgh3lkbplg3y1yl0804f55dlw7v8lcb33ygg8kg39dk60m102"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_TOPMed_freeze5_hg38 = derive2 { name="MafDb.TOPMed.freeze5.hg38"; version="3.7.1"; sha256="1kxk3qqw1igkygqmj8yjl4cp99fan1w84gilh6q35nsaja0fapa8"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_gnomAD_r2_0_1_GRCh38 = derive2 { name="MafDb.gnomAD.r2.0.1.GRCh38"; version="3.7.0"; sha256="0dp82x6dag4ndizvppr2g5x1v8sbj08r6n7mi98c89fn4f7nvqqw"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_gnomAD_r2_0_1_hs37d5 = derive2 { name="MafDb.gnomAD.r2.0.1.hs37d5"; version="3.8.0"; sha256="0kb50g4kmj1b4xm9p8q6j1yzpv5ygxf71vqhkb7c0ajqffqbyznm"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_gnomAD_r2_1_hs37d5 = derive2 { name="MafDb.gnomAD.r2.1.hs37d5"; version="3.8.0"; sha256="00ld23685xlrkx9rpgrcqaycq3zxbxqg734r99avrw8p3lmj4fvc"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_gnomADex_r2_0_1_GRCh38 = derive2 { name="MafDb.gnomADex.r2.0.1.GRCh38"; version="3.7.0"; sha256="0hwyyqa4g3hp85hk4b6qfzm10yk6h20sh0f2mf09yr0hpmkjyl59"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_gnomADex_r2_0_1_hs37d5 = derive2 { name="MafDb.gnomADex.r2.0.1.hs37d5"; version="3.8.0"; sha256="0xz6ayip0cdbal6gsc8wpjyg3rr1kadaddv8flw5k8ky84mckzbc"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MafDb_gnomADex_r2_1_hs37d5 = derive2 { name="MafDb.gnomADex.r2.1.hs37d5"; version="3.8.0"; sha256="06vicw9z05j1pw30sw0f2nkcixc14yn3anq0g3317i3rb1kvmwid"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - MeSH_AOR_db = derive2 { name="MeSH.AOR.db"; version="1.11.0"; sha256="02ysykmbn1b6rv3fbq71g9lnv16gvxyvb9p9smvm0k9brb7s0q24"; depends=[MeSHDbi]; }; - MeSH_Aca_eg_db = derive2 { name="MeSH.Aca.eg.db"; version="1.11.0"; sha256="13x69ki5g99hravrfdll98z2n7nghvf02v920q4g2bgjzzh68sks"; depends=[MeSHDbi]; }; - MeSH_Aga_PEST_eg_db = derive2 { name="MeSH.Aga.PEST.eg.db"; version="1.11.0"; sha256="1sffv89v1vrlgy36kf7q7ixnc2iwfaa2h0dsxrg0pjmzsq669h9s"; depends=[MeSHDbi]; }; - MeSH_Ame_eg_db = derive2 { name="MeSH.Ame.eg.db"; version="1.11.0"; sha256="0ssivaq31rjagw5sdjg9ai3bm73mdvdrkqz0snf3phdgxpvldqms"; depends=[MeSHDbi]; }; - MeSH_Aml_eg_db = derive2 { name="MeSH.Aml.eg.db"; version="1.11.0"; sha256="0cl95vipqcjf1pb9bjzvxa4dc0d5rzac84n9f6l061vhifa2c3pn"; depends=[MeSHDbi]; }; - MeSH_Ana_eg_db = derive2 { name="MeSH.Ana.eg.db"; version="1.11.0"; sha256="190h3pch16bzx0h674kwywcy3pr1y16jbzczbmmvsxg1l2j549zm"; depends=[MeSHDbi]; }; - MeSH_Ani_FGSC_eg_db = derive2 { name="MeSH.Ani.FGSC.eg.db"; version="1.11.0"; sha256="0w6gq9xy1v84ksbd849jpj073s51fbhgss8wl6ax4ybxvfp22m0s"; depends=[MeSHDbi]; }; - MeSH_Ath_eg_db = derive2 { name="MeSH.Ath.eg.db"; version="1.11.0"; sha256="0jdxvnhxrajhd5dr6hzfii7b1n6x874qfc8999pw8y8rwh8c4ln7"; depends=[MeSHDbi]; }; - MeSH_Bfl_eg_db = derive2 { name="MeSH.Bfl.eg.db"; version="1.11.0"; sha256="0vqyanf9n9ji77zkck3vyrrhm87hx3yxiy9fpwal6a0vh31vrjb9"; depends=[MeSHDbi]; }; - MeSH_Bsu_168_eg_db = derive2 { name="MeSH.Bsu.168.eg.db"; version="1.11.0"; sha256="11f9jibxf0amhixhs2pvmx6ir1530qkm9xcjrj09hwyx687bs3z8"; depends=[MeSHDbi]; }; - MeSH_Bta_eg_db = derive2 { name="MeSH.Bta.eg.db"; version="1.11.0"; sha256="03nbmbnbfvpja1p9rnqy1mpamlab0fd2y4fkx456jmnl87m1zk0n"; depends=[MeSHDbi]; }; - MeSH_Cal_SC5314_eg_db = derive2 { name="MeSH.Cal.SC5314.eg.db"; version="1.11.0"; sha256="0pd9gigwrckz9drh3x7n9nvvcq2q2wwmczkhhkqlpp4qhg85yp7g"; depends=[MeSHDbi]; }; - MeSH_Cbr_eg_db = derive2 { name="MeSH.Cbr.eg.db"; version="1.11.0"; sha256="1rjb9ldrn2jg73p2j9mjn61ljw83bhr07yq7482lp4mglhwvqibm"; depends=[MeSHDbi]; }; - MeSH_Cel_eg_db = derive2 { name="MeSH.Cel.eg.db"; version="1.11.0"; sha256="14ywqllqgynwfxyxrkw2d6r7m2n82znx9s15l62d7jb88pvaajn6"; depends=[MeSHDbi]; }; - MeSH_Cfa_eg_db = derive2 { name="MeSH.Cfa.eg.db"; version="1.11.0"; sha256="0b5b5dyh99gykdp3whdz7rjz1862p3w4jigy7s1bjmhv4pm3bn2d"; depends=[MeSHDbi]; }; - MeSH_Cin_eg_db = derive2 { name="MeSH.Cin.eg.db"; version="1.11.0"; sha256="1cbwqyb4ja10j0250lggbpxgpivf0xj1m7hn4l687rdidxgrmy4s"; depends=[MeSHDbi]; }; - MeSH_Cja_eg_db = derive2 { name="MeSH.Cja.eg.db"; version="1.11.0"; sha256="0b5q8yclcx18f8aq45ikv7qyw0xfsksjf1fbl6fprflvzfz2cnir"; depends=[MeSHDbi]; }; - MeSH_Cpo_eg_db = derive2 { name="MeSH.Cpo.eg.db"; version="1.11.0"; sha256="1rd90rzipaa480sahh7pqlv1qzj1wcx543gkshj6mcfkr6r08zci"; depends=[MeSHDbi]; }; - MeSH_Cre_eg_db = derive2 { name="MeSH.Cre.eg.db"; version="1.11.0"; sha256="0xg2mi60qlg76g1zxmybcixci8nivw4ld91qxf13jybcr0mwf9xn"; depends=[MeSHDbi]; }; - MeSH_Dan_eg_db = derive2 { name="MeSH.Dan.eg.db"; version="1.11.0"; sha256="0l80s6v7p2n7p17chbk6a7y5y2b02z38x034jwg3yvyfqy073r11"; depends=[MeSHDbi]; }; - MeSH_Dda_3937_eg_db = derive2 { name="MeSH.Dda.3937.eg.db"; version="1.11.0"; sha256="187zq75qz7jysz8jg5k5sgvxkrpvdyyi8xlsidi774nyb7z5d96l"; depends=[MeSHDbi]; }; - MeSH_Ddi_AX4_eg_db = derive2 { name="MeSH.Ddi.AX4.eg.db"; version="1.11.0"; sha256="1aicyzgw5nx6z9q339cd1iabi7a1yjswla0j94anqwh783lqrpxq"; depends=[MeSHDbi]; }; - MeSH_Der_eg_db = derive2 { name="MeSH.Der.eg.db"; version="1.11.0"; sha256="03rvcxawyhckg693w2ngnk3sljgz7idha6iqyax8p8wagl2h5ipv"; depends=[MeSHDbi]; }; - MeSH_Dgr_eg_db = derive2 { name="MeSH.Dgr.eg.db"; version="1.11.0"; sha256="17d3ankadjsvddfqxqm3hnqcmsr2rknkbvraq6zpdl7xw3r21yfn"; depends=[MeSHDbi]; }; - MeSH_Dme_eg_db = derive2 { name="MeSH.Dme.eg.db"; version="1.11.0"; sha256="1j3wsmspg7w30y04l173pihac9xg633w8zj2scz6jnph6rgxw3p1"; depends=[MeSHDbi]; }; - MeSH_Dmo_eg_db = derive2 { name="MeSH.Dmo.eg.db"; version="1.11.0"; sha256="0640jfik9qp15h5180rn1afd2kv2wh5s0nbv2zjiz6089csb2fnf"; depends=[MeSHDbi]; }; - MeSH_Dpe_eg_db = derive2 { name="MeSH.Dpe.eg.db"; version="1.11.0"; sha256="1y058sma4p48fj5f8v2i79nak5892pkk7rmr3i18jv44c8246zzl"; depends=[MeSHDbi]; }; - MeSH_Dre_eg_db = derive2 { name="MeSH.Dre.eg.db"; version="1.11.0"; sha256="03dybrs5zhnil83jp37hq4rh8ybvyjnqpkr2vwa7f1kd65mq33za"; depends=[MeSHDbi]; }; - MeSH_Dse_eg_db = derive2 { name="MeSH.Dse.eg.db"; version="1.11.0"; sha256="032kjhsm39jck9gxlg15g4x6n4r2iyi339vm6b9v4xcays45h9hi"; depends=[MeSHDbi]; }; - MeSH_Dsi_eg_db = derive2 { name="MeSH.Dsi.eg.db"; version="1.11.0"; sha256="0h60gqkc4cjkbqs8i3x6z774qq4ihp20bssi70wli6fvsiysgbly"; depends=[MeSHDbi]; }; - MeSH_Dvi_eg_db = derive2 { name="MeSH.Dvi.eg.db"; version="1.11.0"; sha256="1c8rg4h6gcs4y5gxz1z66a0ma3xpg4sdp6zwzcyrq02r2vjwj6ls"; depends=[MeSHDbi]; }; - MeSH_Dya_eg_db = derive2 { name="MeSH.Dya.eg.db"; version="1.11.0"; sha256="03aycm5222wkx6rh7x204rkcxnh6amghm2zpzqiy4c5a2a871y9d"; depends=[MeSHDbi]; }; - MeSH_Eco_55989_eg_db = derive2 { name="MeSH.Eco.55989.eg.db"; version="1.11.0"; sha256="0qqwwa3hk8ds2nv7xndqx4z9s00524sqrpgxh690yhdczn1ridqd"; depends=[MeSHDbi]; }; - MeSH_Eco_ED1a_eg_db = derive2 { name="MeSH.Eco.ED1a.eg.db"; version="1.11.0"; sha256="1v47a80lvhhbl7sqx881nx1m4pqi6mprmgd03cvk4vhrgv74ji8f"; depends=[MeSHDbi]; }; - MeSH_Eco_IAI39_eg_db = derive2 { name="MeSH.Eco.IAI39.eg.db"; version="1.11.0"; sha256="0mpabfvji1y1irgm5wkbinabriwbbb6wg6a0rc4mq5vn6j8nia36"; depends=[MeSHDbi]; }; - MeSH_Eco_K12_MG1655_eg_db = derive2 { name="MeSH.Eco.K12.MG1655.eg.db"; version="1.11.0"; sha256="1sb0b82ibvk2n22a88c7qkmb3wch6zcgaah54p920dih2xxx24nb"; depends=[MeSHDbi]; }; - MeSH_Eco_O157_H7_Sakai_eg_db = derive2 { name="MeSH.Eco.O157.H7.Sakai.eg.db"; version="1.11.0"; sha256="1i65691h3w34kvqswfkg6klpj8gm39p6csa8da4hlbwc7q58zzpf"; depends=[MeSHDbi]; }; - MeSH_Eco_UMN026_eg_db = derive2 { name="MeSH.Eco.UMN026.eg.db"; version="1.11.0"; sha256="12yrsy71g0r6w028i56kxknkb4gr34x4d6064m61023234j31j69"; depends=[MeSHDbi]; }; - MeSH_Eqc_eg_db = derive2 { name="MeSH.Eqc.eg.db"; version="1.11.0"; sha256="19ihdqwlrifd6nyi1bbxnjbq7qqb535d47mm5h0f1pz2h6w6jps6"; depends=[MeSHDbi]; }; - MeSH_Gga_eg_db = derive2 { name="MeSH.Gga.eg.db"; version="1.11.0"; sha256="1f2f9vqdaqi6iak6yg3rcgcpvhaz76zl4hywnlz1gi7aszxiff0k"; depends=[MeSHDbi]; }; - MeSH_Gma_eg_db = derive2 { name="MeSH.Gma.eg.db"; version="1.11.0"; sha256="075hhjahc34bznvmqrlc6vnlq25c4ybsyd6ry5qmnzccpxyqhgv8"; depends=[MeSHDbi]; }; - MeSH_Hsa_eg_db = derive2 { name="MeSH.Hsa.eg.db"; version="1.11.0"; sha256="0c7kb73jrr74a05jgyf903bvy92pn23aklflnl2cqqwxqjc6f9hm"; depends=[MeSHDbi]; }; - MeSH_Laf_eg_db = derive2 { name="MeSH.Laf.eg.db"; version="1.11.0"; sha256="1zg7c08z6j02sg74ff1q3hnmy5bszd6g5dyr0hxxqivx28bmirya"; depends=[MeSHDbi]; }; - MeSH_Lma_eg_db = derive2 { name="MeSH.Lma.eg.db"; version="1.11.0"; sha256="1p70v5bvhawsh954mmnxiy734n0z6b0mfl4j3i2g3jijwrds9f6v"; depends=[MeSHDbi]; }; - MeSH_Mdo_eg_db = derive2 { name="MeSH.Mdo.eg.db"; version="1.11.0"; sha256="0997k7iwq49sf2fn88lgx5j3rhsv9g7mldsm2bpsqmw52d8j568f"; depends=[MeSHDbi]; }; - MeSH_Mes_eg_db = derive2 { name="MeSH.Mes.eg.db"; version="1.11.0"; sha256="16pxwy7yycdp59j3nvz58jc8h2y251b4prpk4nn589z7pk37hw52"; depends=[MeSHDbi]; }; - MeSH_Mga_eg_db = derive2 { name="MeSH.Mga.eg.db"; version="1.11.0"; sha256="0dmdfi983i2sf56b06p7q1w7n8ik3j1dkfw1x1cc207wmmns4916"; depends=[MeSHDbi]; }; - MeSH_Miy_eg_db = derive2 { name="MeSH.Miy.eg.db"; version="1.11.0"; sha256="024076n31mpz2fr7dbf5di6gxn1w1gajx95065vl4555zx46i9n1"; depends=[MeSHDbi]; }; - MeSH_Mml_eg_db = derive2 { name="MeSH.Mml.eg.db"; version="1.11.0"; sha256="0rbnysb12i2f1a9xz0869m5n031j60c8bxnj1cp0zxlnylamf7w0"; depends=[MeSHDbi]; }; - MeSH_Mmu_eg_db = derive2 { name="MeSH.Mmu.eg.db"; version="1.11.0"; sha256="1h9jz00bgz54nknl95jf60qqgmn5iyq766sdkxn7r54h9315c9g9"; depends=[MeSHDbi]; }; - MeSH_Mtr_eg_db = derive2 { name="MeSH.Mtr.eg.db"; version="1.11.0"; sha256="1b4nhix3ky4d0cm8hix9m7chcgdyskvd0h7fj3k13a4zxyxvfw9x"; depends=[MeSHDbi]; }; - MeSH_Nle_eg_db = derive2 { name="MeSH.Nle.eg.db"; version="1.11.0"; sha256="16fcswjrv056g5d6ikf2g8af470djf02pyxhp5ib6gk932vl7kp0"; depends=[MeSHDbi]; }; - MeSH_Oan_eg_db = derive2 { name="MeSH.Oan.eg.db"; version="1.11.0"; sha256="08cdkyvwss0cczd6j19j02950jpqhhzi79y9swqnzzh3nydb3aqj"; depends=[MeSHDbi]; }; - MeSH_Ocu_eg_db = derive2 { name="MeSH.Ocu.eg.db"; version="1.11.0"; sha256="09nigd6hc3iy3s2r70ixfyj04la8cnaxhvr5i1k0adapjgf4q1mx"; depends=[MeSHDbi]; }; - MeSH_Oni_eg_db = derive2 { name="MeSH.Oni.eg.db"; version="1.11.0"; sha256="1cwhbrpiznkfbkxchpddkr68jzcxzn0mvn8cy81dm0vj4x8dxjb8"; depends=[MeSHDbi]; }; - MeSH_Osa_eg_db = derive2 { name="MeSH.Osa.eg.db"; version="1.11.0"; sha256="0psaqhdi4hicy5vkngkh7ig5ndsjl768n9fg36zlvqllww58kfis"; depends=[MeSHDbi]; }; - MeSH_PCR_db = derive2 { name="MeSH.PCR.db"; version="1.11.0"; sha256="0jdwxkwinbnvap0mpirzcd4zgfvhsmca2r57s2lzh2i1x24hxa4c"; depends=[MeSHDbi]; }; - MeSH_Pab_eg_db = derive2 { name="MeSH.Pab.eg.db"; version="1.11.0"; sha256="16qcm0d8m53dkwfbcsygbm3xj7x6hblwpa4agds5vnlkb26m48qn"; depends=[MeSHDbi]; }; - MeSH_Pae_PAO1_eg_db = derive2 { name="MeSH.Pae.PAO1.eg.db"; version="1.11.0"; sha256="1w3zqynqjv79ixxnmn3khvj3p6586nq48dx00rap6vzirmhzigqv"; depends=[MeSHDbi]; }; - MeSH_Pfa_3D7_eg_db = derive2 { name="MeSH.Pfa.3D7.eg.db"; version="1.11.0"; sha256="0ryxhk5g07fpnnk72q5a2847k6w509956fcxnrvwvp7f98p3z50x"; depends=[MeSHDbi]; }; - MeSH_Pto_eg_db = derive2 { name="MeSH.Pto.eg.db"; version="1.11.0"; sha256="0i1772rpq95ppzxa809ms1r65d9rk5vqhcl36ndjs2lhzdydw8fz"; depends=[MeSHDbi]; }; - MeSH_Ptr_eg_db = derive2 { name="MeSH.Ptr.eg.db"; version="1.11.0"; sha256="0xgi89vzhxkmqx0y84i58jkxikksqdi64r82p59ir6l1anpyvvc9"; depends=[MeSHDbi]; }; - MeSH_Rno_eg_db = derive2 { name="MeSH.Rno.eg.db"; version="1.11.0"; sha256="0g0fnackq1yjaw0b3ppzbcj0sfx288wm6cv57ly69svfg1n0wlk5"; depends=[MeSHDbi]; }; - MeSH_Sce_S288c_eg_db = derive2 { name="MeSH.Sce.S288c.eg.db"; version="1.11.0"; sha256="1z29d19is5lq8rqrkk1dyifgn0v2i68pbw8i7dlwnnicj2sfpynb"; depends=[MeSHDbi]; }; - MeSH_Sco_A32_eg_db = derive2 { name="MeSH.Sco.A32.eg.db"; version="1.11.0"; sha256="0dcxjlpc9diz1lvrkpbrab5zjz96r837x7ij9786966a3x458xk0"; depends=[MeSHDbi]; }; - MeSH_Sil_eg_db = derive2 { name="MeSH.Sil.eg.db"; version="1.11.0"; sha256="0gpj4i2mls1qkyivxy2gk3b8w9vkxnwf2b0cpmbv5bvpjcsbw47i"; depends=[MeSHDbi]; }; - MeSH_Spu_eg_db = derive2 { name="MeSH.Spu.eg.db"; version="1.11.0"; sha256="14knm1h8mp5qfjbny2wwkj772x72laxgymhsa04m78mb38qhypwq"; depends=[MeSHDbi]; }; - MeSH_Ssc_eg_db = derive2 { name="MeSH.Ssc.eg.db"; version="1.11.0"; sha256="0hwgkq669g99yrkbpk3pjpxbz7q0vwvkcx3rrvdk9dnjinlbcn54"; depends=[MeSHDbi]; }; - MeSH_Syn_eg_db = derive2 { name="MeSH.Syn.eg.db"; version="1.11.0"; sha256="1mz986apgfd6sn62wws948yi46r87fzaszxnv450fgc42l23l0jx"; depends=[MeSHDbi]; }; - MeSH_Tbr_9274_eg_db = derive2 { name="MeSH.Tbr.9274.eg.db"; version="1.11.0"; sha256="0dvz5xbx6vdmqibpq8xmpdjfvvqw7iqq3w4d350sxj5kaw2afp5s"; depends=[MeSHDbi]; }; - MeSH_Tgo_ME49_eg_db = derive2 { name="MeSH.Tgo.ME49.eg.db"; version="1.11.0"; sha256="08hyvaqsvdpcizsqr53ab6bfh1fnlsj8d62pq03lpgr96rlyqi8q"; depends=[MeSHDbi]; }; - MeSH_Tgu_eg_db = derive2 { name="MeSH.Tgu.eg.db"; version="1.11.0"; sha256="0mid3qmv7kxc7kn69vbhgchvrbv4fig97nw9zxsbd0rj66abzas2"; depends=[MeSHDbi]; }; - MeSH_Vvi_eg_db = derive2 { name="MeSH.Vvi.eg.db"; version="1.11.0"; sha256="1pwq58mm7ripnzxcn13k1y157pjasrv30xxmrrqb4rv55nk61vbf"; depends=[MeSHDbi]; }; - MeSH_Xla_eg_db = derive2 { name="MeSH.Xla.eg.db"; version="1.11.0"; sha256="0qd75lkyrs864sy3sci3bablipn9gabk24wbriis9bi0qf7hccv5"; depends=[MeSHDbi]; }; - MeSH_Xtr_eg_db = derive2 { name="MeSH.Xtr.eg.db"; version="1.11.0"; sha256="0djsx876h0xz0h8jhs6yad8iqqjlr72b0fxasqgh89zpfp2hkvwd"; depends=[MeSHDbi]; }; - MeSH_Zma_eg_db = derive2 { name="MeSH.Zma.eg.db"; version="1.11.0"; sha256="08b92lhq2gbvbm7y0q4zc991wi1fjhm68n03b782h2g6syczmlma"; depends=[MeSHDbi]; }; - MeSH_db = derive2 { name="MeSH.db"; version="1.11.0"; sha256="1l6hynwmhb8p666q8n9dnvd0nhjy1f9nz2jg3z2p13dc5jl6syiw"; depends=[MeSHDbi]; }; + MafDb_1Kgenomes_phase1_GRCh38 = derive2 { name="MafDb.1Kgenomes.phase1.GRCh38"; version="3.10.0"; sha256="057531mvxip32lyqak4hh964ms0cil29p5cch5fpjw5vbbzidrlc"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_1Kgenomes_phase1_hs37d5 = derive2 { name="MafDb.1Kgenomes.phase1.hs37d5"; version="3.10.0"; sha256="0vsjik59qa36w402bcrd5z27wc9vyp4gl0ffcwskd9iwjqim0phi"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_1Kgenomes_phase3_GRCh38 = derive2 { name="MafDb.1Kgenomes.phase3.GRCh38"; version="3.10.0"; sha256="0ibww7ml5cfyx8h198fgrnf13vvsxxb5spf7hcmm6z3hha6j2ij0"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_1Kgenomes_phase3_hs37d5 = derive2 { name="MafDb.1Kgenomes.phase3.hs37d5"; version="3.10.0"; sha256="1c2bxgy3bpbszfsqlk262lv45x1fgqyywk9i9nax7bpahlcpp68d"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_ESP6500SI_V2_SSA137_GRCh38 = derive2 { name="MafDb.ESP6500SI.V2.SSA137.GRCh38"; version="3.10.0"; sha256="0z33c0f8janzvlldmkcfzcmz4ymkw94m3qfjf75izc08xhyw1wx8"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_ESP6500SI_V2_SSA137_hs37d5 = derive2 { name="MafDb.ESP6500SI.V2.SSA137.hs37d5"; version="3.10.0"; sha256="1an0s5n4nwzmaqr57qydgkazbqf0gywcs2zhlbbr6nxk97zh8374"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_ExAC_r1_0_GRCh38 = derive2 { name="MafDb.ExAC.r1.0.GRCh38"; version="3.10.0"; sha256="02mlwkx9kal4h1q1h3c2pdragir9bh63vg1wyagmh8capf19zx5c"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_ExAC_r1_0_hs37d5 = derive2 { name="MafDb.ExAC.r1.0.hs37d5"; version="3.10.0"; sha256="18czbllphsccb2hs02g6jz517ylxsvx12czwh4xz7vym6q4br0cz"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_ExAC_r1_0_nonTCGA_GRCh38 = derive2 { name="MafDb.ExAC.r1.0.nonTCGA.GRCh38"; version="3.10.0"; sha256="16rsm24nlz7jdnqk1p0avn9dlxkbbjd50nja5pcg0z18m30srlya"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_ExAC_r1_0_nonTCGA_hs37d5 = derive2 { name="MafDb.ExAC.r1.0.nonTCGA.hs37d5"; version="3.10.0"; sha256="1srwc9n9x0ilipqwvm95khy4w2dnn1fkxyrrlcqfwv96gl7141x5"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_TOPMed_freeze5_hg19 = derive2 { name="MafDb.TOPMed.freeze5.hg19"; version="3.10.0"; sha256="1fxq5jq4g6rys909v0a4lbrcgfdk844wgihn0ary509w8ifdkxdv"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_TOPMed_freeze5_hg38 = derive2 { name="MafDb.TOPMed.freeze5.hg38"; version="3.10.0"; sha256="0yd9r26l2s3ykw5d2lndnx4m1h401g7hsnkk0wywczdc1xa39y4n"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_gnomAD_r2_1_GRCh38 = derive2 { name="MafDb.gnomAD.r2.1.GRCh38"; version="3.10.0"; sha256="1bshq6ncns7xdrpkkc84m4x6a1pnm3ssp02f0d23yhlkhh0h40zd"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_gnomAD_r2_1_hs37d5 = derive2 { name="MafDb.gnomAD.r2.1.hs37d5"; version="3.10.0"; sha256="153dy3lx0islfdkmyik7lxp1w2yzb0bqmia673hlwi4rmvns112h"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_gnomAD_r3_0_GRCh38 = derive2 { name="MafDb.gnomAD.r3.0.GRCh38"; version="3.10.0"; sha256="0f0sbfi6vlgqwhmipsvp59vi5npq33i5fa9g3ilhijsf2hb1xfb9"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_gnomADex_r2_1_GRCh38 = derive2 { name="MafDb.gnomADex.r2.1.GRCh38"; version="3.10.0"; sha256="1v0sdjmn9z8gqn4yj4v04zycj3ngr32r04zqmkp6y41hcgdr8lxw"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MafDb_gnomADex_r2_1_hs37d5 = derive2 { name="MafDb.gnomADex.r2.1.hs37d5"; version="3.10.0"; sha256="0y42ncmilijdxsgqsmskz7gff3il3fdf2kpflknmz1z9kybzaday"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; + MeSH_AOR_db = derive2 { name="MeSH.AOR.db"; version="1.13.0"; sha256="0l55b03072s052ji52glqpqc8x0z7d4fkf392113bskmplgcg3ny"; depends=[MeSHDbi]; }; + MeSH_Aca_eg_db = derive2 { name="MeSH.Aca.eg.db"; version="1.13.0"; sha256="061bp9y592h57y0i4y6aah9vln23f1mk1yzx9fxhimnd4rzmwzl4"; depends=[MeSHDbi]; }; + MeSH_Aga_PEST_eg_db = derive2 { name="MeSH.Aga.PEST.eg.db"; version="1.13.0"; sha256="10253yy1gv96x6h92xz35qhz087ma6whr5pbi69mjdfc21pzyc7a"; depends=[MeSHDbi]; }; + MeSH_Ame_eg_db = derive2 { name="MeSH.Ame.eg.db"; version="1.13.0"; sha256="19aw7vq6iafhjb1n7kgbyaib2di682dia0yjc4r3cnzv7k7kv8z0"; depends=[MeSHDbi]; }; + MeSH_Aml_eg_db = derive2 { name="MeSH.Aml.eg.db"; version="1.13.0"; sha256="0ljijw7p5nxvgda2jb3gf6x03y046ihxz7nl2s90rgf4s1fjciaf"; depends=[MeSHDbi]; }; + MeSH_Ana_eg_db = derive2 { name="MeSH.Ana.eg.db"; version="1.13.0"; sha256="1afv8yf2yggid12id0j5v5gf5qhcdmanfanp2d13cnkzgxkr88js"; depends=[MeSHDbi]; }; + MeSH_Ani_FGSC_eg_db = derive2 { name="MeSH.Ani.FGSC.eg.db"; version="1.13.0"; sha256="1amgb9gr5aa1cgggf2x5ailzm4mfq78lfqnx1yzq1ix3nh5idajf"; depends=[MeSHDbi]; }; + MeSH_Ath_eg_db = derive2 { name="MeSH.Ath.eg.db"; version="1.13.0"; sha256="0byxvlwcix154qbpvpgv9zblyn1wx6npn366303v81r6x5gh4qkh"; depends=[MeSHDbi]; }; + MeSH_Bfl_eg_db = derive2 { name="MeSH.Bfl.eg.db"; version="1.13.0"; sha256="1v1f7b0qyii8nakn7lhckbyqyw43101i2y0dcamp5lds8m79691d"; depends=[MeSHDbi]; }; + MeSH_Bsu_168_eg_db = derive2 { name="MeSH.Bsu.168.eg.db"; version="1.13.0"; sha256="1rr4yr0n2zdkcq2xj7cyv683sgv5mnjwcylz4r8wkrdhji28zyyh"; depends=[MeSHDbi]; }; + MeSH_Bta_eg_db = derive2 { name="MeSH.Bta.eg.db"; version="1.13.0"; sha256="1nz96wyw99rz2wlsa59y36ddxg3i4vz116i4sjvm3ww2q71nimmr"; depends=[MeSHDbi]; }; + MeSH_Cal_SC5314_eg_db = derive2 { name="MeSH.Cal.SC5314.eg.db"; version="1.13.0"; sha256="0irsxad7s1asllwajwy1bl2frs22sgwv60fdgnslgxmngg5v6jbc"; depends=[MeSHDbi]; }; + MeSH_Cbr_eg_db = derive2 { name="MeSH.Cbr.eg.db"; version="1.13.0"; sha256="0qq08f245qsq6c9g38wcbn9gnhhx2wlsas3na1n5fycr5d19qbvz"; depends=[MeSHDbi]; }; + MeSH_Cel_eg_db = derive2 { name="MeSH.Cel.eg.db"; version="1.13.0"; sha256="0mjg8dinlp1qqnf2h1lpyhig9ywa9x99isyvj2z37mrbk9mh6si6"; depends=[MeSHDbi]; }; + MeSH_Cfa_eg_db = derive2 { name="MeSH.Cfa.eg.db"; version="1.13.0"; sha256="1xlcn55v3hyngdqmb5a3v64ll1cmm1yd8gbxw3sbbbnwp349w2jb"; depends=[MeSHDbi]; }; + MeSH_Cin_eg_db = derive2 { name="MeSH.Cin.eg.db"; version="1.13.0"; sha256="13naakq86kgkbd8cif5gi7hzag64xkp8mddrwn4hc67i1dzlfyq0"; depends=[MeSHDbi]; }; + MeSH_Cja_eg_db = derive2 { name="MeSH.Cja.eg.db"; version="1.13.0"; sha256="1b4sl5qiwh0vxm1svwqwsbrz2b88jmf7s14nwhb27431ml5lya03"; depends=[MeSHDbi]; }; + MeSH_Cpo_eg_db = derive2 { name="MeSH.Cpo.eg.db"; version="1.13.0"; sha256="12qak3gzbr7hpg08nmpa69h0qw0v4kdplf10ilycc8ra1nrm9s8x"; depends=[MeSHDbi]; }; + MeSH_Cre_eg_db = derive2 { name="MeSH.Cre.eg.db"; version="1.13.0"; sha256="1gp33ga0gdd09flz1c9q7hf3y8si238zb6hmn1v9pqmkww5pns3g"; depends=[MeSHDbi]; }; + MeSH_Dan_eg_db = derive2 { name="MeSH.Dan.eg.db"; version="1.13.0"; sha256="0v3jlfg95fgh4f5gnqz1prb2lwj1bn7ggparxqzc63j0jws0wmgp"; depends=[MeSHDbi]; }; + MeSH_Dda_3937_eg_db = derive2 { name="MeSH.Dda.3937.eg.db"; version="1.12.0"; sha256="1vhg07r0yk876zlzbn86nj6g91ilrnfrj3p5q2pkrcsic0m5nwcw"; depends=[MeSHDbi]; }; + MeSH_Ddi_AX4_eg_db = derive2 { name="MeSH.Ddi.AX4.eg.db"; version="1.13.0"; sha256="12kc26wsg390hzhi4x2rmnm1s38sqs4nckkvrnmv70mjabg34w49"; depends=[MeSHDbi]; }; + MeSH_Der_eg_db = derive2 { name="MeSH.Der.eg.db"; version="1.13.0"; sha256="171nrhd4nqpgcaaa62gj1di2xdsy3n8pp09lsbyq4slasmcd450w"; depends=[MeSHDbi]; }; + MeSH_Dgr_eg_db = derive2 { name="MeSH.Dgr.eg.db"; version="1.13.0"; sha256="15nb1pbnfkhr83q06irghi4r7la5h6dn993la3sn1f8614hcr2wd"; depends=[MeSHDbi]; }; + MeSH_Dme_eg_db = derive2 { name="MeSH.Dme.eg.db"; version="1.13.0"; sha256="1jgvbp0g4armmvg2w5rpxkx8zclll5nl6j6zbq9d1w7kk4lazw83"; depends=[MeSHDbi]; }; + MeSH_Dmo_eg_db = derive2 { name="MeSH.Dmo.eg.db"; version="1.13.0"; sha256="0p3p4ld74hszgvv6xd5kmd7i9glv1l4mdqigglr1sk4vig1qwg47"; depends=[MeSHDbi]; }; + MeSH_Dpe_eg_db = derive2 { name="MeSH.Dpe.eg.db"; version="1.13.0"; sha256="0pbd49s4n1mar58did4amrq5h78ic54gk6fnlyicddf7xg24qsp5"; depends=[MeSHDbi]; }; + MeSH_Dre_eg_db = derive2 { name="MeSH.Dre.eg.db"; version="1.13.0"; sha256="1bga7nlfkyqqxq4m9c44l6hnswqa3dfbjzbnnyh8xmyp7m91kbj3"; depends=[MeSHDbi]; }; + MeSH_Dse_eg_db = derive2 { name="MeSH.Dse.eg.db"; version="1.13.0"; sha256="0vaz520r54ydbb0why68hnigd924y3vk72357cms363qs6753dij"; depends=[MeSHDbi]; }; + MeSH_Dsi_eg_db = derive2 { name="MeSH.Dsi.eg.db"; version="1.13.0"; sha256="1fjdb5h3dsgxk38c1fff30knnhav9w6pdl7vqdfdhq7642c6a1y4"; depends=[MeSHDbi]; }; + MeSH_Dvi_eg_db = derive2 { name="MeSH.Dvi.eg.db"; version="1.13.0"; sha256="1vqwdf8sj0qid2df0qqhxlwbccmlmw63kmhdmz49fz3hxyr081z5"; depends=[MeSHDbi]; }; + MeSH_Dya_eg_db = derive2 { name="MeSH.Dya.eg.db"; version="1.13.0"; sha256="1ixn62rn6vc17ks23hn9hkfyynp3p7mf9wq3rw9wiyyzpl6xgqw0"; depends=[MeSHDbi]; }; + MeSH_Eco_55989_eg_db = derive2 { name="MeSH.Eco.55989.eg.db"; version="1.13.0"; sha256="118j864y3bn386cgjbwqwvdjflk7f510yzx451w9mcbfm7af8nqh"; depends=[MeSHDbi]; }; + MeSH_Eco_ED1a_eg_db = derive2 { name="MeSH.Eco.ED1a.eg.db"; version="1.13.0"; sha256="094h4w8p0h81pqz4f1ykk0285fq5cayvkv01712bi85qqvyc8vh0"; depends=[MeSHDbi]; }; + MeSH_Eco_IAI39_eg_db = derive2 { name="MeSH.Eco.IAI39.eg.db"; version="1.13.0"; sha256="19xj1x0bnxk8y3n7cjihp7aa1l6vvy6d3m949zv0cs9ia8mw5lrh"; depends=[MeSHDbi]; }; + MeSH_Eco_K12_MG1655_eg_db = derive2 { name="MeSH.Eco.K12.MG1655.eg.db"; version="1.13.0"; sha256="1m2zi73d23hqa7dn8ab6bm3ynjc4mngakcba5wa3fkvv972kba26"; depends=[MeSHDbi]; }; + MeSH_Eco_O157_H7_Sakai_eg_db = derive2 { name="MeSH.Eco.O157.H7.Sakai.eg.db"; version="1.13.0"; sha256="0sgp5hckh3waa1bp43rsnx6hlcvjr7a6yw46m6r3jzwdfpkmbh4v"; depends=[MeSHDbi]; }; + MeSH_Eco_UMN026_eg_db = derive2 { name="MeSH.Eco.UMN026.eg.db"; version="1.13.0"; sha256="17k0h1jfiqwg6396m3mnsq3v042p8rck19wdhrgdasb6vp7rnk7w"; depends=[MeSHDbi]; }; + MeSH_Eqc_eg_db = derive2 { name="MeSH.Eqc.eg.db"; version="1.13.0"; sha256="0z68zs190sv1v7r0059hf5c3mcrv2hil3hx3liycck2fiwarjw8d"; depends=[MeSHDbi]; }; + MeSH_Gga_eg_db = derive2 { name="MeSH.Gga.eg.db"; version="1.13.0"; sha256="0nbc8710nwjlxxcslljcfj72qlq1k64i8p4jvyddjp8fj8anca9f"; depends=[MeSHDbi]; }; + MeSH_Gma_eg_db = derive2 { name="MeSH.Gma.eg.db"; version="1.13.0"; sha256="0s45w1rnz79azqkk852knicviqc6jisxnpkzmm4j6ydjqibz4xv0"; depends=[MeSHDbi]; }; + MeSH_Hsa_eg_db = derive2 { name="MeSH.Hsa.eg.db"; version="1.13.0"; sha256="1azm323gqax1ffixvqqghqbbmv7gfq5jhxhn1qr07raml1z56yiw"; depends=[MeSHDbi]; }; + MeSH_Laf_eg_db = derive2 { name="MeSH.Laf.eg.db"; version="1.13.0"; sha256="0aix6k1lmdd4wms4dcmhw35gsyn07cvir60wslcabsvccjxbip4i"; depends=[MeSHDbi]; }; + MeSH_Lma_eg_db = derive2 { name="MeSH.Lma.eg.db"; version="1.13.0"; sha256="1fb3xhwf08h91pmb7nmkz68zwrg8ac1sk55923baa6bn9bwli2ny"; depends=[MeSHDbi]; }; + MeSH_Mdo_eg_db = derive2 { name="MeSH.Mdo.eg.db"; version="1.13.0"; sha256="0py8r05ix4k6xfm3jnzkgzk59gzc1bj43271rbgsmqlyh42abgay"; depends=[MeSHDbi]; }; + MeSH_Mes_eg_db = derive2 { name="MeSH.Mes.eg.db"; version="1.13.0"; sha256="01mmn4021cscnp9wfz84rxckqqfn4p98bh4g1mlgwb7wsgf5nbc9"; depends=[MeSHDbi]; }; + MeSH_Mga_eg_db = derive2 { name="MeSH.Mga.eg.db"; version="1.13.0"; sha256="1h4y7iqqb4fili8k4k11z5nmgd0hq8rw7p7awjwl6w5v4n9im0fs"; depends=[MeSHDbi]; }; + MeSH_Miy_eg_db = derive2 { name="MeSH.Miy.eg.db"; version="1.13.0"; sha256="03rj89bmw4j2fc9lnpwx479j5m089jcj6iisf339bzcw1rgryi56"; depends=[MeSHDbi]; }; + MeSH_Mml_eg_db = derive2 { name="MeSH.Mml.eg.db"; version="1.13.0"; sha256="1r2c422w1c88w4sh3s8mqpffx10322c3j44qz4ymxgvnarxc3fkh"; depends=[MeSHDbi]; }; + MeSH_Mmu_eg_db = derive2 { name="MeSH.Mmu.eg.db"; version="1.13.0"; sha256="09s2d9hjzzhlig2bnnr5wkpxgf8pj4q9hwvs4sj3ylabvlg5ak09"; depends=[MeSHDbi]; }; + MeSH_Mtr_eg_db = derive2 { name="MeSH.Mtr.eg.db"; version="1.13.0"; sha256="0l0w4px7wp58rqry4xbz2qh5jc97mmw7pvc1dnhkknr6n96fcpik"; depends=[MeSHDbi]; }; + MeSH_Nle_eg_db = derive2 { name="MeSH.Nle.eg.db"; version="1.13.0"; sha256="1v4jcsdww7j0rnck3r30g8p57419ai676qlawmra1w6sdflqcpj9"; depends=[MeSHDbi]; }; + MeSH_Oan_eg_db = derive2 { name="MeSH.Oan.eg.db"; version="1.13.0"; sha256="0a6mxwmvsh6zcyqw83y7y1axviqrzy2kdbalh2w8xa3yn72z65ln"; depends=[MeSHDbi]; }; + MeSH_Ocu_eg_db = derive2 { name="MeSH.Ocu.eg.db"; version="1.13.0"; sha256="1n197svyc3p4xf3lc5qdjnhlkiadra43bxdqisk2w60jdijnxyh0"; depends=[MeSHDbi]; }; + MeSH_Oni_eg_db = derive2 { name="MeSH.Oni.eg.db"; version="1.13.0"; sha256="1h7iqb9kcxcgslm8rab4469vvay3msd3w08bxv3h0mq7q870z0r8"; depends=[MeSHDbi]; }; + MeSH_Osa_eg_db = derive2 { name="MeSH.Osa.eg.db"; version="1.13.0"; sha256="0mxs9bjs0pnj9aszfdydkw2kljcixwflvwcaz94my30444c1pi9l"; depends=[MeSHDbi]; }; + MeSH_PCR_db = derive2 { name="MeSH.PCR.db"; version="1.13.0"; sha256="03fcidamz9x0xgyl5fsvphc7l5v2hvr4izf6ma2g34a1l1qhs0g1"; depends=[MeSHDbi]; }; + MeSH_Pab_eg_db = derive2 { name="MeSH.Pab.eg.db"; version="1.13.0"; sha256="0vyi7awyy3v851ylc95xrn5wvbprq1qq3x1ypsb31qqny940m5rf"; depends=[MeSHDbi]; }; + MeSH_Pae_PAO1_eg_db = derive2 { name="MeSH.Pae.PAO1.eg.db"; version="1.13.0"; sha256="18amkwn9wglj3a5hh9b0zfd23vizmj1nfa90jz93w1adksjlky7v"; depends=[MeSHDbi]; }; + MeSH_Pfa_3D7_eg_db = derive2 { name="MeSH.Pfa.3D7.eg.db"; version="1.13.0"; sha256="1yrx8dj0lx77qny0dha68lwy3x3c9d4rkb8gng3by55zgp6hghms"; depends=[MeSHDbi]; }; + MeSH_Pto_eg_db = derive2 { name="MeSH.Pto.eg.db"; version="1.13.0"; sha256="18x1q7md0zvb233qw1x6qs8k55hjkh1nd1cvizs2vhsbvzfw9yjz"; depends=[MeSHDbi]; }; + MeSH_Ptr_eg_db = derive2 { name="MeSH.Ptr.eg.db"; version="1.13.0"; sha256="1fqi308z4psspykj1dkq76v94641wq9mnxwj3yzd9j49c8x45294"; depends=[MeSHDbi]; }; + MeSH_Rno_eg_db = derive2 { name="MeSH.Rno.eg.db"; version="1.13.0"; sha256="0kakfkkmvmlk22g1aa86grahfbvk8hainar1760r5j8zrny8dvvr"; depends=[MeSHDbi]; }; + MeSH_Sce_S288c_eg_db = derive2 { name="MeSH.Sce.S288c.eg.db"; version="1.13.0"; sha256="09gzlfp958bfkvas0hxaw6r319y02sygmb7ywxvdqj41sxyv63zp"; depends=[MeSHDbi]; }; + MeSH_Sco_A32_eg_db = derive2 { name="MeSH.Sco.A32.eg.db"; version="1.13.0"; sha256="0cm3352chz3qaknq0an8gfsk2xbfn0jw5rqss3lrxcq35x1qk21a"; depends=[MeSHDbi]; }; + MeSH_Sil_eg_db = derive2 { name="MeSH.Sil.eg.db"; version="1.13.0"; sha256="1hpj2cr8gixqlvfhnqvr5m3m1ngfdrvavqipf38m5cnm1wlqk9ll"; depends=[MeSHDbi]; }; + MeSH_Spu_eg_db = derive2 { name="MeSH.Spu.eg.db"; version="1.13.0"; sha256="1ryrr1mr7w6h8xs4f79zmnnv8j4mkjckxjk4npcdiilfb2zg1y3j"; depends=[MeSHDbi]; }; + MeSH_Ssc_eg_db = derive2 { name="MeSH.Ssc.eg.db"; version="1.13.0"; sha256="10ygdjx63ajd1vsgrn2f8isvaxdf2p6yg45yqrmjv3zhbvi1aav1"; depends=[MeSHDbi]; }; + MeSH_Syn_eg_db = derive2 { name="MeSH.Syn.eg.db"; version="1.13.0"; sha256="153i3ln2m8rb0445hjplnim4h8dvvmf370zglcc5ww9dcx9m93nb"; depends=[MeSHDbi]; }; + MeSH_Tbr_9274_eg_db = derive2 { name="MeSH.Tbr.9274.eg.db"; version="1.13.0"; sha256="0sm2sg246w35vfv9dam40x85mdv18fpi5j1k31432chrda867rf0"; depends=[MeSHDbi]; }; + MeSH_Tgo_ME49_eg_db = derive2 { name="MeSH.Tgo.ME49.eg.db"; version="1.13.0"; sha256="0xqapk2fkaj719ih818rpb1ciiblw6zr6a83y0xpwrm8y29m3qh5"; depends=[MeSHDbi]; }; + MeSH_Tgu_eg_db = derive2 { name="MeSH.Tgu.eg.db"; version="1.13.0"; sha256="0zfrjhrw2jrk6yzkmjnxfqws1a2sylpz1rz2im5n3xnlk6l5d0zn"; depends=[MeSHDbi]; }; + MeSH_Vvi_eg_db = derive2 { name="MeSH.Vvi.eg.db"; version="1.13.0"; sha256="0v6g4wqsph3jhxziayijqn63cjp9z4i6jpm5wk431qp9zhr3vw4w"; depends=[MeSHDbi]; }; + MeSH_Xla_eg_db = derive2 { name="MeSH.Xla.eg.db"; version="1.13.0"; sha256="1v2blabzcd1vdmc47m9rfknlf4865ppvfx8p2nm9cilrwp29w1pk"; depends=[MeSHDbi]; }; + MeSH_Xtr_eg_db = derive2 { name="MeSH.Xtr.eg.db"; version="1.13.0"; sha256="0ymc65z935yzz0dxvrlx1wj40zmd7192jdav3736syhq6jrwmq3d"; depends=[MeSHDbi]; }; + MeSH_Zma_eg_db = derive2 { name="MeSH.Zma.eg.db"; version="1.13.0"; sha256="1vnh6y9jr03cmncyka886wq59qnbpk1d3sqryxjd3d3hyhg7jz7b"; depends=[MeSHDbi]; }; + MeSH_db = derive2 { name="MeSH.db"; version="1.13.0"; sha256="1fdqzbka0bbpzphr64sjabddr1a7mrk310mzjfrwd6sll54am9q8"; depends=[MeSHDbi]; }; MmAgilentDesign026655_db = derive2 { name="MmAgilentDesign026655.db"; version="3.2.3"; sha256="00d0yjcb5id7zacx4bzdwy4q6f4qvnnx8ph4d4xz1fmcbspz2qiz"; depends=[AnnotationDbi org_Mm_eg_db]; }; MoExExonProbesetLocation = derive2 { name="MoExExonProbesetLocation"; version="1.15.0"; sha256="0bvj3bji4bwwmxjz4b57n1aqypdibdmry30rfwmlxss1hav96sl7"; depends=[AnnotationDbi]; }; Mu15v1_db = derive2 { name="Mu15v1.db"; version="3.2.3"; sha256="0qchqkbx6ybijab8qhflxj33kwksfll1d3d3917vydjac9fzw1lz"; depends=[AnnotationDbi org_Mm_eg_db]; }; @@ -256,8 +263,8 @@ in with self; { Mus_musculus = derive2 { name="Mus.musculus"; version="1.3.1"; sha256="143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"; depends=[AnnotationDbi GenomicFeatures GO_db org_Mm_eg_db OrganismDbi TxDb_Mmusculus_UCSC_mm10_knownGene]; }; Norway981_db = derive2 { name="Norway981.db"; version="3.2.3"; sha256="04ngc2hilqi9m7933mnm7jcvkxlz68vqqh5b628db575vcxql9b9"; depends=[AnnotationDbi org_Hs_eg_db]; }; OperonHumanV3_db = derive2 { name="OperonHumanV3.db"; version="3.2.3"; sha256="082gff88cwk2p50q8g9bixggacaclgqcvk6w5dc11h9fkgvd160i"; depends=[AnnotationDbi org_Hs_eg_db]; }; - PANTHER_db = derive2 { name="PANTHER.db"; version="1.0.4"; sha256="1vl8anixkhcb9axlszk479yaw48bz1hhgmff41nqk8k8w4jkyn1y"; depends=[AnnotationDbi RSQLite]; }; - PFAM_db = derive2 { name="PFAM.db"; version="3.7.0"; sha256="0ih3xz8vk80xzqwgv6ff3rp1a24qhwd1v1frkq1m6d981g7ymdap"; depends=[AnnotationDbi]; }; + PANTHER_db = derive2 { name="PANTHER.db"; version="1.0.10"; sha256="05jyss22q68j7i773ss29g9z1yifi5xsp7qjaq3f5gwy3131x485"; depends=[AnnotationDbi AnnotationHub BiocFileCache RSQLite]; }; + PFAM_db = derive2 { name="PFAM.db"; version="3.10.0"; sha256="0n71xwg062pvlwvx882m8615d5h9rcxsl20b1sn314p6bkwqi203"; depends=[AnnotationDbi]; }; POCRCannotation_db = derive2 { name="POCRCannotation.db"; version="3.2.3"; sha256="0ybvs4hrxpivdkhm0fxpib11vlxqqdk8prlyj78vj5qzyb3iy89d"; depends=[AnnotationDbi org_Hs_eg_db]; }; PartheenMetaData_db = derive2 { name="PartheenMetaData.db"; version="3.2.3"; sha256="0d37c5b7s3fgkkvg7sj7gl9ksrjk5pyyv54vkys8w3qwgsm8yrdz"; depends=[AnnotationDbi org_Hs_eg_db]; }; PolyPhen_Hsapiens_dbSNP131 = derive2 { name="PolyPhen.Hsapiens.dbSNP131"; version="1.0.2"; sha256="1kikygkli41sn3rqihz0924prmqg2264ifj29vmg1a7qccm0kf7c"; depends=[AnnotationDbi RSQLite VariantAnnotation]; }; @@ -282,35 +289,41 @@ in with self; { TxDb_Athaliana_BioMart_plantsmart22 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart22"; version="3.0.1"; sha256="0j2zr4cddad7z1lxx9m9kfgyy7jajjnblpk9j8igd39ia3ixrpzc"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Athaliana_BioMart_plantsmart25 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart25"; version="3.1.3"; sha256="0a6v0l6p13zmiysi3k8dxzdlxng552qqj9rnlbdavdiidla0pvm3"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Athaliana_BioMart_plantsmart28 = derive2 { name="TxDb.Athaliana.BioMart.plantsmart28"; version="3.2.2"; sha256="1yjyvrbx55y024lqg3b2rlf8pngqw5xi3p83j5ipan05wf0aq6ir"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Btaurus_UCSC_bosTau8_refGene = derive2 { name="TxDb.Btaurus.UCSC.bosTau8.refGene"; version="3.4.4"; sha256="18gmx57savyvvdkgnrvmc4xj3xrakybyx4pkfmpabnqy29z6n71q"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Celegans_UCSC_ce11_refGene = derive2 { name="TxDb.Celegans.UCSC.ce11.refGene"; version="3.4.4"; sha256="04jcx40z2380x760wbl686zvm780y38kls1js215jhmw7hff8md5"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Btaurus_UCSC_bosTau8_refGene = derive2 { name="TxDb.Btaurus.UCSC.bosTau8.refGene"; version="3.10.0"; sha256="1pg08ks4nk5zqfmrjnf5cl46sfv7n4r1kvq31xvsgdl01lkq5yh1"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Btaurus_UCSC_bosTau9_refGene = derive2 { name="TxDb.Btaurus.UCSC.bosTau9.refGene"; version="3.10.0"; sha256="1v7q9jaaj1n2vabjj6ij6pz0g89nqlyy4y4g65irz6cm5mvik4q9"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Celegans_UCSC_ce11_ensGene = derive2 { name="TxDb.Celegans.UCSC.ce11.ensGene"; version="3.4.6"; sha256="0pnqmyi5v9gsk2b56pfxf9qam9nvdmg5j1zag166yzzx0hipasm8"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Celegans_UCSC_ce11_refGene = derive2 { name="TxDb.Celegans.UCSC.ce11.refGene"; version="3.4.6"; sha256="1aq4jhn2c67wibq02l8drrjscmicbj6z35d0jksq8mwhz8k30zn6"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Celegans_UCSC_ce6_ensGene = derive2 { name="TxDb.Celegans.UCSC.ce6.ensGene"; version="3.2.2"; sha256="1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Cfamiliaris_UCSC_canFam3_refGene = derive2 { name="TxDb.Cfamiliaris.UCSC.canFam3.refGene"; version="3.4.4"; sha256="1rl7yc2csc3fs2iri0kkvpjv34jnhkzc0jhh2a3hnyvhv55lzmf0"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Cfamiliaris_UCSC_canFam3_refGene = derive2 { name="TxDb.Cfamiliaris.UCSC.canFam3.refGene"; version="3.10.0"; sha256="0n6zlaq9ysfsas75j9ysa3zdgy2y01phdq16gisqh1limsdwalky"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Dmelanogaster_UCSC_dm3_ensGene = derive2 { name="TxDb.Dmelanogaster.UCSC.dm3.ensGene"; version="3.2.2"; sha256="1337x23rdmiiza83ms225kri37h16q5hw1lw0m577abcgip3d7c7"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Dmelanogaster_UCSC_dm6_ensGene = derive2 { name="TxDb.Dmelanogaster.UCSC.dm6.ensGene"; version="3.4.4"; sha256="18nwjnkbrvrkk6g5jns3h55874hk92fdbrfyjvvxk4daw0p7gii8"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Drerio_UCSC_danRer10_refGene = derive2 { name="TxDb.Drerio.UCSC.danRer10.refGene"; version="3.4.4"; sha256="1ck4ymlxj0fjrbgxzgdqgbyl3z4nqyc6bczw1cgwblmcv52h3cj0"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Ggallus_UCSC_galGal4_refGene = derive2 { name="TxDb.Ggallus.UCSC.galGal4.refGene"; version="3.4.4"; sha256="1cxdrdg3pqwi0rfk5bzik05r1hvxwsva862b7cf7pfcf202dkqg5"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Ggallus_UCSC_galGal5_refGene = derive2 { name="TxDb.Ggallus.UCSC.galGal5.refGene"; version="3.4.4"; sha256="15laq4kdm85755lk176lqsi2aryi9i85b4c1arrj4qgjkjrbylvq"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Dmelanogaster_UCSC_dm6_ensGene = derive2 { name="TxDb.Dmelanogaster.UCSC.dm6.ensGene"; version="3.4.6"; sha256="05nmvqshin09k0rzxr8kn38b7h6bv5g8ycdvi4bvq5pq0q5p59bw"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Drerio_UCSC_danRer10_refGene = derive2 { name="TxDb.Drerio.UCSC.danRer10.refGene"; version="3.4.6"; sha256="1isd4idvh9flvirrq760cw5lc1nwqjx0q76p9dp01wbbbsb3rfnk"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Drerio_UCSC_danRer11_refGene = derive2 { name="TxDb.Drerio.UCSC.danRer11.refGene"; version="3.4.6"; sha256="0p5pr0fq1l9bp019w2214szf78y3nbw0p4819jcnba1v50y3336l"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Ggallus_UCSC_galGal4_refGene = derive2 { name="TxDb.Ggallus.UCSC.galGal4.refGene"; version="3.10.0"; sha256="05ssas7dgyz5zz6r5m1fs2pzcvgkzn5pjpw7lrka7jjghi4a4cfh"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Ggallus_UCSC_galGal5_refGene = derive2 { name="TxDb.Ggallus.UCSC.galGal5.refGene"; version="3.10.0"; sha256="1xlpxaay56mgnz03mm351xw1xdpc80d70dvvqmllwmnmq1p5s70m"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Ggallus_UCSC_galGal6_refGene = derive2 { name="TxDb.Ggallus.UCSC.galGal6.refGene"; version="3.10.0"; sha256="0ddibdn6shlhqfmlajnq754z4vad7gi55vb5y8j89nc2k1sc5a3i"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Hsapiens_BioMart_igis = derive2 { name="TxDb.Hsapiens.BioMart.igis"; version="2.3.2"; sha256="0590a2hkrpm33hmjg5g0gm6sig3xvc09m0q6lwmafgaajf90h6ky"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Hsapiens_UCSC_hg18_knownGene = derive2 { name="TxDb.Hsapiens.UCSC.hg18.knownGene"; version="3.2.2"; sha256="1yk9ggclkqqfzrdp8gcqyplvif824pa7df54ck5gb1xb9q5s975w"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Hsapiens_UCSC_hg19_knownGene = derive2 { name="TxDb.Hsapiens.UCSC.hg19.knownGene"; version="3.2.2"; sha256="1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Hsapiens_UCSC_hg19_lincRNAsTranscripts = derive2 { name="TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts"; version="3.2.2"; sha256="0bmbp7kydvviczw8axgxq2wdlwq6fdas90jk9bg56avjq5syws2g"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Hsapiens_UCSC_hg38_knownGene = derive2 { name="TxDb.Hsapiens.UCSC.hg38.knownGene"; version="3.4.0"; sha256="0i0xw0mcn403r911ijqdnrwg9k5bspdnjibfjvnhxq4h8vcfprn5"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Mmulatta_UCSC_rheMac3_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac3.refGene"; version="3.4.4"; sha256="13nv7l71piwf0frnwplwbac82ad7vxbw31yrfnqvnd1knh7ns99x"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Mmulatta_UCSC_rheMac8_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac8.refGene"; version="3.4.4"; sha256="1qgm66hnhqb3jyal8s43yri96k1xwb3vamb83894n86bh2g6nlca"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Hsapiens_UCSC_hg38_knownGene = derive2 { name="TxDb.Hsapiens.UCSC.hg38.knownGene"; version="3.10.0"; sha256="0lqir16l8wphhpaizmvgmjzk40p90rzgqndgvbms7ickinrpg59s"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Mmulatta_UCSC_rheMac10_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac10.refGene"; version="3.10.0"; sha256="1d1gvs6877649zwgja1z5x0mgci2kirbj7pzhb22xyinif3bhz26"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Mmulatta_UCSC_rheMac3_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac3.refGene"; version="3.10.0"; sha256="073w43cm09wj4y7xaml8f0wls7kskymlb4rw5cijhifjbp17kpyh"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Mmulatta_UCSC_rheMac8_refGene = derive2 { name="TxDb.Mmulatta.UCSC.rheMac8.refGene"; version="3.10.0"; sha256="08l242l9j6r17ghmlxgmz3chdq781kv5zaayhh487qp7rsyz3scg"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Mmusculus_UCSC_mm10_ensGene = derive2 { name="TxDb.Mmusculus.UCSC.mm10.ensGene"; version="3.4.0"; sha256="0saxi1fdiwd38sfvy1rynd3v44rbp158jv6sjqcivvaqnd84zg9s"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Mmusculus_UCSC_mm10_knownGene = derive2 { name="TxDb.Mmusculus.UCSC.mm10.knownGene"; version="3.4.4"; sha256="01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Mmusculus_UCSC_mm10_knownGene = derive2 { name="TxDb.Mmusculus.UCSC.mm10.knownGene"; version="3.10.0"; sha256="0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Mmusculus_UCSC_mm9_knownGene = derive2 { name="TxDb.Mmusculus.UCSC.mm9.knownGene"; version="3.2.2"; sha256="16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Ptroglodytes_UCSC_panTro4_refGene = derive2 { name="TxDb.Ptroglodytes.UCSC.panTro4.refGene"; version="3.4.4"; sha256="12fdcs4vv4l0d3sksdq76nwwj88f8psiy84rd1jhfw8kbxqrhh8y"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Ptroglodytes_UCSC_panTro5_refGene = derive2 { name="TxDb.Ptroglodytes.UCSC.panTro5.refGene"; version="3.4.4"; sha256="00mirzp38iqm0l0py1a7mlslnbmkfzzk1krcg6jdyr8gan2sskpi"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Ptroglodytes_UCSC_panTro4_refGene = derive2 { name="TxDb.Ptroglodytes.UCSC.panTro4.refGene"; version="3.10.0"; sha256="18kqikxrcln4mbl216jrs4wx20a9l7x8v23kapy91svi2br900f5"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Ptroglodytes_UCSC_panTro5_refGene = derive2 { name="TxDb.Ptroglodytes.UCSC.panTro5.refGene"; version="3.10.0"; sha256="05ydg49rh8idjqxyvrcfc3mwsb1xj4bnjww46gnpgm4hp9na9swy"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Ptroglodytes_UCSC_panTro6_refGene = derive2 { name="TxDb.Ptroglodytes.UCSC.panTro6.refGene"; version="3.10.0"; sha256="0z4lq7wy48kkxnx29zmrbmrq4qjrj3digwxkw3x54qq80nvzxiza"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Rnorvegicus_BioMart_igis = derive2 { name="TxDb.Rnorvegicus.BioMart.igis"; version="2.3.2"; sha256="1099vkk8g3lxbgjxsm1p1m3mjj08nsw282mqxgzpnrxf7m6jll76"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Rnorvegicus_UCSC_rn4_ensGene = derive2 { name="TxDb.Rnorvegicus.UCSC.rn4.ensGene"; version="3.2.2"; sha256="0gv8bynfxxa471ap069mjvfrb1d7a0c4w5k8hxkr4hnsm44mschm"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Rnorvegicus_UCSC_rn5_refGene = derive2 { name="TxDb.Rnorvegicus.UCSC.rn5.refGene"; version="3.4.4"; sha256="1h9vmsp8lcr8yyvd1mjm81p8l660bjsx2kyhg3wm96izxgd4i7gn"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Rnorvegicus_UCSC_rn6_refGene = derive2 { name="TxDb.Rnorvegicus.UCSC.rn6.refGene"; version="3.4.4"; sha256="1k4g78kh52ppr4fd5z4bwzzgw8jg6j3zi129fnny4ks6zkadhlw6"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Rnorvegicus_UCSC_rn5_refGene = derive2 { name="TxDb.Rnorvegicus.UCSC.rn5.refGene"; version="3.10.0"; sha256="1n9x827chp71cv8jm3mm3srr2id4iifnpwmvmrd68a82j03pxljh"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Rnorvegicus_UCSC_rn6_refGene = derive2 { name="TxDb.Rnorvegicus.UCSC.rn6.refGene"; version="3.4.6"; sha256="1piqli0wdq3r289is8lmijnshm8rmx7rphp2qfymlvc0jmvgs9wr"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Scerevisiae_UCSC_sacCer2_sgdGene = derive2 { name="TxDb.Scerevisiae.UCSC.sacCer2.sgdGene"; version="3.2.2"; sha256="0l5gcwhbvzx60p9hjhd31angamb0hkgdg2avga7341j77rd5pwza"; depends=[AnnotationDbi GenomicFeatures]; }; TxDb_Scerevisiae_UCSC_sacCer3_sgdGene = derive2 { name="TxDb.Scerevisiae.UCSC.sacCer3.sgdGene"; version="3.2.2"; sha256="1sjwl7fb3l3zxxbk8gkvzxwdsind0xjj7kmh7dachm6fi17hpb3d"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Sscrofa_UCSC_susScr11_refGene = derive2 { name="TxDb.Sscrofa.UCSC.susScr11.refGene"; version="3.4.4"; sha256="1c6kbkp6iq6zzpg6wpnbgclp1vsdhh19g220va8b61jhgcccr2c6"; depends=[AnnotationDbi GenomicFeatures]; }; - TxDb_Sscrofa_UCSC_susScr3_refGene = derive2 { name="TxDb.Sscrofa.UCSC.susScr3.refGene"; version="3.4.4"; sha256="1yvjwsq9cn9kyjir53n20fbi8nyf1m64zim18w5mv05w9rn86gdl"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Sscrofa_UCSC_susScr11_refGene = derive2 { name="TxDb.Sscrofa.UCSC.susScr11.refGene"; version="3.10.0"; sha256="02xfl6265wp5qbjnyj45w5lwlx2sfnarxy69cckpf5x0az910i52"; depends=[AnnotationDbi GenomicFeatures]; }; + TxDb_Sscrofa_UCSC_susScr3_refGene = derive2 { name="TxDb.Sscrofa.UCSC.susScr3.refGene"; version="3.10.0"; sha256="0kvnxzkvjra9a3wf2qgv3lq89h1hk6fa0x7v9afwwi99xhfww2yc"; depends=[AnnotationDbi GenomicFeatures]; }; XtraSNPlocs_Hsapiens_dbSNP141_GRCh38 = derive2 { name="XtraSNPlocs.Hsapiens.dbSNP141.GRCh38"; version="0.99.12"; sha256="0a27y0ngg760y5wwcja4dpd7cjd8h5zg1s2b3a1r54s21k65zny3"; depends=[BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; XtraSNPlocs_Hsapiens_dbSNP144_GRCh37 = derive2 { name="XtraSNPlocs.Hsapiens.dbSNP144.GRCh37"; version="0.99.12"; sha256="0k823fvqjmdkmd47m7wyra6jxmv8lnk2i1xl4pp0mh3zgb87hgfb"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; XtraSNPlocs_Hsapiens_dbSNP144_GRCh38 = derive2 { name="XtraSNPlocs.Hsapiens.dbSNP144.GRCh38"; version="0.99.12"; sha256="0d4q32ij2x4726wvw06sgmivid0n94vfdmszdyh607xlcahqxa5z"; depends=[BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; @@ -320,22 +333,22 @@ in with self; { agprobe = derive2 { name="agprobe"; version="2.18.0"; sha256="1vnawamcpz16na8nmlq2czfxcr325fwdnngxl65mmnbd0f4lmy3k"; depends=[AnnotationDbi]; }; alternativeSplicingEvents_hg19 = derive2 { name="alternativeSplicingEvents.hg19"; version="1.0.1"; sha256="1v714abdpzhwa450zr66s1yjpxl6lkwi3wjbwn8phn87cgf8rj7q"; depends=[AnnotationHub]; }; alternativeSplicingEvents_hg38 = derive2 { name="alternativeSplicingEvents.hg38"; version="1.0.1"; sha256="0im87mrh1n6kv84q6lm4y15lb93rih88zdpa0jms5az91lyvsf25"; depends=[AnnotationHub]; }; - anopheles_db0 = derive2 { name="anopheles.db0"; version="3.7.1"; sha256="0f940ybh7kr30d9pkqhr0w2yrwsqa25yxbhzhlccn4a6a6svzcwb"; depends=[AnnotationDbi]; }; - arabidopsis_db0 = derive2 { name="arabidopsis.db0"; version="3.7.1"; sha256="1d7cnhbm44dv0g6mjv76sdr8dgni34fbffzkk95rqikdqag8s9cy"; depends=[AnnotationDbi]; }; + anopheles_db0 = derive2 { name="anopheles.db0"; version="3.10.0"; sha256="0rpani2ma6mg0nhlja67m2nm7jfb15c9nhrvjaa8i35z1hryhz6b"; depends=[AnnotationDbi]; }; + arabidopsis_db0 = derive2 { name="arabidopsis.db0"; version="3.10.0"; sha256="14hxvyz8xzkrsirpjy88lzfras99hchzggcs2lvhg2lx858sv0i2"; depends=[AnnotationDbi]; }; ath1121501_db = derive2 { name="ath1121501.db"; version="3.2.3"; sha256="1zrf26cfhlmrb5pyfawwk4v8l1mflx8c43zsxrwkbmxzc1jnc7dv"; depends=[AnnotationDbi org_At_tair_db]; }; ath1121501cdf = derive2 { name="ath1121501cdf"; version="2.18.0"; sha256="1naq8f8dwgbmndx178nm2pw6hjx5ljx0w1wb4dfjifnl4bs5rqcc"; depends=[AnnotationDbi]; }; ath1121501probe = derive2 { name="ath1121501probe"; version="2.18.0"; sha256="0a2nd8zhp3ybis780l3rrmwcxskbl3a111g8w6m8qfwsw5vnlqg1"; depends=[AnnotationDbi]; }; barley1cdf = derive2 { name="barley1cdf"; version="2.18.0"; sha256="0rbij5cqr2sz33y5waybv85nrcgf70iwj5gk13g0xn9p1l1zxyn2"; depends=[AnnotationDbi]; }; barley1probe = derive2 { name="barley1probe"; version="2.18.0"; sha256="1kh5r748b4vkmvlfaclmrh07ypbrzgxn90liqfz1rwkabh6rfk71"; depends=[AnnotationDbi]; }; bovine_db = derive2 { name="bovine.db"; version="3.2.3"; sha256="1i8mgk60hlmvngb4c727wajix9mca9gfg0pzxrnfcjwi87rpw7fy"; depends=[AnnotationDbi org_Bt_eg_db]; }; - bovine_db0 = derive2 { name="bovine.db0"; version="3.7.1"; sha256="17q8hkfips8znwnkk062m8xsvcpaf6ynpf2jjszrcm02495vbw45"; depends=[AnnotationDbi]; }; + bovine_db0 = derive2 { name="bovine.db0"; version="3.10.0"; sha256="07dg88d10cb4b5cwr7la9lj4wmn6hmhl90ilhgd5i9ai1n4v925d"; depends=[AnnotationDbi]; }; bovinecdf = derive2 { name="bovinecdf"; version="2.18.0"; sha256="13mf0yy0dypkm5n2ghl04xm6ayb9bn9qijqhgynksghi7s2k34mb"; depends=[AnnotationDbi]; }; bovineprobe = derive2 { name="bovineprobe"; version="2.18.0"; sha256="0i4afa5dksnir2nfrfh2cynjm59sm6vfaqa9wyag8cxg7c2nlm1i"; depends=[AnnotationDbi]; }; bsubtiliscdf = derive2 { name="bsubtiliscdf"; version="2.18.0"; sha256="1rihrjim37b49rhqr4nxga8sp67qri9xqlqc141mhbngh6cw3iyl"; depends=[AnnotationDbi]; }; bsubtilisprobe = derive2 { name="bsubtilisprobe"; version="2.18.0"; sha256="0k99hvgaswn96x4yanvr9cy8bdy69sd5q7yp6dj9synxj7s1fcw9"; depends=[AnnotationDbi]; }; cMAP = derive2 { name="cMAP"; version="1.15.1"; sha256="0pzizm27rgcaic7wsh52z30v1jwarmz4cwh1mksbygp63k54mwiv"; depends=[]; }; canine_db = derive2 { name="canine.db"; version="3.2.3"; sha256="0wbyzhk827l49yxzimvznx9z6yag5nd4djm2hddysf5nk1ndapqs"; depends=[AnnotationDbi org_Cf_eg_db]; }; - canine_db0 = derive2 { name="canine.db0"; version="3.7.1"; sha256="1z691m0ap7x5sb7pbxlk8cs5s6hwvgvdbjjdxlfp8vilciwrsgwn"; depends=[AnnotationDbi]; }; + canine_db0 = derive2 { name="canine.db0"; version="3.10.0"; sha256="1zi3g22iagpxs4j9p07g5lss0bvxmhp0lkq3dwchzd0bddph8xnn"; depends=[AnnotationDbi]; }; canine2_db = derive2 { name="canine2.db"; version="3.2.3"; sha256="1gzd2x23dkfiwnwqz9pdn5lp4l8aby525mhscn3xakw633si4dvz"; depends=[AnnotationDbi org_Cf_eg_db]; }; canine2cdf = derive2 { name="canine2cdf"; version="2.18.0"; sha256="077cmmnhjdk0vxjzm1kqf3q5kgx6chwkm59dr4s5dy019rqb6sqr"; depends=[AnnotationDbi]; }; canine2probe = derive2 { name="canine2probe"; version="2.18.0"; sha256="1l849a1dqy4kpcsxs0lvb48ag81i0f0ys0w4757rw4kp8ry59z4b"; depends=[AnnotationDbi]; }; @@ -345,10 +358,10 @@ in with self; { celeganscdf = derive2 { name="celeganscdf"; version="2.18.0"; sha256="0a6w0a48azg0i21j3aqb7fnxck3ff9w3gsi89bnlfh0zx6pknx7p"; depends=[AnnotationDbi]; }; celegansprobe = derive2 { name="celegansprobe"; version="2.18.0"; sha256="05k7si3f8pzkyb8jv0r2vkavbrqxsn4nawl92gcphfsylrwcddqb"; depends=[AnnotationDbi]; }; chicken_db = derive2 { name="chicken.db"; version="3.2.3"; sha256="1rq9afkpcpv8qi75shvnsw8di3ycai4ylv7jq9zwj51zlwlw9cpq"; depends=[AnnotationDbi org_Gg_eg_db]; }; - chicken_db0 = derive2 { name="chicken.db0"; version="3.7.1"; sha256="0jib8pamnqzppk2x1i8c7szrwvhhilsxbk2x83ajzbzk3df3rvnd"; depends=[AnnotationDbi]; }; + chicken_db0 = derive2 { name="chicken.db0"; version="3.10.0"; sha256="0k4qwid7pf385l1q76hijmv79dwll1d84812l3hjcy40v7vn2x3k"; depends=[AnnotationDbi]; }; chickencdf = derive2 { name="chickencdf"; version="2.18.0"; sha256="09hhim5s9xj7n2b5rhn1svf5qly2mn0rr2v2ls25hfzyrqcbxlz1"; depends=[AnnotationDbi]; }; chickenprobe = derive2 { name="chickenprobe"; version="2.18.0"; sha256="1fdsiwfyg7fwslrr7xs3gny7sw24bzg5k1fvlyzb1477sgj0pid3"; depends=[AnnotationDbi]; }; - chimp_db0 = derive2 { name="chimp.db0"; version="3.7.1"; sha256="0bgn2yjj1jg0dswn5m4n78lydlzz7qb8fxpm8pl7909xrkcd1lpw"; depends=[AnnotationDbi]; }; + chimp_db0 = derive2 { name="chimp.db0"; version="3.10.0"; sha256="0yays3mn92k9b5ardq7bav9qd2v5pr6pm5zrsn0n26yqb585rhqv"; depends=[AnnotationDbi]; }; citruscdf = derive2 { name="citruscdf"; version="2.18.0"; sha256="1326mj1xf3k4v5iyyn46whx24qfng0x3cv6rvckdr1ycc1v887dn"; depends=[AnnotationDbi]; }; citrusprobe = derive2 { name="citrusprobe"; version="2.18.0"; sha256="0bf1wic136cxwgs4j13wsyqasnyvr0jw1hzg6qizndmy7g8hrb87"; depends=[AnnotationDbi]; }; clariomdhumanprobeset_db = derive2 { name="clariomdhumanprobeset.db"; version="8.7.0"; sha256="039bsywnim0nr8b3w6vkj4m20j0pggnm6ajjz24bnlikm9zzrs6l"; depends=[AnnotationDbi org_Hs_eg_db]; }; @@ -371,14 +384,14 @@ in with self; { ecoli2_db = derive2 { name="ecoli2.db"; version="3.2.3"; sha256="07vc5fl2zq2f65ndcldyzvwfpl65snp6ygvw658j4036lbb7cpjl"; depends=[AnnotationDbi org_EcK12_eg_db]; }; ecoli2cdf = derive2 { name="ecoli2cdf"; version="2.18.0"; sha256="1rkxrwadq9kg9685z9pg6rgc4bblkx5p3c6snsl4gv2k188dva9r"; depends=[AnnotationDbi]; }; ecoli2probe = derive2 { name="ecoli2probe"; version="2.18.0"; sha256="11q4ka0ncjapahic49xdl9919vm9frrwlqgj101krgkg262lfm8n"; depends=[AnnotationDbi]; }; - ecoliK12_db0 = derive2 { name="ecoliK12.db0"; version="3.7.1"; sha256="075ngixclxh1qqgn5p1afxyx8610rfxj1ax3iqmbvqqlyq9nc9ar"; depends=[AnnotationDbi]; }; - ecoliSakai_db0 = derive2 { name="ecoliSakai.db0"; version="3.7.1"; sha256="1p3lvf92l44kqn47jhgwd6nqnjl0ksnvmsj1052lrbalh5xl3rcd"; depends=[AnnotationDbi]; }; + ecoliK12_db0 = derive2 { name="ecoliK12.db0"; version="3.10.0"; sha256="1vhb7dlva48arf1rqgnyzv9zk34sy1r1j4fhd7j1gyyhzgikih1x"; depends=[AnnotationDbi]; }; + ecoliSakai_db0 = derive2 { name="ecoliSakai.db0"; version="3.10.0"; sha256="1zcfpra075yqycfghmdplqsrw6ywwmzpjph5cxh2l7kar4pmir3c"; depends=[AnnotationDbi]; }; ecoliasv2cdf = derive2 { name="ecoliasv2cdf"; version="2.18.0"; sha256="16i6has9qgmzakcy24racc1h9j331wndv5c87qp5r1zrai61zyav"; depends=[AnnotationDbi]; }; ecoliasv2probe = derive2 { name="ecoliasv2probe"; version="2.18.0"; sha256="1hfrnal170cdigc2fmnynb75jjsiq77p4x6ws9gah558hvx87nk3"; depends=[AnnotationDbi]; }; ecolicdf = derive2 { name="ecolicdf"; version="2.18.0"; sha256="18g5prjykn356k35m131ifn128k5mhij2x26balqav0azigzjqsn"; depends=[AnnotationDbi]; }; ecoliprobe = derive2 { name="ecoliprobe"; version="2.18.0"; sha256="17g5zxfzsak7a0w51irc0w1w2i5ngdkx9db6rhv1fyp8mfjgaphd"; depends=[AnnotationDbi]; }; fitCons_UCSC_hg19 = derive2 { name="fitCons.UCSC.hg19"; version="3.7.1"; sha256="19isa4x8js0pdb4k8a11bw3bzmzv6jc4jphzrvav7piqkvrgykzx"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - fly_db0 = derive2 { name="fly.db0"; version="3.7.1"; sha256="0l617pksrcgb96bm25qsxlyjz7jp7hqk1sfba516l2gd2rvbp7rs"; depends=[AnnotationDbi]; }; + fly_db0 = derive2 { name="fly.db0"; version="3.10.0"; sha256="02n01bc14igh5raffv3q7wlhc4g4jcqff5ai09jhvgrrcrn6nflc"; depends=[AnnotationDbi]; }; geneplast_data_string_v91 = derive2 { name="geneplast.data.string.v91"; version="0.99.6"; sha256="0mc26d0sgmpmfmqsqinqv5k6vhg0hlc8hsjkcnvf369yav224nq1"; depends=[]; }; genomewidesnp5Crlmm = derive2 { name="genomewidesnp5Crlmm"; version="1.0.6"; sha256="06dmwnjy3gb53y6nr02dmp22qzfl5d63wppazrabcqbzwimhnvp8"; depends=[]; }; genomewidesnp6Crlmm = derive2 { name="genomewidesnp6Crlmm"; version="1.0.7"; sha256="16qcxa32fmbdcv5dck0grsnqyfcqql7wpxa1l6andv9hrvabv2jx"; depends=[]; }; @@ -453,6 +466,7 @@ in with self; { hom_Mm_inp_db = derive2 { name="hom.Mm.inp.db"; version="3.1.2"; sha256="034b9wiis7w7zj3647s0fh1jspyfn654yf0lm5ymp65sww965cxh"; depends=[AnnotationDbi]; }; hom_Rn_inp_db = derive2 { name="hom.Rn.inp.db"; version="3.1.2"; sha256="02smfm88y72dgmj2kna9v7sbcg5dxr8b4sqgy6i8b3zw3a6776yp"; depends=[AnnotationDbi]; }; hom_Sc_inp_db = derive2 { name="hom.Sc.inp.db"; version="3.1.2"; sha256="0l9nly3k7jnf6g1qnwyw22ga1hdyjdvn3hrlway8pb9rv7279bil"; depends=[AnnotationDbi]; }; + hpAnnot = derive2 { name="hpAnnot"; version="1.0.1"; sha256="16isg9byqc9ghipg7626mrijcs0bngz6n6hxz3m616v21cjyingj"; depends=[]; }; hs25kresogen_db = derive2 { name="hs25kresogen.db"; version="2.5.0"; sha256="1yp25ifm3bwzkzm8vimlxw5slini7drhvmh5ggh0z80sfrjyndyf"; depends=[AnnotationDbi org_Hs_eg_db]; }; hspeccdf = derive2 { name="hspeccdf"; version="0.99.1"; sha256="07azl9zpg552ic7li14p6n09ba3jbqqclwffjfpd2vc249x0n4fw"; depends=[AnnotationDbi]; }; hta20probeset_db = derive2 { name="hta20probeset.db"; version="8.7.0"; sha256="12m58w0av2b806w75df7spg72d0v7mr7vlhsgdc9h221r0g06vgx"; depends=[AnnotationDbi org_Hs_eg_db]; }; @@ -509,7 +523,7 @@ in with self; { hugene20sttranscriptcluster_db = derive2 { name="hugene20sttranscriptcluster.db"; version="8.7.0"; sha256="0ba3yvizj9ya61rr9ik2hdxhy0q67908x16n58jjjfq8wf96h7sp"; depends=[AnnotationDbi org_Hs_eg_db]; }; hugene21stprobeset_db = derive2 { name="hugene21stprobeset.db"; version="8.7.0"; sha256="0chkxxpfl696qqiai3i30ylpsihyicbs0hbcni6nmnhfz9k5800g"; depends=[AnnotationDbi org_Hs_eg_db]; }; hugene21sttranscriptcluster_db = derive2 { name="hugene21sttranscriptcluster.db"; version="8.7.0"; sha256="0wk2lg74zkgxh6frmikhk4bxndiyvc1j7mhvz65w8fxfqiwfyf5i"; depends=[AnnotationDbi org_Hs_eg_db]; }; - human_db0 = derive2 { name="human.db0"; version="3.7.1"; sha256="1vikw70n828prccs1vlnw3f4rwp5lsp5cb02f56hih4n3mapky9f"; depends=[AnnotationDbi]; }; + human_db0 = derive2 { name="human.db0"; version="3.10.0"; sha256="0wmp5rr41bdn2p9lna82sdfd0fy55l2c3i7ljijchsp1kb5hnlah"; depends=[AnnotationDbi]; }; human1mduov3bCrlmm = derive2 { name="human1mduov3bCrlmm"; version="1.0.4"; sha256="1p7qpzk6svafgdafljhh4k0z7pcs78qmwwfd80r0a1yhkssmp0v9"; depends=[]; }; human1mv1cCrlmm = derive2 { name="human1mv1cCrlmm"; version="1.0.3"; sha256="1qlph3qrjv52ddzlj8pwa93zzh70x4mbdrdr7q9pan427lpck9gx"; depends=[]; }; human370quadv3cCrlmm = derive2 { name="human370quadv3cCrlmm"; version="1.0.3"; sha256="1chjx9vsmqz2whslw1l7jn7nfn7zx6pcjfmqqm9mh81i74rzrdik"; depends=[]; }; @@ -547,7 +561,7 @@ in with self; { m20kcod_db = derive2 { name="m20kcod.db"; version="3.4.0"; sha256="1p2sm5j4b50iqzwcb984qrh74c3hf6yml7b8mvxlhhhvxz4iy1np"; depends=[AnnotationDbi org_Mm_eg_db]; }; maizecdf = derive2 { name="maizecdf"; version="2.18.0"; sha256="0yfz5gjhsq4wz6j63s1b1hxjz03gsmrlfs2cdc8smq6azp3zdid4"; depends=[AnnotationDbi]; }; maizeprobe = derive2 { name="maizeprobe"; version="2.18.0"; sha256="01h5dv5i0zaqlphkii9ipxy9wswv1srgprrpr5vmi01c9d98qsk0"; depends=[AnnotationDbi]; }; - malaria_db0 = derive2 { name="malaria.db0"; version="3.7.1"; sha256="1ljk5xfshp96pibw9k1yb5cl664iashb9rhc1y1bjalyidraznk7"; depends=[AnnotationDbi]; }; + malaria_db0 = derive2 { name="malaria.db0"; version="3.10.0"; sha256="12s4gyh0w0dsj47yxx1irm91ap4jgq8pgk57py1jwi8mnanjsk96"; depends=[AnnotationDbi]; }; medicagocdf = derive2 { name="medicagocdf"; version="2.18.0"; sha256="1clz679cc887x98c6jk93cphijkbg5r2nd9idrj5901yvh6p9n5q"; depends=[AnnotationDbi]; }; medicagoprobe = derive2 { name="medicagoprobe"; version="2.18.0"; sha256="0w6j1pfkvb3npc8srpjifq2ywnqxhc9q090jqzmkx22x36cw9cl5"; depends=[AnnotationDbi]; }; mgu74a_db = derive2 { name="mgu74a.db"; version="3.2.3"; sha256="0xd2gbvry061409kiwq99i13641g8x6m9kbgg4yr0x6m9dh7hxa8"; depends=[AnnotationDbi org_Mm_eg_db]; }; @@ -601,7 +615,7 @@ in with self; { mogene20sttranscriptcluster_db = derive2 { name="mogene20sttranscriptcluster.db"; version="8.7.0"; sha256="1s7cdjglrc9qqf3gsmhsyycfa0h5qrbk28i4z3z4mb9g6242r1r4"; depends=[AnnotationDbi org_Mm_eg_db]; }; mogene21stprobeset_db = derive2 { name="mogene21stprobeset.db"; version="8.7.0"; sha256="0l8y2zbhykzqs9hbjhj1cys1mzdjhmi4rjv4l3v0sv5969h6sl96"; depends=[AnnotationDbi org_Mm_eg_db]; }; mogene21sttranscriptcluster_db = derive2 { name="mogene21sttranscriptcluster.db"; version="8.7.0"; sha256="1mkw3997mqr7ssa60zpwhlyajda51smcrnlnxwif78g99yj0nrxb"; depends=[AnnotationDbi org_Mm_eg_db]; }; - mouse_db0 = derive2 { name="mouse.db0"; version="3.7.1"; sha256="1fyawqxf1m6cnl6p41q1bqb75k59n8ixn3kw8gf4kq34cldl0h9k"; depends=[AnnotationDbi]; }; + mouse_db0 = derive2 { name="mouse.db0"; version="3.10.0"; sha256="12780ydznzh1l5vdd6q92zaz7m27cb05giwm91x9ig9d1ilh6hhd"; depends=[AnnotationDbi]; }; mouse4302_db = derive2 { name="mouse4302.db"; version="3.2.3"; sha256="1wdgqawqzkr39xwl32cap4ksr59p7r7i83g82h1ss4q3lm58gxpm"; depends=[AnnotationDbi org_Mm_eg_db]; }; mouse4302cdf = derive2 { name="mouse4302cdf"; version="2.18.0"; sha256="1mpyma4x8zfs2fmmx57xw4cfs2cf9lhw71nc3icl72d7vmwidswc"; depends=[AnnotationDbi]; }; mouse4302frmavecs = derive2 { name="mouse4302frmavecs"; version="1.5.0"; sha256="04clwkfz1gqqwrnqbavkka3hv480w6vi6c4q947qqnhw8j5jjp7s"; depends=[]; }; @@ -638,25 +652,26 @@ in with self; { nugomm1a520177cdf = derive2 { name="nugomm1a520177cdf"; version="3.4.0"; sha256="0skd5b76si0vydzk5qhg4f1a1j655alxflm9sqci8fi8safwj96a"; depends=[AnnotationDbi]; }; nugomm1a520177probe = derive2 { name="nugomm1a520177probe"; version="3.4.0"; sha256="1n70k0mhv146983myjgk1cgkr9rmmcpqdv8wpkcr320qcvgf9bn7"; depends=[AnnotationDbi]; }; oligoData = derive2 { name="oligoData"; version="1.8.0"; sha256="1d1yfms3jv2c4s255xnh8yxwijrj35skw3nxds7l46y88lg3qn8y"; depends=[oligo]; }; - org_Ag_eg_db = derive2 { name="org.Ag.eg.db"; version="3.7.0"; sha256="101xvx62y1y2kbiv9j427879zhjindm1hzb9iscinmf10lwhyj8q"; depends=[AnnotationDbi]; }; - org_At_tair_db = derive2 { name="org.At.tair.db"; version="3.7.0"; sha256="0i5dv4lc8dh27ipf37wk84y75fmnbja0bbllzbchb459c9bpwcf9"; depends=[AnnotationDbi]; }; - org_Bt_eg_db = derive2 { name="org.Bt.eg.db"; version="3.7.0"; sha256="0vdfgh2yrawz8bbszgxl5vvq6iqvn25p5l01j7zhlmx035jcbfak"; depends=[AnnotationDbi]; }; - org_Ce_eg_db = derive2 { name="org.Ce.eg.db"; version="3.7.0"; sha256="1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"; depends=[AnnotationDbi]; }; - org_Cf_eg_db = derive2 { name="org.Cf.eg.db"; version="3.7.0"; sha256="1y3kda375f327bv31cfp470546hvcdw5a8bl3z5h1dm6c556z7cl"; depends=[AnnotationDbi]; }; - org_Dm_eg_db = derive2 { name="org.Dm.eg.db"; version="3.7.0"; sha256="1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"; depends=[AnnotationDbi]; }; - org_Dr_eg_db = derive2 { name="org.Dr.eg.db"; version="3.7.0"; sha256="1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"; depends=[AnnotationDbi]; }; - org_EcK12_eg_db = derive2 { name="org.EcK12.eg.db"; version="3.7.0"; sha256="0ii3k9b0rr6bkb16m108if9liinw7md4mgh8fz4yd4gh8a7zcli7"; depends=[AnnotationDbi]; }; - org_EcSakai_eg_db = derive2 { name="org.EcSakai.eg.db"; version="3.7.0"; sha256="1zcqbr4sds24mcggg71g4j6v0wp7fri75d1l0bhp0x245b9k5vnw"; depends=[AnnotationDbi]; }; - org_Gg_eg_db = derive2 { name="org.Gg.eg.db"; version="3.7.0"; sha256="0lyzznrnyyw9lsdp58a0sc5jw2lrccsv44dvrza2ix8mx46gplis"; depends=[AnnotationDbi]; }; - org_Hs_eg_db = derive2 { name="org.Hs.eg.db"; version="3.7.0"; sha256="1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"; depends=[AnnotationDbi]; }; - org_Mm_eg_db = derive2 { name="org.Mm.eg.db"; version="3.7.0"; sha256="1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"; depends=[AnnotationDbi]; }; - org_Mmu_eg_db = derive2 { name="org.Mmu.eg.db"; version="3.7.0"; sha256="1c6mwknyf8cq824qm3cax0a2l3wd2h9dw6pylhwm0x7viz2xf2iz"; depends=[AnnotationDbi]; }; - org_Pf_plasmo_db = derive2 { name="org.Pf.plasmo.db"; version="3.7.0"; sha256="0s3ibaqvjw3sg1j22pfgzw1gcb9pv9b8a4livj9ph73jqhx03r5i"; depends=[AnnotationDbi]; }; - org_Pt_eg_db = derive2 { name="org.Pt.eg.db"; version="3.7.0"; sha256="1n9qd34gjkjgbbz07h6ibzgbq9id81z6ni01vmaki3554gmfk3dl"; depends=[AnnotationDbi]; }; - org_Rn_eg_db = derive2 { name="org.Rn.eg.db"; version="3.7.0"; sha256="10293py12jar1ab3s1b872c5gxpw9d2d5sxk4iq5g38i0gcf5gsc"; depends=[AnnotationDbi]; }; - org_Sc_sgd_db = derive2 { name="org.Sc.sgd.db"; version="3.7.0"; sha256="0dwaw9v4c1d5wr6skaf97s013wqwqm31bybhggm1fm59aa6mkdwv"; depends=[AnnotationDbi]; }; - org_Ss_eg_db = derive2 { name="org.Ss.eg.db"; version="3.7.0"; sha256="1s5zizma3ba00z8q1k9h4fajxwj3f2jg1034rfwqlhsscwrhv5ih"; depends=[AnnotationDbi]; }; - org_Xl_eg_db = derive2 { name="org.Xl.eg.db"; version="3.7.0"; sha256="002i6aacrirvyzi14r26fgr6cqc0bfwn0wg83sbligp2dwqm0bb4"; depends=[AnnotationDbi]; }; + org_Ag_eg_db = derive2 { name="org.Ag.eg.db"; version="3.10.0"; sha256="1hq037fbz2rgk2wisk9bky3gl5axicfrq9sk65bfnagr29x2hyr4"; depends=[AnnotationDbi]; }; + org_At_tair_db = derive2 { name="org.At.tair.db"; version="3.10.0"; sha256="1lkicfq5k1924kn0l00qya358zshmw41zijzxiiaj51ilg84qlhh"; depends=[AnnotationDbi]; }; + org_Bt_eg_db = derive2 { name="org.Bt.eg.db"; version="3.10.0"; sha256="0yaipiqrbnhd501b50icgig74a2943c40gpvfivs2jj33b1fwys8"; depends=[AnnotationDbi]; }; + org_Ce_eg_db = derive2 { name="org.Ce.eg.db"; version="3.10.1"; sha256="0ixzdinb97ffhfsfrnyazb44n5082f0lhxb0zl6igabbnyl0fpm7"; depends=[AnnotationDbi]; }; + org_Cf_eg_db = derive2 { name="org.Cf.eg.db"; version="3.10.0"; sha256="1hvg6xqzb4jkgf9647bphwm0yjjb7kkmryf5c70xp1m1x793dh00"; depends=[AnnotationDbi]; }; + org_Dm_eg_db = derive2 { name="org.Dm.eg.db"; version="3.10.0"; sha256="1w9yxz3jcmq8dwi7xd0sqdvqp7vq4jp982nrdp5rsfxrjsmwypng"; depends=[AnnotationDbi]; }; + org_Dr_eg_db = derive2 { name="org.Dr.eg.db"; version="3.10.0"; sha256="0j269mvdhsn6gj5g6gygi35cb3a8mlddn70bsk0hdsilyzfi0gyz"; depends=[AnnotationDbi]; }; + org_EcK12_eg_db = derive2 { name="org.EcK12.eg.db"; version="3.10.0"; sha256="1bp3pbc2f4rknnzqwnj37l7ylmkld4gf6951v92dnbz2k9w5cmrz"; depends=[AnnotationDbi]; }; + org_EcSakai_eg_db = derive2 { name="org.EcSakai.eg.db"; version="3.10.0"; sha256="09zxzr8l35wxrki9fn6w2sd58igvwws6naskkcqjymjcqzdqi21z"; depends=[AnnotationDbi]; }; + org_Gg_eg_db = derive2 { name="org.Gg.eg.db"; version="3.10.0"; sha256="1gd2y2ggarj051wspf0gfmb2asa1q0xhxwswgy84iszfh8j8xr1h"; depends=[AnnotationDbi]; }; + org_Hs_eg_db = derive2 { name="org.Hs.eg.db"; version="3.10.0"; sha256="1v3g2i5xvf2pmrirvhdm86z5298idcm2bgy50d16lqmpcnharj44"; depends=[AnnotationDbi]; }; + org_Mm_eg_db = derive2 { name="org.Mm.eg.db"; version="3.10.0"; sha256="17s75fvwspbps4875wf7yv4snbls64z087l3rv6vj6m3g3jrsl34"; depends=[AnnotationDbi]; }; + org_Mmu_eg_db = derive2 { name="org.Mmu.eg.db"; version="3.10.0"; sha256="16fkfqnq2g6l6li1nryv0nk0k2ifgwxj0ls7fcwnwn6q6x9k0naj"; depends=[AnnotationDbi]; }; + org_Mxanthus_db = derive2 { name="org.Mxanthus.db"; version="1.0.27"; sha256="1jqwsdjz1d8fwqhq26lavb2kq739ddlb8khsh4b096vhnwv3dxg5"; depends=[AnnotationDbi AnnotationHub BiocFileCache BiocStyle]; }; + org_Pf_plasmo_db = derive2 { name="org.Pf.plasmo.db"; version="3.10.0"; sha256="0h434vpyrm2br2c8ahmswgw41ml9d6mq9sd6lga32kvk49wpapvc"; depends=[AnnotationDbi]; }; + org_Pt_eg_db = derive2 { name="org.Pt.eg.db"; version="3.10.0"; sha256="0ibn8x8vywv1p8m36604jm4ibfvkplb6qwris91igms2d3fx6khb"; depends=[AnnotationDbi]; }; + org_Rn_eg_db = derive2 { name="org.Rn.eg.db"; version="3.10.0"; sha256="11hwpz907300qc78f013kjrxm053qx6fxjc7m9qwx1rhlyar8049"; depends=[AnnotationDbi]; }; + org_Sc_sgd_db = derive2 { name="org.Sc.sgd.db"; version="3.10.0"; sha256="1jkbbhrazg4zvxfshsm1m0i4fmajc52dnbz9w4rwxv691n30b08j"; depends=[AnnotationDbi]; }; + org_Ss_eg_db = derive2 { name="org.Ss.eg.db"; version="3.10.0"; sha256="1yg6am15d38qxmwpvxxl077lna426hsv3hsx3gv0ykgywk9j061q"; depends=[AnnotationDbi]; }; + org_Xl_eg_db = derive2 { name="org.Xl.eg.db"; version="3.10.0"; sha256="1m8zsfqqr3d5972257yr99kzp7wl13lyzdfgi22gyjjhdcpff552"; depends=[AnnotationDbi]; }; paeg1acdf = derive2 { name="paeg1acdf"; version="2.18.0"; sha256="127pgxxp5wp3hgmafbzdzsk4gqnllq1m1gcsfyzkvpkvmbn4aa9n"; depends=[AnnotationDbi]; }; paeg1aprobe = derive2 { name="paeg1aprobe"; version="2.18.0"; sha256="0hbyd402wf9nzy2g93nhnf2zsi9jvhgfk0llxlyfk0kqxs0y4byy"; depends=[AnnotationDbi]; }; pd_081229_hg18_promoter_medip_hx1 = derive2 { name="pd.081229.hg18.promoter.medip.hx1"; version="0.99.4"; sha256="1h4925dmw0vfsnhllg55gswq3sxfmx9rcjzifdvgs9y27399psrr"; depends=[Biostrings DBI IRanges oligo oligoClasses RSQLite]; }; @@ -833,7 +848,7 @@ in with self; { phastCons100way_UCSC_hg19 = derive2 { name="phastCons100way.UCSC.hg19"; version="3.7.2"; sha256="1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; phastCons100way_UCSC_hg38 = derive2 { name="phastCons100way.UCSC.hg38"; version="3.7.1"; sha256="0dka39rvx4d3wbcjypcgvc19s6cnxkkfywa4irv23kpibq1sjyv0"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; phastCons7way_UCSC_hg38 = derive2 { name="phastCons7way.UCSC.hg38"; version="3.7.1"; sha256="105isdrb3nsy30wd8yy9vrrv8b7c8izc11xqqixg6rcriacd0rl0"; depends=[BSgenome GenomeInfoDb GenomicRanges GenomicScores IRanges S4Vectors]; }; - pig_db0 = derive2 { name="pig.db0"; version="3.7.1"; sha256="06hwggby003y64mhrk4b48zxnh3csqi5hm9y42iccz17qs7j1jmi"; depends=[AnnotationDbi]; }; + pig_db0 = derive2 { name="pig.db0"; version="3.10.0"; sha256="1nc6sy09g3lvka71ph6h6imf4xmffklz8n7i9c80525a79jhxh4d"; depends=[AnnotationDbi]; }; plasmodiumanophelescdf = derive2 { name="plasmodiumanophelescdf"; version="2.18.0"; sha256="1vs36091djinn3g6rjhmy9xfdyi58365zbcjc9mf50adnp2i5fq9"; depends=[AnnotationDbi]; }; plasmodiumanophelesprobe = derive2 { name="plasmodiumanophelesprobe"; version="2.18.0"; sha256="03hfq51nrpmx8ihc48jiih6bk99irrgal9x7i7mgcv8xd508gcsy"; depends=[AnnotationDbi]; }; poplarcdf = derive2 { name="poplarcdf"; version="2.18.0"; sha256="0j28czs936j2wgwp63qbwl1mjcflcrx7ir88jzxkkw7411ch1gl1"; depends=[AnnotationDbi]; }; @@ -862,14 +877,15 @@ in with self; { ragene20sttranscriptcluster_db = derive2 { name="ragene20sttranscriptcluster.db"; version="8.7.0"; sha256="135cgn92raa6f9yiw4k25rn04rpg5mdnf969l66x4s1jcc0rwscq"; depends=[AnnotationDbi org_Rn_eg_db]; }; ragene21stprobeset_db = derive2 { name="ragene21stprobeset.db"; version="8.7.0"; sha256="0lp4prymrm3cp8yq1hba9bylw22hcvlx7piqpvjx51hj79yrwdig"; depends=[AnnotationDbi org_Rn_eg_db]; }; ragene21sttranscriptcluster_db = derive2 { name="ragene21sttranscriptcluster.db"; version="8.7.0"; sha256="1b7s2r4w1yy2v3srs6n931zc64qf58nq4apmq2ag5nx50wspima1"; depends=[AnnotationDbi org_Rn_eg_db]; }; - rat_db0 = derive2 { name="rat.db0"; version="3.7.1"; sha256="1k7vx0iihb5sgaicrxbv33fi7kjwqfskbwn37aj769nqxq66fx8h"; depends=[AnnotationDbi]; }; + rat_db0 = derive2 { name="rat.db0"; version="3.10.0"; sha256="0sj65idfspzc6crzhqmys5jk3zyx2hx3lkrggy4cn0giip5c9lvd"; depends=[AnnotationDbi]; }; rat2302_db = derive2 { name="rat2302.db"; version="3.2.3"; sha256="0vj4vkx091m34xqjh6gv6m2iqszvn5rq3kvnpyq3fin5v42wrsr1"; depends=[AnnotationDbi org_Rn_eg_db]; }; rat2302cdf = derive2 { name="rat2302cdf"; version="2.18.0"; sha256="1748rc6yypd7y8wgr1qg632pcsxx0fkxjz6b3z4fhblgdllhy9wk"; depends=[AnnotationDbi]; }; + rat2302frmavecs = derive2 { name="rat2302frmavecs"; version="0.99.11"; sha256="0qy5hf86lrkn20yg6d46kcw9fjc0qhsbzbyavaj1v2zl34xvr1ii"; depends=[affy frma]; }; rat2302probe = derive2 { name="rat2302probe"; version="2.18.0"; sha256="1zwjgbcb9d4ib6z1iyjz8x11lq0b5gqs08y6j3idb5wf3i2p521v"; depends=[AnnotationDbi]; }; ratCHRLOC = derive2 { name="ratCHRLOC"; version="2.1.6"; sha256="0mgk6lwvvdwjzjh4r1q1q6nfnx4vqx9iy6gmbrb9f31jf30hqnsb"; depends=[]; }; rattoxfxcdf = derive2 { name="rattoxfxcdf"; version="2.18.0"; sha256="0q84lfaxnnj2zbm5q8xswa1md15fjj4i0djnqr835ixzn7px4yqn"; depends=[AnnotationDbi]; }; rattoxfxprobe = derive2 { name="rattoxfxprobe"; version="2.18.0"; sha256="1kp159553rkcn9yh6x3yph3yjz2ja21wi9j5ax03qnhwlsl1x8ik"; depends=[AnnotationDbi]; }; - reactome_db = derive2 { name="reactome.db"; version="1.66.0"; sha256="18kh68sx9825bi92904xcygjh9jsbxyhsp4ghw1wh160na65gy3v"; depends=[AnnotationDbi]; }; + reactome_db = derive2 { name="reactome.db"; version="1.70.0"; sha256="05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"; depends=[AnnotationDbi]; }; rgu34a_db = derive2 { name="rgu34a.db"; version="3.2.3"; sha256="1s2sd5bqlj4qhamhrnb9byxn8nc7z265mqy7zzkgxcd6a2k472vp"; depends=[AnnotationDbi org_Rn_eg_db]; }; rgu34acdf = derive2 { name="rgu34acdf"; version="2.18.0"; sha256="08z9f16xp1m2mwl9vlmbffxl4zyyl8cgzf6wp66rrm32lvl0nbwq"; depends=[AnnotationDbi]; }; rgu34aprobe = derive2 { name="rgu34aprobe"; version="2.18.0"; sha256="1gjxyq9128jgv3ic386f84rajgf3wz7yi2dja80y0ff4m0a48dlh"; depends=[AnnotationDbi]; }; @@ -883,7 +899,7 @@ in with self; { rgug4105a_db = derive2 { name="rgug4105a.db"; version="3.2.3"; sha256="0lq8k95qm0q7j65nf16p3f09dn9zs87n3k561wxrgi2lb0pf6j40"; depends=[AnnotationDbi org_Rn_eg_db]; }; rgug4130a_db = derive2 { name="rgug4130a.db"; version="3.2.3"; sha256="0zlcn9spw23bj3px9z1l2f5afn09zbr6rv0nbd2h6dd12wrvy1zk"; depends=[AnnotationDbi org_Rn_eg_db]; }; rgug4131a_db = derive2 { name="rgug4131a.db"; version="3.2.3"; sha256="1r272jf9cflf1yf4bznp4d59h7bd7adh1i3rf890h5ffc0xzf5cq"; depends=[AnnotationDbi org_Rn_eg_db]; }; - rhesus_db0 = derive2 { name="rhesus.db0"; version="3.7.1"; sha256="1k695lwbwznk4i03dqpfyk0nx4s9n1qlgh9ccfxjy591lraj7b4j"; depends=[AnnotationDbi]; }; + rhesus_db0 = derive2 { name="rhesus.db0"; version="3.10.0"; sha256="0ddrjv0xcz8c9kcp6gkqbsvfkvsn9cf5caggr5wlrvigl662fvgi"; depends=[AnnotationDbi]; }; rhesuscdf = derive2 { name="rhesuscdf"; version="2.18.0"; sha256="0q2alkxm80wkzaf0q80df27q30qkswybavz05x6ywsihbs9h0nb8"; depends=[AnnotationDbi]; }; rhesusprobe = derive2 { name="rhesusprobe"; version="2.18.0"; sha256="0fd8pvwvpcmx41k80nbccjxllh39fvjf7l9dr8facisl1x7gsfil"; depends=[AnnotationDbi]; }; ri16cod_db = derive2 { name="ri16cod.db"; version="3.4.0"; sha256="1xz533vxjdyxx1wkks0kgk6b90sxs44iqcsvyds0xcm573bx8c6q"; depends=[AnnotationDbi org_Rn_eg_db]; }; @@ -922,8 +938,8 @@ in with self; { vitisviniferaprobe = derive2 { name="vitisviniferaprobe"; version="2.18.0"; sha256="1ggz1s37dwvrkhj4vx2civyhap7bgqsshy33lk14z4fjsayfi39a"; depends=[AnnotationDbi]; }; wheatcdf = derive2 { name="wheatcdf"; version="2.18.0"; sha256="1gmbrdilqvm54h6nkb1cm01ki8aipiywd4qj8gpwlm2hqrimr8kr"; depends=[AnnotationDbi]; }; wheatprobe = derive2 { name="wheatprobe"; version="2.18.0"; sha256="1fifi3pvzdrg356idwz0kx7qlf5mssdxlyvwpn3cjgw0z7n7cnw8"; depends=[AnnotationDbi]; }; - worm_db0 = derive2 { name="worm.db0"; version="3.7.1"; sha256="0p5rzmkars7kl4y4mlq6jbmgp1mdfw3jcnvhl50dnpqc7h28y4xf"; depends=[AnnotationDbi]; }; - xenopus_db0 = derive2 { name="xenopus.db0"; version="3.7.1"; sha256="067vs7b2slmragqqnfpgy6m187cz1rx9r5agizrjycndzdzkpy3k"; depends=[AnnotationDbi]; }; + worm_db0 = derive2 { name="worm.db0"; version="3.10.1"; sha256="0chpahw95y05kvwkf5rvy0plfs7id40mly4i8fkm8wz9ikmc1jci"; depends=[AnnotationDbi]; }; + xenopus_db0 = derive2 { name="xenopus.db0"; version="3.10.0"; sha256="1vgmbbax4dc7fmd610zjmm4v26q04na0f5zd363kfbi5ilj050fr"; depends=[AnnotationDbi]; }; xenopuslaeviscdf = derive2 { name="xenopuslaeviscdf"; version="2.18.0"; sha256="1bcz1hr7gxw6ac4qvw0giph6hfcf5i9b11s274ypq512qc1d32iq"; depends=[AnnotationDbi]; }; xenopuslaevisprobe = derive2 { name="xenopuslaevisprobe"; version="2.18.0"; sha256="0prb14zn2gvgxq8w0y21x1ng51cn3bgjhkppf7zkmnq1xkzvq0pw"; depends=[AnnotationDbi]; }; xlaevis_db = derive2 { name="xlaevis.db"; version="3.2.3"; sha256="0cdi71c8pflb8n4yfxc0wmfi51w6z0dlz7nw5hv0hkx547v79d53"; depends=[AnnotationDbi org_Xl_eg_db]; }; @@ -935,7 +951,7 @@ in with self; { ye6100subbcdf = derive2 { name="ye6100subbcdf"; version="2.18.0"; sha256="1169hv56981b915rlr5w5sn6ppyjd8as7f4k1hbjzadrdrl3glwp"; depends=[AnnotationDbi]; }; ye6100subccdf = derive2 { name="ye6100subccdf"; version="2.18.0"; sha256="0mhr4zd33gfvvivc17k7fb6nvmhq6h3q0xbx2zl09zd6qk09kizm"; depends=[AnnotationDbi]; }; ye6100subdcdf = derive2 { name="ye6100subdcdf"; version="2.18.0"; sha256="11b1fflgc34lrj4yf1p7way5n83cm9c7znsbxpzlwddwyy8qib30"; depends=[AnnotationDbi]; }; - yeast_db0 = derive2 { name="yeast.db0"; version="3.7.1"; sha256="1shjbflvlxipiyapwd6jpqs9mp8nyr3j63wcpnaznmxv0z5k0fw8"; depends=[AnnotationDbi]; }; + yeast_db0 = derive2 { name="yeast.db0"; version="3.10.1"; sha256="1iw5514n1k3gzqyywz99mljply5nz11fmpjv8rsjlq5mj6rc2sa3"; depends=[AnnotationDbi]; }; yeast2_db = derive2 { name="yeast2.db"; version="3.2.3"; sha256="1xns0129ifklipbardybkjyxfwnlklavq0k6s15wk2iwk7vxa33s"; depends=[AnnotationDbi org_Sc_sgd_db]; }; yeast2cdf = derive2 { name="yeast2cdf"; version="2.18.0"; sha256="0c68val9x8bfnv4xx0vag9dxwsx5q8dzbj0dpha3nshh12jw48w9"; depends=[AnnotationDbi]; }; yeast2probe = derive2 { name="yeast2probe"; version="2.18.0"; sha256="125nif693qcmxc0nnnz917f9avggcdr8g9rfvx2qdc54a2l7vdb7"; depends=[AnnotationDbi]; }; @@ -944,7 +960,7 @@ in with self; { ygs98frmavecs = derive2 { name="ygs98frmavecs"; version="1.3.0"; sha256="1xrm1209xnknwvad7nvg1a0mbxz15z12yd4x5bia3cq03zcmzf9m"; depends=[]; }; ygs98probe = derive2 { name="ygs98probe"; version="2.18.0"; sha256="0awf6z4j2vb2jk9a9j2r512yd3m31660y68pasa9mp488m270a3q"; depends=[AnnotationDbi]; }; zebrafish_db = derive2 { name="zebrafish.db"; version="3.2.3"; sha256="1n6p04hlm5c32fnficx294s7n7izy5460avagw8hx1g5xryhdzqk"; depends=[AnnotationDbi org_Dr_eg_db]; }; - zebrafish_db0 = derive2 { name="zebrafish.db0"; version="3.7.1"; sha256="1x9s6sxxgijjnrvg4fggnqhv10zwsfw6hy1qa93rjmpgqpr7ad20"; depends=[AnnotationDbi]; }; + zebrafish_db0 = derive2 { name="zebrafish.db0"; version="3.10.0"; sha256="1q3wsns5dqjidqbn7hvhxqqyyrl3y8bfbfmalqdmbqjgnkr7rrs9"; depends=[AnnotationDbi]; }; zebrafishcdf = derive2 { name="zebrafishcdf"; version="2.18.0"; sha256="0sq1xqhblbilvaiabhqyl9gxdj3jg576vgq8v0cls1zvvx0isrx0"; depends=[AnnotationDbi]; }; zebrafishprobe = derive2 { name="zebrafishprobe"; version="2.18.0"; sha256="1pb8z2rdhq11hq391xyi236scyafbp56kbhhwsnha36yygz5drw0"; depends=[AnnotationDbi]; }; } diff --git a/pkgs/development/r-modules/bioc-experiment-packages.nix b/pkgs/development/r-modules/bioc-experiment-packages.nix index 04f4d25def24b..67a107d23b9cd 100644 --- a/pkgs/development/r-modules/bioc-experiment-packages.nix +++ b/pkgs/development/r-modules/bioc-experiment-packages.nix @@ -4,363 +4,391 @@ # Rscript generate-r-packages.R bioc-experiment >new && mv new bioc-experiment-packages.nix { self, derive }: -let derive2 = derive { biocVersion = "3.8"; }; +let derive2 = derive { biocVersion = "3.10"; }; in with self; { - ABAData = derive2 { name="ABAData"; version="1.11.0"; sha256="0ihr0av55kfg36igb1dn5q132q4gnyaf041xqi4rw7n67525qdap"; depends=[]; }; - ALL = derive2 { name="ALL"; version="1.23.0"; sha256="1m3bx001qngwx0h64kv187q7bsxm22prfm1npbjrfzhg4vjn8rnf"; depends=[Biobase]; }; - ALLMLL = derive2 { name="ALLMLL"; version="1.21.0"; sha256="14pwfwndrapk1h824hw6dyxlkicxqylx56kky9zg8q0qfm5w1ygf"; depends=[affy]; }; - ARRmData = derive2 { name="ARRmData"; version="1.17.0"; sha256="1y6lld8ijxw2g1qxs1bzvjppwfax6yv1ww18axn9553ibjznis7b"; depends=[]; }; - ASICSdata = derive2 { name="ASICSdata"; version="1.1.0"; sha256="050ihbi20chjd5gvyf5jcmjhb1kvdvz80nh5aw1yp8ydfgdnqqwg"; depends=[]; }; - Affyhgu133A2Expr = derive2 { name="Affyhgu133A2Expr"; version="1.17.0"; sha256="1zcai5p4vgpmdv4zdnrqkdszg6wiq6ajj4vbas4hcyp5yglfby3h"; depends=[]; }; - Affyhgu133Plus2Expr = derive2 { name="Affyhgu133Plus2Expr"; version="1.15.0"; sha256="144wb8sniifglqdryfvpnxx7hv1v2c6djqzbk4mq4lkrp64a251n"; depends=[]; }; - Affyhgu133aExpr = derive2 { name="Affyhgu133aExpr"; version="1.19.0"; sha256="0glp22hqblylqc9n8jcx19k2p7ld9ykdnvqgr7nbipsvm4zgnkn1"; depends=[]; }; - AffymetrixDataTestFiles = derive2 { name="AffymetrixDataTestFiles"; version="0.19.0"; sha256="0nf3260aqz4831q8i83nqlcf5hq9b988ly5rhrwyb8mv2ncs0z9k"; depends=[]; }; - Affymoe4302Expr = derive2 { name="Affymoe4302Expr"; version="1.19.0"; sha256="05w1w7fqvhf2xi2d0d5rzigv3sriwy5jxak7j8bvmbwnx31inv5k"; depends=[]; }; - AmpAffyExample = derive2 { name="AmpAffyExample"; version="1.21.0"; sha256="1k1qzxakbavm10bd0ybs1gk97w1y825iqvwimn0cr128qw2xxkyj"; depends=[affy]; }; - AneuFinderData = derive2 { name="AneuFinderData"; version="1.9.0"; sha256="0m3pvsdd2y1947zl582791bsip95j41fc6g9gbin3cg51y7lb6xr"; depends=[]; }; - AshkenazimSonChr21 = derive2 { name="AshkenazimSonChr21"; version="1.11.0"; sha256="08r5430gqsmkbh4n49ac2fl0m24zmqjnc9yxppw5mr0d4n5l26y5"; depends=[]; }; - AssessORFData = derive2 { name="AssessORFData"; version="0.99.2"; sha256="0yi2vxzg21nkqlywcpv6n2vzksl77cvkc42ii9p7gy9kpv56553k"; depends=[DECIPHER]; }; - BeadArrayUseCases = derive2 { name="BeadArrayUseCases"; version="1.19.1"; sha256="08c7aqnh4wnhnalrvchcyhy5vmxq5xkq26pmp9xjn2x4zwf4156y"; depends=[beadarray GEOquery limma]; }; - BloodCancerMultiOmics2017 = derive2 { name="BloodCancerMultiOmics2017"; version="1.1.4"; sha256="1hh1l134cmbcmyc40fwfrwrbx6qyiv9a3bz8hp9vbdf1vslhcnpk"; depends=[beeswarm Biobase DESeq2 devtools dplyr ggdendro ggplot2 glmnet gtable ipflasso RColorBrewer reshape2 scales SummarizedExperiment survival tibble]; }; - CCl4 = derive2 { name="CCl4"; version="1.19.0"; sha256="1j4q7mm4lwi3rcf0y6zj36xc6n7c8y6l8iv9ac4avbgvr1rvlxaq"; depends=[Biobase limma]; }; - CLL = derive2 { name="CLL"; version="1.21.0"; sha256="103lmn87zw73sx30ln6g4382ydpi97b1zsm7www8bwlnw6zx7k7g"; depends=[affy Biobase]; }; - CLLmethylation = derive2 { name="CLLmethylation"; version="1.1.1"; sha256="1vbvxb3bnwx4ngxkk6vrhshcfyrv0fvs3vhlqk0j9q1mhxg8p3a9"; depends=[ExperimentHub SummarizedExperiment]; }; - COHCAPanno = derive2 { name="COHCAPanno"; version="1.17.0"; sha256="199xz5qwp06kr3smr25vx2w25hmzf7qbpaw18aj7bvccsdsyvky9"; depends=[]; }; - CONFESSdata = derive2 { name="CONFESSdata"; version="1.9.0"; sha256="091ydgxqldrcr3b73pqyk6555yyclnnr4yizi0kknqasx33sb802"; depends=[]; }; - COPDSexualDimorphism_data = derive2 { name="COPDSexualDimorphism.data"; version="1.17.0"; sha256="1pgfqrp6cx94marm96swqq8c9nr00xdmlf62hvmacqwspsajbnya"; depends=[]; }; - COSMIC_67 = derive2 { name="COSMIC.67"; version="1.17.0"; sha256="0qd0xbc8hy25hyy8bilim2w5inhwz88rypbqc8vjlg54r2yl12nh"; depends=[GenomicRanges SummarizedExperiment VariantAnnotation]; }; - CRCL18 = derive2 { name="CRCL18"; version="1.1.0"; sha256="1hxh7fldfy2v9sii5clwi9i568dcc742nd4da0048p4pm87qxcsv"; depends=[Biobase]; }; - CardinalWorkflows = derive2 { name="CardinalWorkflows"; version="1.13.0"; sha256="1rjp3ybc0yx8sjqp4ahadgymlld2l2hn3dxxvpng06qpp5jch0zq"; depends=[Cardinal]; }; - CellMapperData = derive2 { name="CellMapperData"; version="1.7.0"; sha256="0zjssdm2z7i6bcp781x9lz09dmh5krvvxg5a0la79dj5vvs72cjp"; depends=[CellMapper ExperimentHub]; }; - ChAMPdata = derive2 { name="ChAMPdata"; version="2.13.0"; sha256="1xa5lcxf7npb8mykqpx84vpjavl9xzwl24nlsaaw3gk75cfrhpkx"; depends=[BiocGenerics GenomicRanges]; }; - ChIC_data = derive2 { name="ChIC.data"; version="1.1.4"; sha256="0s8nm65kwk2cbs8g66zc46q31nd66fdm0kk0d6gxl6zhv0p3d8dv"; depends=[caret]; }; - ChIPXpressData = derive2 { name="ChIPXpressData"; version="1.19.0"; sha256="1f32hzqgpiclby25223ksp63xlhdk7d52sf2xc97hpjig0571630"; depends=[bigmemory]; }; - ChIPexoQualExample = derive2 { name="ChIPexoQualExample"; version="1.5.0"; sha256="0y2s4hw7hbfspy1hjsqkaw72pm26k911699k6sw4jhvjh7mkvjbf"; depends=[]; }; - ChimpHumanBrainData = derive2 { name="ChimpHumanBrainData"; version="1.19.0"; sha256="1i2aj1vxak6b53mpcd36q2xwgpddllqpqz3wii7rrsa9mg2gaaza"; depends=[affy hexbin limma qvalue statmod]; }; - ConnectivityMap = derive2 { name="ConnectivityMap"; version="1.17.0"; sha256="1zz0vq192jfnp494mp61xmkxyd94bbh9xs268jd7ynnlpjp9phsx"; depends=[]; }; - CopyNeutralIMA = derive2 { name="CopyNeutralIMA"; version="0.99.14"; sha256="1lvdacdazpp071grc75gjxmhwjzkm22lhwzjvf6baclq9qfjgqp2"; depends=[ExperimentHub Rdpack]; }; - CopyhelpeR = derive2 { name="CopyhelpeR"; version="1.13.1"; sha256="014jissvpkj2d0sz3r1dr5c5qs29hbvs9jvm8bl86mld8ff3nlkc"; depends=[]; }; - DAPARdata = derive2 { name="DAPARdata"; version="1.11.4"; sha256="06qwja8qkbix6ial81yv1q3bxrdmqrgridina094p1xrxbfrn5sb"; depends=[knitr MSnbase]; }; - DLBCL = derive2 { name="DLBCL"; version="1.21.0"; sha256="0advvjkd6skynjjnz4s9mdnh0l9l2zhn4n9x0kg23dmsg4r8vqm7"; depends=[Biobase]; }; - DMRcatedata = derive2 { name="DMRcatedata"; version="1.17.0"; sha256="1a669jjvkjjklbh2kxrv3y2clfps067w6w19y1yr2a8wc7crbl4a"; depends=[GenomicRanges]; }; - DREAM4 = derive2 { name="DREAM4"; version="1.17.0"; sha256="0s3y3wgg487p5fswbin4237mrm9kzbq12a84jiixhql1j2ysbhcs"; depends=[SummarizedExperiment]; }; - DeSousa2013 = derive2 { name="DeSousa2013"; version="1.17.2"; sha256="1xz1l83my34kwr4wk6vq3q5yzd3i0ky5qm44wx65f4d92hn7k3v5"; depends=[affy AnnotationDbi Biobase cluster ConsensusClusterPlus frma frmaTools gplots hgu133plus2_db hgu133plus2frmavecs pamr rgl ROCR siggenes survival sva]; }; - DmelSGI = derive2 { name="DmelSGI"; version="1.13.1"; sha256="0v25rb5myhki1vvmmzyhpa8n0vv623zj6lh26a10iq4i5bvda9c5"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; }; - DonaPLLP2013 = derive2 { name="DonaPLLP2013"; version="1.19.1"; sha256="1sbhq0m67v5swyafrn74cjz4h3r6d1qmn2skkz3xwjgm70qpbjrb"; depends=[EBImage]; }; - DrugVsDiseasedata = derive2 { name="DrugVsDiseasedata"; version="1.17.0"; sha256="05xykgmiakw6n8f1b86wbyjzs9v6b7qz8119pwvbfjgncgwqmcx9"; depends=[]; }; - DuoClustering2018 = derive2 { name="DuoClustering2018"; version="0.99.2"; sha256="0f4ps36wd1yll9w4zkx6n4kz0svqfajmb11a5c51b55572siq203"; depends=[dplyr ExperimentHub ggplot2 ggthemes magrittr mclust purrr reshape2 tidyr viridis]; }; - DvDdata = derive2 { name="DvDdata"; version="1.17.0"; sha256="0x5crrym68rw2r9nmb33j1n1f5rxpj5rzn8b5j403ikxywfwxblh"; depends=[]; }; - EGSEAdata = derive2 { name="EGSEAdata"; version="1.9.0"; sha256="1bmxm535h9ilnpbm196rf40543kh1yf5ldqxilhiyx5k0qaaihmz"; depends=[]; }; - ELMER_data = derive2 { name="ELMER.data"; version="2.5.5"; sha256="192jdmxl17m8s1r95c2lizh2r5zpazvx0az8xj22dva0mrazql9c"; depends=[GenomicRanges]; }; - EatonEtAlChIPseq = derive2 { name="EatonEtAlChIPseq"; version="0.19.0"; sha256="0w3bcssqpbzgb03ld9j9jv57bvn8yfpkglhb4minbkqbhslv4j52"; depends=[GenomicRanges rtracklayer ShortRead]; }; - FANTOM3and4CAGE = derive2 { name="FANTOM3and4CAGE"; version="1.17.0"; sha256="0iz0f467d2wh5cly3cf2y7kkrv8pwihsccf6zsdrqpq4a1ijiml7"; depends=[]; }; - FIs = derive2 { name="FIs"; version="1.9.0"; sha256="135r3vc8rdjrhl0a6s85052mzranlxd5jkiwxbymsjg6mglsjyvh"; depends=[]; }; - Fletcher2013a = derive2 { name="Fletcher2013a"; version="1.17.0"; sha256="05kvsbr46yjpkdnn7rwxhj3wnlrgz92fgg35b8i781131vpy4lzh"; depends=[Biobase gplots limma VennDiagram]; }; - Fletcher2013b = derive2 { name="Fletcher2013b"; version="1.17.0"; sha256="1rfsb49fcn127nzykwndzp7gapd36j3r01dvvhn87w6ryy9yc98c"; depends=[Fletcher2013a igraph RColorBrewer RedeR RTN]; }; - FlowSorted_Blood_450k = derive2 { name="FlowSorted.Blood.450k"; version="1.19.0"; sha256="0ngh5zwikm83rzv9aykhxijf7nj345nnak2207jn4frdq8qahh3l"; depends=[minfi]; }; - FlowSorted_Blood_EPIC = derive2 { name="FlowSorted.Blood.EPIC"; version="0.99.37"; sha256="1kfh6x69r3vc7v3in1q1n8frbsha5z8gmds7dcgy39wvry16c6lm"; depends=[ExperimentHub genefilter IlluminaHumanMethylationEPICanno_ilm10b4_hg19 minfi nlme quadprog S4Vectors SummarizedExperiment]; }; - FlowSorted_CordBlood_450k = derive2 { name="FlowSorted.CordBlood.450k"; version="1.9.0"; sha256="1ib9g4zy3zwk7m6hl9ggi030qwrjch9jnip6d7a4b27cjzlf0sdq"; depends=[minfi]; }; - FlowSorted_CordBloodNorway_450k = derive2 { name="FlowSorted.CordBloodNorway.450k"; version="1.7.0"; sha256="04i701nl8w8sdc85z1y8gzg076n3znnd9fkp35a7pq7sczkfih90"; depends=[minfi]; }; - FlowSorted_DLPFC_450k = derive2 { name="FlowSorted.DLPFC.450k"; version="1.17.0"; sha256="1d9xq8ha0p1injk8l16vggfkzk7xlsgaqb227gvl6xc49q8dmh5m"; depends=[minfi]; }; - FunciSNP_data = derive2 { name="FunciSNP.data"; version="1.17.0"; sha256="1vp55zd2ifamxm248jskvf2y29cgjyx98jw41h2pbly31qxq4h49"; depends=[IRanges rtracklayer]; }; - GGdata = derive2 { name="GGdata"; version="1.19.0"; sha256="0mr6l11bgg8ncga9ivwdps6jp6zbcjs5jxvcpf834qaj92h63mrg"; depends=[AnnotationDbi Biobase GGBase illuminaHumanv1_db snpStats]; }; - GIGSEAdata = derive2 { name="GIGSEAdata"; version="0.99.11"; sha256="1rn6dmji5ja1p83gai18bcmdc9vi0fm4pq4yk7wdsbv6p334cqlq"; depends=[]; }; - GSBenchMark = derive2 { name="GSBenchMark"; version="1.1.0"; sha256="1a9hlgcz9m36gzkmxkq4i308hsm617hmsxmwq09yd5cxq8dl80g4"; depends=[]; }; - GSE62944 = derive2 { name="GSE62944"; version="1.9.0"; sha256="1s28rkr5nm91vnl6cx0gifib4nw70gs8bhmv003f9kbpiq420i8k"; depends=[Biobase GEOquery]; }; - GSVAdata = derive2 { name="GSVAdata"; version="1.17.0"; sha256="1gjc9psmx0i25bwki6l74d8jg3mrvfzjdnxs5bhbqnzab6fzdfh0"; depends=[Biobase GSEABase hgu95a_db]; }; - GWASdata = derive2 { name="GWASdata"; version="1.19.0"; sha256="0i09njrq0fzwvzj6lqsa7kdnwi35lm7z0akywh0mr87i6dlqj8sq"; depends=[GWASTools]; }; - GeuvadisTranscriptExpr = derive2 { name="GeuvadisTranscriptExpr"; version="1.9.0"; sha256="1h6ghr75h1i87lbarsganiw6mgjyiha4zv4hbjdjljc464s11b0d"; depends=[]; }; - HD2013SGI = derive2 { name="HD2013SGI"; version="1.21.1"; sha256="1m3q08m21vim5j520wgiwszrp6nnkrsfqf6wac8cyzw1qs3cp1s6"; depends=[EBImage geneplotter gplots limma LSD RColorBrewer splots vcd]; }; - HDCytoData = derive2 { name="HDCytoData"; version="1.1.2"; sha256="1ay7r0aya0b6rxwscg3lwzlgl9iaj9ykii52lmzpxx40yc6szpnv"; depends=[ExperimentHub flowCore SummarizedExperiment]; }; - HEEBOdata = derive2 { name="HEEBOdata"; version="1.19.0"; sha256="1z8qb5xrzadg6fxg8cx04dpad3qiab5m8vhgdqw4xs8xdaqd4g1m"; depends=[]; }; - HIVcDNAvantWout03 = derive2 { name="HIVcDNAvantWout03"; version="1.21.0"; sha256="0pgb0r6zp6v0wq16c5zjxzjjwb6cjjp3cn8jnh4p91rwf43za4rh"; depends=[]; }; - HMP16SData = derive2 { name="HMP16SData"; version="1.1.4"; sha256="0qjqf7ipczv3rs4r4l5ynagi46ksb98b8mylgvbclrqp7ny2wcbq"; depends=[AnnotationHub assertthat dplyr ExperimentHub kableExtra knitr magrittr readr S4Vectors SummarizedExperiment tibble]; }; - HSMMSingleCell = derive2 { name="HSMMSingleCell"; version="1.1.0"; sha256="0fl3r3sdnnn3s9h5sn0bmgpi0hj965cwgca51qkwcvll4rjamyq2"; depends=[]; }; - HarmanData = derive2 { name="HarmanData"; version="1.9.0"; sha256="1c6avjny0fasj99q0a2dm8p3h68jalcglx51b90fnyjgvqgx3h2g"; depends=[]; }; - HarmonizedTCGAData = derive2 { name="HarmonizedTCGAData"; version="1.3.0"; sha256="07fvdf6kzipa42r5dmmld7p2chbi074d248da0xmlm8lm1i0wkc9"; depends=[ExperimentHub]; }; - HelloRangesData = derive2 { name="HelloRangesData"; version="1.7.0"; sha256="05yr2mklxwfij6yzmhpk83mlrq7zfcn8finf2m4lrvdbdzl1bkki"; depends=[]; }; - HiCDataHumanIMR90 = derive2 { name="HiCDataHumanIMR90"; version="1.1.0"; sha256="0nmd7iqa6cg74xvz1a2x9ahyzs3kwd4fnhz5nkh62sgndj1pv62l"; depends=[]; }; - HiCDataLymphoblast = derive2 { name="HiCDataLymphoblast"; version="1.17.0"; sha256="0hjhlq7vx71lwv37vidwlb819hm617dx7g39hgf20ggccmp310rh"; depends=[]; }; - Hiiragi2013 = derive2 { name="Hiiragi2013"; version="1.17.0"; sha256="17mnwnpsam62mc8bqdwjfh9fiayasbkx1gd3bbp0k82w3az9yzbf"; depends=[affy Biobase boot clue cluster genefilter geneplotter gplots gtools KEGGREST lattice latticeExtra MASS mouse4302_db RColorBrewer xtable]; }; - HumanAffyData = derive2 { name="HumanAffyData"; version="1.7.0"; sha256="02hp2a7h0ivzdfql3vsrvxrn4answlr7hrhw5azdjw8jh895dd1j"; depends=[Biobase ExperimentHub]; }; - IHWpaper = derive2 { name="IHWpaper"; version="1.9.6"; sha256="19fg4ca9hhlh4as0nyd3qkkgqphghgvlcs57279pl42nphzz1hw0"; depends=[Biobase BiocGenerics BiocParallel cowplot DESeq2 dplyr fdrtool genefilter ggplot2 IHW qvalue Rcpp SummarizedExperiment]; }; - ITALICSData = derive2 { name="ITALICSData"; version="2.19.0"; sha256="0i09g3dj3rz0yr4n35g9fhc5df957i928vbinsx2bl3jsj7xrf6f"; depends=[]; }; - Illumina450ProbeVariants_db = derive2 { name="Illumina450ProbeVariants.db"; version="1.17.0"; sha256="1y219yqipskv3mzf7g75rmzwsp5sq2r9cqacbpyc2gk28z6dfnix"; depends=[]; }; - IlluminaDataTestFiles = derive2 { name="IlluminaDataTestFiles"; version="1.19.0"; sha256="0b6zhvkhpjhz9wr3cfcvyy16l1kvd6aq9p58y78ql9rgpbhz7dcz"; depends=[]; }; - Iyer517 = derive2 { name="Iyer517"; version="1.23.0"; sha256="0986lrh1w5c1y3rlc0rx06046h0nw8cdqp1mbsddllpibnbj4ii3"; depends=[Biobase]; }; - JASPAR2014 = derive2 { name="JASPAR2014"; version="1.17.0"; sha256="13hrxj4q2r9bdzwnl0qm5ap92051483876rwq73bz6hy5xg73abx"; depends=[Biostrings]; }; - JASPAR2016 = derive2 { name="JASPAR2016"; version="1.9.0"; sha256="1gx14sjv9v5705h1763p5js37jrvvlkiqdm7nrawjs4n6y4cpsdf"; depends=[]; }; - JctSeqData = derive2 { name="JctSeqData"; version="1.11.0"; sha256="1zrnmvs1mmg07s5fi8m5yqb975kb1nkx98j0shpk9xi5jdbf7x0d"; depends=[]; }; - KEGGandMetacoreDzPathwaysGEO = derive2 { name="KEGGandMetacoreDzPathwaysGEO"; version="1.1.0"; sha256="1d4qg0svrmfc6v7dhgxbsn0xfhyplizfh113n26z64y97nfhc21p"; depends=[Biobase BiocGenerics]; }; - KEGGdzPathwaysGEO = derive2 { name="KEGGdzPathwaysGEO"; version="1.19.0"; sha256="0w2a3yjp5xhbxq0vhzyka8sx17a095ddnpm4jhac65s6zmndgqr3"; depends=[Biobase BiocGenerics]; }; - KOdata = derive2 { name="KOdata"; version="1.7.0"; sha256="0grvn2pc38zv133v60hvjh1jx9dsbrwxrz9c6fb977z1rznrkzz8"; depends=[]; }; - LiebermanAidenHiC2009 = derive2 { name="LiebermanAidenHiC2009"; version="0.19.0"; sha256="1i6rl8mziv8apxxa2hlmsg6ramq4aasbg9nxj963lsk9b6gnrzlf"; depends=[IRanges KernSmooth]; }; - ListerEtAlBSseq = derive2 { name="ListerEtAlBSseq"; version="1.13.0"; sha256="1p3f67zdihy5prbgqm27bdpnz3gmag3jnya0y7gxaqn3lkdd1vns"; depends=[methylPipe]; }; - LungCancerACvsSCCGEO = derive2 { name="LungCancerACvsSCCGEO"; version="1.17.0"; sha256="0rgbx36c4hdjc67jsmhrbzyhk3ib8vgmif2g131rly2057zs43f2"; depends=[]; }; - LungCancerLines = derive2 { name="LungCancerLines"; version="0.19.0"; sha256="11yycm8l0ykkb22h9rppaqrkvyyphz7q8k5zgha06c4h0lcf9zqi"; depends=[Rsamtools]; }; - M3DExampleData = derive2 { name="M3DExampleData"; version="1.7.0"; sha256="0iaaxz3k7kw2qfaq5c7nx8jbyy4lg3csvsgnci7aknm4iqdgzc7v"; depends=[]; }; - MAQCsubset = derive2 { name="MAQCsubset"; version="1.19.0"; sha256="1c9gng9mr56h0pqc6xsr489d8m6xixg1iyw6ivdjdm38yg9l5q8h"; depends=[affy Biobase lumi]; }; - MAQCsubsetAFX = derive2 { name="MAQCsubsetAFX"; version="1.19.0"; sha256="1901vmaq8k8ip508w3s37bdvrhzbd1f36zgz4z7i2f93464yh188"; depends=[affy Biobase]; }; - MAQCsubsetILM = derive2 { name="MAQCsubsetILM"; version="1.19.0"; sha256="1qknpl7k22rbn3v5m4jqs0xiiw2n8wz32qbqsdy13300ynwlvvkn"; depends=[Biobase lumi]; }; - MEDIPSData = derive2 { name="MEDIPSData"; version="1.17.0"; sha256="0pazyx7xsvxsv36yhhxjbiyfdmd19ifrbbbfj685hgdx0mpiz8qa"; depends=[]; }; - MEEBOdata = derive2 { name="MEEBOdata"; version="1.19.0"; sha256="1naapb5mskfr482lfs5z1ya2bbsz3jwcpm3mm15dhrxl7rrd7z98"; depends=[]; }; - MIGSAdata = derive2 { name="MIGSAdata"; version="1.5.0"; sha256="15v3gva9xprr24fv3p49lvwgnh56g9x3nj2qqdd410i1avwn6j8n"; depends=[]; }; - MMDiffBamSubset = derive2 { name="MMDiffBamSubset"; version="1.17.0"; sha256="1bjkdyf0knkdbzdmlas81dhnm5k7yslq6km3yzffrvn1kssml47i"; depends=[]; }; - MSBdata = derive2 { name="MSBdata"; version="0.99.1"; sha256="1bgzzrynb4066xps7wagawb2pjd64qab7n9il2znsidfprm03bxj"; depends=[]; }; - MSstatsBioData = derive2 { name="MSstatsBioData"; version="1.3.0"; sha256="10i3gg9fbhcj6fz4fz1jzmqmabdf9c39ys8yp40qs60glv9gj3qa"; depends=[]; }; - MUGAExampleData = derive2 { name="MUGAExampleData"; version="1.1.0"; sha256="18y2ljddzk0g7cn5v8cpc151mrdfzhvj0ah4c988lmc6xlqcyjsv"; depends=[]; }; - MetaGxBreast = derive2 { name="MetaGxBreast"; version="1.1.1"; sha256="1lzqv8alxccmfp6s4ylyam9ljwga9p9q5ndnhsljnfiyw820md78"; depends=[AnnotationHub Biobase ExperimentHub impute lattice]; }; - MetaGxOvarian = derive2 { name="MetaGxOvarian"; version="1.1.1"; sha256="1djqlmms5a24g8n6mimp4fib3h6qd17p1cl9anzmvl3zscz23p8y"; depends=[AnnotationHub Biobase ExperimentHub impute lattice]; }; - MetaGxPancreas = derive2 { name="MetaGxPancreas"; version="1.1.1"; sha256="17vjfnlxrkmdxifmbpfq81zqzzpdhkm5s1aagcnrhgzkv9prszms"; depends=[AnnotationHub Biobase ExperimentHub impute lattice]; }; - MethylAidData = derive2 { name="MethylAidData"; version="1.13.0"; sha256="157qvzvw8hhw25qnzv7xax3vzmq38bw4fp0k34jfwgq944srv0h5"; depends=[MethylAid]; }; - Mulder2012 = derive2 { name="Mulder2012"; version="0.21.1"; sha256="1ypxdys24g8k98jd50sldqggy28fmjy1cq7gc3pxa10rww6g9h57"; depends=[HTSanalyzeR igraph KEGG_db MASS org_Hs_eg_db PANR pvclust RedeR]; }; - NCIgraphData = derive2 { name="NCIgraphData"; version="1.17.0"; sha256="090s04iwbnhdbgprcy15hl596vmgq8x97v34w2xvmsdld5b8z58d"; depends=[]; }; - NGScopyData = derive2 { name="NGScopyData"; version="1.1.0"; sha256="13dlsznbg3kk7pi0gdzwnh9i3qdk538qh4rnjbpxr6iw61hwl0zd"; depends=[]; }; - Neve2006 = derive2 { name="Neve2006"; version="0.19.0"; sha256="0fn77ic133wfdjrnh5vdk95rwx51nigfmznb7i94n8h5hddmpnbc"; depends=[annotate Biobase hgu133a_db]; }; - OMICsPCAdata = derive2 { name="OMICsPCAdata"; version="0.99.11"; sha256="1w38ii5wsaiar4lbn5428pyinzg07zvw4c7fac6a3nx70mhpnxn5"; depends=[MultiAssayExperiment]; }; - OnassisJavaLibs = derive2 { name="OnassisJavaLibs"; version="1.3.0"; sha256="0ih472qrzx183pyk0k8agwybn5bycx3hx1j2amjkp42p7hml4iqj"; depends=[rJava]; }; - PCHiCdata = derive2 { name="PCHiCdata"; version="1.9.0"; sha256="19cmbyhsi84pi89fy623f7r5yld7qifnqfpvwcb3n7ads5idq1qm"; depends=[Chicago]; }; - PGPC = derive2 { name="PGPC"; version="1.9.0"; sha256="10z8r98lp92dh14wpf2hs5n3jzw9y3dw6mf5ssx469368hhaypma"; depends=[ChemmineR EBImage geneplotter ggplot2 gplots imageHTS limma plyr RColorBrewer reshape2 SearchTrees splots]; }; - PREDAsampledata = derive2 { name="PREDAsampledata"; version="0.21.0"; sha256="1h7x57vvplxbmsxwalgnkbxwnl91qnfyrn1j6cwyak9pzh58aqh0"; depends=[affy annotate Biobase PREDA]; }; - PWMEnrich_Dmelanogaster_background = derive2 { name="PWMEnrich.Dmelanogaster.background"; version="4.15.0"; sha256="1gq65gl4dkas9nl3k31k7xjwdry5c2bgj841w1llbb48wy9w06d8"; depends=[PWMEnrich]; }; - PWMEnrich_Hsapiens_background = derive2 { name="PWMEnrich.Hsapiens.background"; version="4.15.0"; sha256="1ryrrw0fdi7bmw8h7pdi02yq9y39dkl0vppyf4ycasnbyn14ddrv"; depends=[PWMEnrich]; }; - PWMEnrich_Mmusculus_background = derive2 { name="PWMEnrich.Mmusculus.background"; version="4.15.0"; sha256="1py3rsnd4s9x7r2mhzsp7hqaflg3ip2fgq3cf10f136fdrfcbf1k"; depends=[PWMEnrich]; }; - PasillaTranscriptExpr = derive2 { name="PasillaTranscriptExpr"; version="1.9.0"; sha256="1lkqz0kp1jfsi1bvkqhvlqapp658qfm7b1p9kiwk9qakfl0nm7x6"; depends=[]; }; - PathNetData = derive2 { name="PathNetData"; version="1.17.0"; sha256="02wdp23y583p9sinhaqkv6lxp836m6kh7na8b2wv6qajanibzhl1"; depends=[]; }; - ProData = derive2 { name="ProData"; version="1.19.0"; sha256="0idv9icfzr52k96gij5mlyqyd48mjwka7jg1nhawiaj7g4c005yc"; depends=[Biobase]; }; - PtH2O2lipids = derive2 { name="PtH2O2lipids"; version="1.7.1"; sha256="1ypwwrk643shfng4nqs7jpy25058ni2fqq4jhx2yc1j73bx8k834"; depends=[CAMERA LOBSTAHS xcms]; }; - QDNAseq_hg19 = derive2 { name="QDNAseq.hg19"; version="1.11.0"; sha256="134mzg2r3bpzcpag5vf2fq8g0xczb5qxyvqqcjzqw654mbafgczr"; depends=[QDNAseq]; }; - QDNAseq_mm10 = derive2 { name="QDNAseq.mm10"; version="1.11.0"; sha256="1j5qzwbc7a9h9hlda6c6f53pm6vqm4kdja4z144j4snyac88xclm"; depends=[QDNAseq]; }; - QUBICdata = derive2 { name="QUBICdata"; version="1.9.0"; sha256="1r1wcmd7s17gm5q682siy8ld65w6ylch9jamqjlbp8qiqqvfmzdd"; depends=[]; }; - RGMQLlib = derive2 { name="RGMQLlib"; version="1.1.0"; sha256="0ijyjgqnap1zmfh6jf4gz9xjiwyzzhyyghvydh6rwkyys46ci8zl"; depends=[]; }; - RIPSeekerData = derive2 { name="RIPSeekerData"; version="1.17.0"; sha256="11hrk3cf86jgc7vf14wlyarar2vsnjs0i9wyzvmk76draq9frg30"; depends=[RIPSeeker]; }; - RITANdata = derive2 { name="RITANdata"; version="1.5.0"; sha256="0yn8nfvni9h4k9ngzccsqgbjrjvql5gp3haqyg9x334sjsi212c8"; depends=[]; }; - RMassBankData = derive2 { name="RMassBankData"; version="1.19.0"; sha256="172x6x7fnzjczi76ibmscbb51l8185lqgiypyyvlisp145mxssdn"; depends=[]; }; - RNASeqRData = derive2 { name="RNASeqRData"; version="0.99.8"; sha256="0mfgfmbngx87h9ymbqcdabla5rb26p1kh4rvp3g307rp3hraivcp"; depends=[]; }; - RNAinteractMAPK = derive2 { name="RNAinteractMAPK"; version="1.19.1"; sha256="1c90s1vjp4w065zldlzrn64qakwnhfg3s6w3ddmx6hynbrc8lk8j"; depends=[fields gdata genefilter MASS RNAinteract sparseLDA]; }; - RNAseqData_HNRNPC_bam_chr14 = derive2 { name="RNAseqData.HNRNPC.bam.chr14"; version="0.19.0"; sha256="0z1b986jvinzh3c1yl9q8wa66wgq8hp8rjbs23glxna77znvkp87"; depends=[]; }; - RRBSdata = derive2 { name="RRBSdata"; version="1.1.0"; sha256="18xm228jlpvv5z5r5k3nyjnnmizsyg5lkml4kdrkw8mv7gljgcyb"; depends=[BiSeq]; }; - RTCGA_CNV = derive2 { name="RTCGA.CNV"; version="1.9.2"; sha256="19lwjkzs0wrvrgm5a81wq2qcqv2xa1irfnqbv6yrx9c3g3sk6zqi"; depends=[RTCGA]; }; - RTCGA_PANCAN12 = derive2 { name="RTCGA.PANCAN12"; version="1.9.2"; sha256="1ain3wscy6n1jjcb8wajpn9h7flhppih01mjjv6y3dxyyiqqchim"; depends=[RTCGA]; }; - RTCGA_RPPA = derive2 { name="RTCGA.RPPA"; version="1.9.2"; sha256="0fisrp4mgl035lcwg4pj1zcrmfafsc0kgc6788h9nx9b1vh6s7w9"; depends=[RTCGA]; }; - RTCGA_clinical = derive2 { name="RTCGA.clinical"; version="20151101.11.0"; sha256="1y63vnj59sv73zcrnwqd4ikdjx45y9sqb2pj1lnsrhvfbmjazi5z"; depends=[RTCGA]; }; - RTCGA_mRNA = derive2 { name="RTCGA.mRNA"; version="1.9.2"; sha256="1bb9b83y3f9012gnr19c2wacj1fkqvbqnymdv3qyc2pn6qhzid93"; depends=[RTCGA]; }; - RTCGA_methylation = derive2 { name="RTCGA.methylation"; version="1.9.2"; sha256="1a97cdwm7rn9mipw3v904r4j4ay6p26rv3f8lx2znhz5hg44gnaq"; depends=[RTCGA]; }; - RTCGA_miRNASeq = derive2 { name="RTCGA.miRNASeq"; version="1.9.2"; sha256="1lkywq2nvpil8wi8nv73hfxs3hsi71d85n9if7ra4c6ib3frwiwb"; depends=[RTCGA]; }; - RTCGA_mutations = derive2 { name="RTCGA.mutations"; version="20151101.11.0"; sha256="1wyiz22rw400hiqqnw41mqpvy8bbj1vxwx3v4vnz6x81drv2sc1n"; depends=[RTCGA]; }; - RTCGA_rnaseq = derive2 { name="RTCGA.rnaseq"; version="20151101.11.0"; sha256="0z2k651pd0m9lxl3n62xf41xhk65n33cgf7d5zfwd03hbc07d0gq"; depends=[RTCGA]; }; - RUVnormalizeData = derive2 { name="RUVnormalizeData"; version="1.1.0"; sha256="002q9rc6d0cr6gip9irlafi67ds4jlvxfnil2if30aw4h6l4apkn"; depends=[Biobase]; }; - RcisTarget_hg19_motifDBs_cisbpOnly_500bp = derive2 { name="RcisTarget.hg19.motifDBs.cisbpOnly.500bp"; version="1.1.1"; sha256="08p1r5vpz92i7nmgdjsp0i5wzypb46lsdnlykci21nzf9ip12mc9"; depends=[data_table]; }; - RegParallel = derive2 { name="RegParallel"; version="0.99.9"; sha256="0n0qyiz2bqw5wi35f8rszrx668dl6hqw054lqakb2dpfpjlzz57y"; depends=[arm data_table doParallel foreach iterators MASS stringr survival]; }; - RforProteomics = derive2 { name="RforProteomics"; version="1.19.4"; sha256="1mm1cfsazajkhaim4grz2zi7ar4x2ljn5vq4rlv20gra3d4b82ca"; depends=[BiocManager biocViews MSnbase R_utils shiny]; }; - RnBeads_hg19 = derive2 { name="RnBeads.hg19"; version="1.13.1"; sha256="1l3za4hbrg38p9sh38qsj17hgg03cbgqga4zg0c4lcipifrpbbfj"; depends=[GenomicRanges]; }; - RnBeads_hg38 = derive2 { name="RnBeads.hg38"; version="1.13.0"; sha256="1wyy4m3p40i12hlwvz9ixqps8i4d5703gl0pcgl4i2485d78yv9v"; depends=[GenomicRanges]; }; - RnBeads_mm10 = derive2 { name="RnBeads.mm10"; version="1.13.0"; sha256="1kjvy1v0dbdm959cmsf2d5mnrbnisjpff12wl5gn44n2cg7bb65g"; depends=[GenomicRanges]; }; - RnBeads_mm9 = derive2 { name="RnBeads.mm9"; version="1.13.0"; sha256="1s1iy8x1x53ny1pyfgwwkiwc3jpjhdkcd9vpwyv2ix5g22jf8ag7"; depends=[GenomicRanges]; }; - RnBeads_rn5 = derive2 { name="RnBeads.rn5"; version="1.13.0"; sha256="1pp9y94rdk5wwapc4jbvs35x1z2agv4xvzxy3fl3h7hp22gaqr9p"; depends=[GenomicRanges]; }; - RnaSeqSampleSizeData = derive2 { name="RnaSeqSampleSizeData"; version="1.13.1"; sha256="1cqannbgpr0s9qr1cx4d23rwjy6k63x25khdr7qx5939chz0r21a"; depends=[edgeR]; }; - SCLCBam = derive2 { name="SCLCBam"; version="1.13.1"; sha256="1b6da5i20w7w08jv3s2xdpp71qf7y1nxyv3qj3fz5jkw2aavds5f"; depends=[]; }; - SNAData = derive2 { name="SNAData"; version="1.27.0"; sha256="182pramjd14g1p0aawcjrv51xlyqkp9mhm84v3gnd9gnmkb69b31"; depends=[graph]; }; - SNAGEEdata = derive2 { name="SNAGEEdata"; version="1.17.0"; sha256="15l23gw5ckxgr6pscl07jqwb1lz58g5893wnlzz4zpk3sd46d2p6"; depends=[]; }; - SNPhoodData = derive2 { name="SNPhoodData"; version="1.11.0"; sha256="1zm0zhf2987hls15b47jv6krn1cc8kp6jm64k4wqhp4dsjxwbaqd"; depends=[]; }; - SVM2CRMdata = derive2 { name="SVM2CRMdata"; version="1.13.0"; sha256="0qhkhnxrcy5i7cs4cl5axc8y9dbzhzfl00c17qp9r4bf8292xf1d"; depends=[]; }; - Single_mTEC_Transcriptomes = derive2 { name="Single.mTEC.Transcriptomes"; version="1.9.0"; sha256="1xnsilyjls3s048kl1jwqcs6sb4r33khga0z2zipsgk6aqnx81cc"; depends=[]; }; - SomatiCAData = derive2 { name="SomatiCAData"; version="1.19.0"; sha256="0aj84aljp7ih849qnyhmsibnsvg7cshj7xah67xhn5grzwk7v9hi"; depends=[]; }; - SomaticCancerAlterations = derive2 { name="SomaticCancerAlterations"; version="1.17.0"; sha256="0bprp4cddjf9zlhv38q5y08zrzizqaxj4338wbzjq1ypnjyip2qj"; depends=[exomeCopy GenomicRanges IRanges S4Vectors stringr]; }; - SpikeIn = derive2 { name="SpikeIn"; version="1.23.0"; sha256="1yjlljcy1wnxkxrcxaw26f96vkyvhqh9zq52l9s8d7gnrsfj44ak"; depends=[affy]; }; - SpikeInSubset = derive2 { name="SpikeInSubset"; version="1.21.0"; sha256="1z6fbq2z2ry2v3sv48n20c07bi96gb1nfg81g5ylh4q7w79g8lvf"; depends=[affy Biobase]; }; - TBX20BamSubset = derive2 { name="TBX20BamSubset"; version="1.17.0"; sha256="15521vpi6h1ydl8vw43h0plrgy7baj5bprzg8rs50yxgkphh9nns"; depends=[Rsamtools xtable]; }; - TCGAMethylation450k = derive2 { name="TCGAMethylation450k"; version="1.17.0"; sha256="090y4vyipnlxxg78yxva7q5y81gawfpmkgjrsqiqr1smfalvx9yw"; depends=[]; }; - TCGAWorkflowData = derive2 { name="TCGAWorkflowData"; version="1.5.0"; sha256="0kbab7fjy7waq5r6k2w0c8x811xd62v39p17acd5gk8gbw9gy919"; depends=[SummarizedExperiment]; }; - TCGAbiolinksGUI_data = derive2 { name="TCGAbiolinksGUI.data"; version="1.1.1"; sha256="0lg2xmf9crcd3328sikjynicrapm32ffq8ay9p0r484rx0m5yvbp"; depends=[]; }; - TCGAcrcmRNA = derive2 { name="TCGAcrcmRNA"; version="1.1.0"; sha256="160gj5q4n08l3llfqd0iim2054v8jd3a2pvvd7454amangnrrjd1"; depends=[Biobase]; }; - TCGAcrcmiRNA = derive2 { name="TCGAcrcmiRNA"; version="1.1.0"; sha256="1njy5ab0a8p97gi8ci0bad1byl5k42a5shjrss8z9k3a0n9jzpxm"; depends=[Biobase]; }; - TENxBrainData = derive2 { name="TENxBrainData"; version="1.1.2"; sha256="1m4cajmp1h5mahlxbvyfvslqq3yfbcy8k46m5p0b73phvnw44846"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; }; - TENxPBMCData = derive2 { name="TENxPBMCData"; version="0.99.3"; sha256="00xjm8xr5f1dzghmr6p3mcjcir6a81gd99kgzznj5k90assggr45"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; }; - TabulaMurisData = derive2 { name="TabulaMurisData"; version="0.99.2"; sha256="185y3cxdkgj4gl4ai0nc0684nz357qscfsah559wdvvvqny25dmk"; depends=[ExperimentHub]; }; - TargetScoreData = derive2 { name="TargetScoreData"; version="1.17.0"; sha256="12bmw3qmkw9blmr5ikgx0qyfv1x6hda8d41fiy8gsb74fa4nifsv"; depends=[]; }; - TargetSearchData = derive2 { name="TargetSearchData"; version="1.19.1"; sha256="1hwfqsz1rivqq14x5z9d8nphxajfxhm70mgbi0pjzlzsravg487w"; depends=[]; }; - TimerQuant = derive2 { name="TimerQuant"; version="1.11.0"; sha256="1a49jaxgjhwl756a7wijswa90z03fz61ffp6w5h00v9qfzgnyf79"; depends=[deSolve dplyr ggplot2 gridExtra locfit shiny]; }; - VariantToolsData = derive2 { name="VariantToolsData"; version="1.5.0"; sha256="1kkz3zvba4mc237pxwj6z0c2jvbrgfaz3n5vm55bz6j47aas3i4j"; depends=[BiocGenerics GenomicRanges VariantAnnotation]; }; - WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.13.0"; sha256="0f3llqwkc5d4av47871d45lfqghmncww9g5rgf58pydrnw7n93xv"; depends=[]; }; - XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.19.0"; sha256="1kac43fvng1pwa8hlbivd8pxan7agp9csp0nmh062x4kwamny3hm"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; }; - affycompData = derive2 { name="affycompData"; version="1.19.0"; sha256="14ss2b854dj36rzhx1z854r5hkxy0yqzlm5k0690gn5bwlah6rk6"; depends=[affycomp Biobase]; }; - affydata = derive2 { name="affydata"; version="1.29.0"; sha256="0sv5q59xfvlyk97ihki5sqdzy9nldjccxiscx3ii1xpp4xk44i3c"; depends=[affy]; }; - airway = derive2 { name="airway"; version="1.1.0"; sha256="0daywdjalqbqx6gxrg4fwiasa62h9jh8ibg9kh0vrd35mdazh7b4"; depends=[SummarizedExperiment]; }; - allenpvc = derive2 { name="allenpvc"; version="0.99.2"; sha256="04f6y2zk7c8prk22yl15qp9xf81dickn2ida8b5jdhzby6a4p1d1"; depends=[AnnotationHub ExperimentHub SingleCellExperiment]; }; - alpineData = derive2 { name="alpineData"; version="1.7.1"; sha256="1gdj474nc2s92i2m1f02ganr5vsv93315mk3dqdyyk05xr9banbw"; depends=[AnnotationHub ExperimentHub GenomicAlignments]; }; - antiProfilesData = derive2 { name="antiProfilesData"; version="1.17.0"; sha256="0wyjfc02wm5x5d61fs6cs7g3s0j4aibpqkdiwx0d8cbbkl38ih3f"; depends=[Biobase]; }; - aracne_networks = derive2 { name="aracne.networks"; version="1.7.0"; sha256="1acngnqvg7vl402yfcw65rqs27a7sncl1xfz2893abfli2ccpbzx"; depends=[viper]; }; - bcellViper = derive2 { name="bcellViper"; version="1.17.0"; sha256="0rzzj4pla57z9825jcs2kx177xrcqfnh7jai41m8dwfxln6ccz25"; depends=[Biobase]; }; - beadarrayExampleData = derive2 { name="beadarrayExampleData"; version="1.19.0"; sha256="13g7p6jrg9qa43zv8nhkgfz2pq7b3v6chgqmydyyz25q6jy28iqp"; depends=[beadarray Biobase]; }; - beta7 = derive2 { name="beta7"; version="1.19.0"; sha256="1gd1l8rh73k27sm1cjfy9rmsplrkji3zhzrzcldjmaaixl5nfjql"; depends=[marray]; }; - biotmleData = derive2 { name="biotmleData"; version="1.5.0"; sha256="0ccx398761qdnnsrjwrrg6qjrq01fv88999f2llyq9gpd3f43lgs"; depends=[]; }; - bladderbatch = derive2 { name="bladderbatch"; version="1.19.0"; sha256="0n9vwbj8cii67rhxvb1ps72k99rv251zcdr4w3r1jkbvcd61nvh0"; depends=[Biobase]; }; - blimaTestingData = derive2 { name="blimaTestingData"; version="1.1.0"; sha256="0r51zz7kh16zgadr2vzgrm5fywfs03mk2jk5qywb27agqbw5y40s"; depends=[]; }; - brainImageRdata = derive2 { name="brainImageRdata"; version="0.99.6"; sha256="0wbj8y1qskc23gqdwc815racv7kqplmh1v12y5y094fcgs6cq62p"; depends=[ExperimentHub]; }; - breakpointRdata = derive2 { name="breakpointRdata"; version="0.99.2"; sha256="13mfnd2ms1fnk6zmyz8l10qw8xhfmb8qjyc2r7hn1qmap6ld578f"; depends=[]; }; - breastCancerMAINZ = derive2 { name="breastCancerMAINZ"; version="1.19.0"; sha256="0pn48n81vx2wq425q5wnga6n32apgajk0bwq78ri983plh7ik2b1"; depends=[]; }; - breastCancerNKI = derive2 { name="breastCancerNKI"; version="1.19.0"; sha256="0b6z16m6kqkd8rfrdvjp6p4fbqs78s25fbiswnw0k8jzvz5yw5x7"; depends=[]; }; - breastCancerTRANSBIG = derive2 { name="breastCancerTRANSBIG"; version="1.19.0"; sha256="0slagz3x2q1qykvjcfnh7k3ggpn2g34j4iqvnv7j3mdcc085hn1d"; depends=[]; }; - breastCancerUNT = derive2 { name="breastCancerUNT"; version="1.19.0"; sha256="0470r0i59phz2rcnmi0sb2hvw87nvm5dq6s4dj6s6z5mn85g8hd4"; depends=[]; }; - breastCancerUPP = derive2 { name="breastCancerUPP"; version="1.19.0"; sha256="0qgz0dsds0xd8d6assqd0715zfyk2y92251m3zq108ndqh5gn4bm"; depends=[]; }; - breastCancerVDX = derive2 { name="breastCancerVDX"; version="1.19.0"; sha256="0ma62g72md7is365pbnqbdskacxqvvcnc65jzv8b7g1dwvayswp6"; depends=[]; }; - brgedata = derive2 { name="brgedata"; version="1.3.0"; sha256="0w9h12ns984h6k5zhz2x9ria4fa1wxp3k04f6qg5k1zw20v4q2d6"; depends=[Biobase SummarizedExperiment]; }; - bronchialIL13 = derive2 { name="bronchialIL13"; version="1.19.0"; sha256="1jg9jz03ab3fki6g293c0jclk8cfpj9qb6yzzskdpcz99xmhs2xv"; depends=[affy]; }; - bsseqData = derive2 { name="bsseqData"; version="0.19.1"; sha256="0gqwyx0l0xmd2aa46shq4kr11nfi1imj2pwfjc9026r47af5b84h"; depends=[bsseq]; }; - cMap2data = derive2 { name="cMap2data"; version="1.17.0"; sha256="11973w3gjz0qayxacx41mlbf4ji345js8jgjkn2aba0ahnyzb6vw"; depends=[]; }; - cancerdata = derive2 { name="cancerdata"; version="1.19.0"; sha256="02zi60lh6jsg6hlyyq6wzg9lzxjr8m9418kywlk3x3c6kkgkrh69"; depends=[Biobase]; }; - ccTutorial = derive2 { name="ccTutorial"; version="1.19.3"; sha256="1bghwfpdm2xzh6w1z2pinv9wxy3f5vx8aabyl5vj9smfmplgcmxx"; depends=[affy Biobase Ringo topGO]; }; - ccdata = derive2 { name="ccdata"; version="1.7.0"; sha256="1vdsldxl1xnjdi9ai346a1zx9jp6kw33884vwwy86xmj7799j3y1"; depends=[]; }; - celarefData = derive2 { name="celarefData"; version="0.99.0"; sha256="118rdgkz4vlhk5n5c683sl28xsjqds6m08w3nfsw8z7ki6kng9sx"; depends=[]; }; - ceu1kg = derive2 { name="ceu1kg"; version="0.19.0"; sha256="0vs60mflfc1pnc7s725wsyq2jrj44jrvxwzpw4bhlj0qbs602s8l"; depends=[Biobase GGBase GGtools]; }; - ceu1kgv = derive2 { name="ceu1kgv"; version="0.23.0"; sha256="10jnbc8y386racq3ac1hf1dp76wvzlfm8p66c94pk3f2m0w45psv"; depends=[Biobase GGBase]; }; - ceuhm3 = derive2 { name="ceuhm3"; version="0.19.0"; sha256="1qdp85ps5xrlx1pl769j91aig2rgxcix4pdzrsa249nyyq1avdym"; depends=[Biobase GGBase GGtools]; }; - cgdv17 = derive2 { name="cgdv17"; version="0.19.0"; sha256="1n67nx1har6mswv5p2cb1xfrawkkhzrzxy7fpc6091yy3ypw1s5w"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors VariantAnnotation]; }; - charmData = derive2 { name="charmData"; version="1.17.0"; sha256="0hgac6z9k3frw648479jf8m6n2wlljhln7n8y13lbsdv5wakln87"; depends=[charm pd_charm_hg18_example]; }; - chipenrich_data = derive2 { name="chipenrich.data"; version="2.5.0"; sha256="0j9zdc0xrxi7vjyl3dzkvr8g24cxc1kcvw52vplrd5njyyka5vw1"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicRanges IRanges readr rtracklayer S4Vectors]; }; - chromstaRData = derive2 { name="chromstaRData"; version="1.7.0"; sha256="0arxcqr1yrs00i7a8xncprixzm8lc8ljrbh371ckjdr7641g63gq"; depends=[]; }; - cnvGSAdata = derive2 { name="cnvGSAdata"; version="1.17.0"; sha256="1inxvj6sfl7n3cxzswkllbjbjwz0rm803hkycy4wxcsq7416sj21"; depends=[cnvGSA]; }; - colonCA = derive2 { name="colonCA"; version="1.23.0"; sha256="1mm0zb003izia6j502n4m91vad6iz3ymf8nn4f9wlj20di66fvx6"; depends=[Biobase]; }; - curatedBladderData = derive2 { name="curatedBladderData"; version="1.17.0"; sha256="14xwq55g83pvwyxm7kl6hq9c4j2bd6vp63afir619d5binl6i7ln"; depends=[affy]; }; - curatedBreastData = derive2 { name="curatedBreastData"; version="2.9.0"; sha256="024sx3am50vsaaixmj8gfp3f905rf7g7qyn47sdakpv6sx48k1zl"; depends=[Biobase BiocStyle ggplot2 impute XML]; }; - curatedCRCData = derive2 { name="curatedCRCData"; version="2.13.0"; sha256="1f6m6sllbxzca27lwyvav2d4si65w7fs9mh4mksw2sn8n8x5452v"; depends=[BiocGenerics nlme]; }; - curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="1.11.5"; sha256="1rcznh6h7vrwicf545jfxabrjwqf1npxqpp6hdfnf5bylkfrc1d9"; depends=[AnnotationHub Biobase dplyr ExperimentHub magrittr S4Vectors tidyr]; }; - curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.19.0"; sha256="0yvc1kpy4ql2sd467dggi6kpwxrvvqyasr0mgc61s1snmakvm06y"; depends=[affy BiocGenerics]; }; - curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.3.5"; sha256="01m4kld5cp0ff5wlwk2wln15vyjxgahzbk3xkzlg81yvs67ai2vr"; depends=[AnnotationHub ExperimentHub MultiAssayExperiment S4Vectors]; }; - davidTiling = derive2 { name="davidTiling"; version="1.21.0"; sha256="18ivz1z0il8s9sk6c5mzgipsbs8xswbq7swwm422ji1yp75lkd9p"; depends=[Biobase GO_db tilingArray]; }; - derfinderData = derive2 { name="derfinderData"; version="1.99.0"; sha256="1dv6j91c9xs19pynza54gs127qqf5xk66rwin6rby0dcv58ng6s4"; depends=[]; }; - diffloopdata = derive2 { name="diffloopdata"; version="1.9.0"; sha256="12a5338djyhg94q7wdahij4c9dnrx5qx04a1g9304wpk5z6cmxni"; depends=[]; }; - diggitdata = derive2 { name="diggitdata"; version="1.13.0"; sha256="09b1mk68mg3jqf63c54xdh805vd79hbnnh02rf6qb3pq6w9b6z64"; depends=[Biobase viper]; }; - dressCheck = derive2 { name="dressCheck"; version="0.19.0"; sha256="0k3h5i86345xx0d31qim1d1aw25axwy48hiq717fbnz2mpwsggj7"; depends=[Biobase]; }; - dsQTL = derive2 { name="dsQTL"; version="0.19.0"; sha256="0lwgnkvzpipqnzfh3vlqgk568ys1bqjyfih97c7vb8mn57i100fz"; depends=[Biobase GGBase SummarizedExperiment]; }; - dyebiasexamples = derive2 { name="dyebiasexamples"; version="1.21.0"; sha256="0k99wgjm4a7mjs76p48mwfp2y17xn4r2bral2c1hbyj2y4bl1ycz"; depends=[GEOquery marray]; }; - ecoliLeucine = derive2 { name="ecoliLeucine"; version="1.21.0"; sha256="1pbindvfhr7lf01r0kncp23f6jxlwmkd362mix2gw2g006a83y4f"; depends=[affy ecolicdf]; }; - estrogen = derive2 { name="estrogen"; version="1.27.0"; sha256="1m0q2k6p6ydp7ykqwi9a079knxmp14xlrpcwncklsapibcvyz8lr"; depends=[]; }; - etec16s = derive2 { name="etec16s"; version="1.9.0"; sha256="0ljn90gf4sm7615xw25dil15kgf81gl0hvbp24snx4nbflnhns4q"; depends=[Biobase metagenomeSeq]; }; - faahKO = derive2 { name="faahKO"; version="1.21.0"; sha256="19dxcf3yfgy8h8xn76h7x2ihvgy90923a28j3b2k972r84zzy7gk"; depends=[xcms]; }; - fabiaData = derive2 { name="fabiaData"; version="1.19.0"; sha256="104c70pp9cnkx3y2mm6yxj4vj6k2mqrhw1n2cibhxnnqnl2lnwnr"; depends=[Biobase]; }; - facopy_annot = derive2 { name="facopy.annot"; version="1.1.0"; sha256="0snc9v8jy3dnxidk7g9lppxcp35flgdgp132sap8qkh6d1qc2rwd"; depends=[]; }; - facsDorit = derive2 { name="facsDorit"; version="1.23.0"; sha256="0xxdz1xfb661pnrqji6vxsmmr90h1v1i195k9gb4dll6hwbq0n11"; depends=[prada]; }; - ffpeExampleData = derive2 { name="ffpeExampleData"; version="1.19.0"; sha256="0jjaj492k4akc30yvr4q8y31wdi152iq5s3pl5i10sl9xrbg80hj"; depends=[lumi]; }; - fibroEset = derive2 { name="fibroEset"; version="1.23.0"; sha256="1g22av8zj4nq9prnps7zgrzvva9d5a6h016llg0brpf9qjpg58p3"; depends=[Biobase]; }; - fission = derive2 { name="fission"; version="1.1.0"; sha256="04rwbx0dd6fjyg76jw62vimllq40lb432bzmpf051x9gjqfyx0v2"; depends=[SummarizedExperiment]; }; - flowFitExampleData = derive2 { name="flowFitExampleData"; version="1.17.0"; sha256="1ahg5g9ypxbhm7jrsbq1hjk5r5fmgvirawfd2xqfiaw5x9pkmrai"; depends=[flowCore]; }; - flowPloidyData = derive2 { name="flowPloidyData"; version="1.7.0"; sha256="0f3cnq2s215a6wrz2cbp90219smvhr4zsvl02wbd40xb8902zhdc"; depends=[]; }; - flowQBData = derive2 { name="flowQBData"; version="1.7.0"; sha256="1xla98i06j1qi2w88x1v8agvqcljzwxfcxakw0fl6phwl07hz9na"; depends=[]; }; - flowWorkspaceData = derive2 { name="flowWorkspaceData"; version="2.17.0"; sha256="058q46w84jd7rf50pn26fiyh1n312jvxbcdrm5i2mmzg358hrr6y"; depends=[]; }; - frmaExampleData = derive2 { name="frmaExampleData"; version="1.17.0"; sha256="10lr219ghj409himn3g080s5saln3k355x9jhrk9fx69r8g127d7"; depends=[]; }; - furrowSeg = derive2 { name="furrowSeg"; version="1.9.0"; sha256="1a4gwrbqliz3cwn9iqwsn27qhmq9l3rh9k59ca94vsjmkrqx7bjk"; depends=[abind dplyr EBImage locfit tiff]; }; - gageData = derive2 { name="gageData"; version="2.19.0"; sha256="1zrps414095nkc49f90a7f8zy224ll60dm6b46sfkajd35bprafj"; depends=[]; }; - gaschYHS = derive2 { name="gaschYHS"; version="1.19.0"; sha256="0alxcrnk8kyjrs73idgihwvz42hbn4d6laayl849rzcna1fp48sp"; depends=[Biobase]; }; - gatingMLData = derive2 { name="gatingMLData"; version="2.21.0"; sha256="16gwgign7bq4yccq36wav2w8xl193c6aca6bgh9l8fv0z0rdgxnv"; depends=[]; }; - gcspikelite = derive2 { name="gcspikelite"; version="1.19.0"; sha256="197lx2a6jlsrv5bg3ih28maikyb8jk91krifk80xys3yfhp9dhyb"; depends=[]; }; - geneLenDataBase = derive2 { name="geneLenDataBase"; version="1.17.0"; sha256="0qxdhn5is2d47iv01z7in8gd3s2dzrgir8s8j4611f7sgy9s9px4"; depends=[GenomicFeatures rtracklayer]; }; - genomationData = derive2 { name="genomationData"; version="1.13.0"; sha256="02fq74q6vkraivdrka8l0hascvsxg2ys6p40774vjhrhrcvmnfkm"; depends=[]; }; - geuvPack = derive2 { name="geuvPack"; version="1.13.0"; sha256="07h53q19zg89rvzjk3aqgp52gynlxg5frxm5h2q3q5ihidp118cr"; depends=[SummarizedExperiment]; }; - geuvStore2 = derive2 { name="geuvStore2"; version="1.11.0"; sha256="1ggac70x9pblbnzm6wg6rpmbgrkf802b2vgnfah1516grx0dwrkd"; depends=[BatchJobs GenomicRanges gQTLBase]; }; - golubEsets = derive2 { name="golubEsets"; version="1.23.0"; sha256="1h45rwz6z4wgibbyafv8946vfs303km7ixcradml4ymbpwibp4ib"; depends=[Biobase]; }; - grndata = derive2 { name="grndata"; version="1.13.0"; sha256="1ybgk5nf9nqrmw4mchpf183zyik6szzsm2cxh619fv27f0i3hjzk"; depends=[]; }; - gskb = derive2 { name="gskb"; version="1.13.1"; sha256="1jpl7vm2r28bf70mv2sy0dkdn6yn27w96ja2a0yynbpd509v8fwg"; depends=[]; }; - h5vcData = derive2 { name="h5vcData"; version="2.1.0"; sha256="036bvqd8glpk2armbv42wxv28k6rqg301l7i04wp85d94ipgn6yk"; depends=[]; }; - hapmap100khind = derive2 { name="hapmap100khind"; version="1.23.0"; sha256="07r1nsl92awkkw41midkb9iv4c93my7c222li2f4mym8hn4ahn8p"; depends=[]; }; - hapmap100kxba = derive2 { name="hapmap100kxba"; version="1.23.0"; sha256="0dvb3b2ls7g66vsv9qzl29kkjmdd6mwrhqxzj0a1d7qnkg48kgy1"; depends=[]; }; - hapmap500knsp = derive2 { name="hapmap500knsp"; version="1.23.0"; sha256="0jqyvd1khz84l1qw31xk2szb9ycsp76yrs1h81ahg64sslygnfg0"; depends=[]; }; - hapmap500ksty = derive2 { name="hapmap500ksty"; version="1.23.0"; sha256="128p97qmp7br5vwmn934akkh0h4xgirpzc4q7kaxh3w211rch7rm"; depends=[]; }; - hapmapsnp5 = derive2 { name="hapmapsnp5"; version="1.23.0"; sha256="0a1n93nin8hpqh0qswbl9phlwgllam0xxpa2qxr63dyd5k1liwz6"; depends=[]; }; - hapmapsnp6 = derive2 { name="hapmapsnp6"; version="1.23.0"; sha256="1m17r4va3vbiml0avlb7xp2qhh82vig934h3gpmz9190hy6ikds4"; depends=[]; }; - harbChIP = derive2 { name="harbChIP"; version="1.19.0"; sha256="1566kxfblk6z4dia4f3gl3v0dsz8lx343nlflbp2wfb6gd314dl6"; depends=[Biobase Biostrings IRanges]; }; - healthyFlowData = derive2 { name="healthyFlowData"; version="1.19.0"; sha256="052kvg8gvfbqc4fpr8np1q9li7f52daq1rndpg7zmc5zn4nqjzrn"; depends=[flowCore]; }; - hgu133abarcodevecs = derive2 { name="hgu133abarcodevecs"; version="1.19.0"; sha256="1c113f0aj51mdvdizi6m2wmm0v7zxsa3pkp3bjq2426v449qr3ls"; depends=[]; }; - hgu133plus2CellScore = derive2 { name="hgu133plus2CellScore"; version="1.1.1"; sha256="1h1n76j6l0nqqf18a5w5c8vmjd579jdh2ix84j70s30nkzbyxhyw"; depends=[Biobase]; }; - hgu133plus2barcodevecs = derive2 { name="hgu133plus2barcodevecs"; version="1.19.0"; sha256="005llh7vpfc01qbq1wnq1nribqgh1kj7mw0rz59dsmr92czm7lbi"; depends=[]; }; - hgu2beta7 = derive2 { name="hgu2beta7"; version="1.21.0"; sha256="1d80nxbf8ffmh7ipvxw2smvhgq4xvjhnhmwpwmkwn30yghrm46wj"; depends=[]; }; - hmyriB36 = derive2 { name="hmyriB36"; version="1.17.0"; sha256="1s1gsysv8wsk9fzd34fjw2rp6jk8nysg1wd6dhay5mqphv92abkh"; depends=[Biobase GGBase]; }; - humanStemCell = derive2 { name="humanStemCell"; version="0.21.0"; sha256="02y71ydwlygn6yickjx3gjsmrhp6dnvqk5319is70gwd214466r1"; depends=[Biobase hgu133plus2_db]; }; - iontreeData = derive2 { name="iontreeData"; version="1.17.2"; sha256="1y3jawc5rs1fhv90yygkjghp1ir4zw540hi2ncml4lm003d42ghq"; depends=[]; }; - kidpack = derive2 { name="kidpack"; version="1.23.0"; sha256="1ib24nbvqgids10k1glvpswavnv0qd14nvx9bw13bk09vndagkyi"; depends=[Biobase]; }; - leeBamViews = derive2 { name="leeBamViews"; version="1.17.0"; sha256="1mldlpdpnivfi60rnsbz7466jf9ssyfgb2xv9ipwc8nlmszd6g45"; depends=[Biobase BSgenome GenomicAlignments GenomicRanges Rsamtools]; }; - leukemiasEset = derive2 { name="leukemiasEset"; version="1.17.0"; sha256="15c31vzfn83pfjj8bmvg4sl0hynlvaz2wcg3fzlxmlpbf6b5rqd7"; depends=[Biobase]; }; - lumiBarnes = derive2 { name="lumiBarnes"; version="1.21.0"; sha256="043w39jdc35pgblprh2p4crpxcix39ya9kg3g4q8dcajasr13dag"; depends=[Biobase lumi]; }; - lungExpression = derive2 { name="lungExpression"; version="0.19.0"; sha256="1rbbkjv3vjrk6d22k7msnq124y47a8pb4vdf388f1a8j9403jfpi"; depends=[Biobase]; }; - lydata = derive2 { name="lydata"; version="1.7.0"; sha256="0lq17l0klsn081m2nd9hrx50nxksvf7186drby66qvq6bhw3vhms"; depends=[]; }; - mAPKLData = derive2 { name="mAPKLData"; version="1.13.0"; sha256="1h4x00a7rziqm3cqkddpp7ahrb36045yq71lskdjyp43k066jplw"; depends=[]; }; - mCSEAdata = derive2 { name="mCSEAdata"; version="1.1.0"; sha256="0rcfyk6mwlxgkk7q40djbcbd4kx4vyy79h6dxb37zd7mpzxj03nx"; depends=[]; }; - mammaPrintData = derive2 { name="mammaPrintData"; version="1.17.2"; sha256="0015cz3czxzzrx7ba8lqr1a5i4nh1mns114br660y9d32j1nsw0f"; depends=[]; }; - maqcExpression4plex = derive2 { name="maqcExpression4plex"; version="1.25.0"; sha256="14m82492wb7jmqwjllnqak9rivyky1prcqgp1yn0g05c406fj0r9"; depends=[]; }; - mcsurvdata = derive2 { name="mcsurvdata"; version="0.99.4"; sha256="0kv2gq9vr0z2sg8v7mv0ky66gvwf2hbaisw2g02a81bzhjvyjky8"; depends=[AnnotationHub Biobase ExperimentHub]; }; - metaMSdata = derive2 { name="metaMSdata"; version="1.17.0"; sha256="0j6h0s75w50jp3lcfs5cilqaqhhinlfn9c6zlpki6906fj1q6dxx"; depends=[]; }; - methyvimData = derive2 { name="methyvimData"; version="1.3.0"; sha256="0jacj9jyqs5x11xds6bindab6q96br95r37dxmgxw5gxl9lcn6ql"; depends=[minfi]; }; - miRNATarget = derive2 { name="miRNATarget"; version="1.19.0"; sha256="05x4vl8x2brm3bj04kddzcqjnm72jw29prmcwr1ildbaadmzh3fg"; depends=[Biobase]; }; - miRcompData = derive2 { name="miRcompData"; version="1.11.0"; sha256="1qgzplmv16anh7c760nf51fh671z0lmxqmkn0qfmj55d54gfgfmh"; depends=[]; }; - microRNAome = derive2 { name="microRNAome"; version="1.3.0"; sha256="0hbs64bhd129cq098y5ijf6q2nvn2w382d29isws92q1ln12r36b"; depends=[SummarizedExperiment]; }; - minfiData = derive2 { name="minfiData"; version="0.27.0"; sha256="1h7mb52p73bw66rxwjjfmaan6scs9pc6rj2f9wb5hx9hddwz5xy4"; depends=[IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest minfi]; }; - minfiDataEPIC = derive2 { name="minfiDataEPIC"; version="1.7.0"; sha256="119sr9yb82dlcjgddlqwzgn72c7zghz26kzdda48s9zxlf31f9yp"; depends=[IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest minfi]; }; - minionSummaryData = derive2 { name="minionSummaryData"; version="1.11.0"; sha256="1i5ilakb9a4w7zf4zwymmpxyqn8s4y7295gdw2spgafgny0ayvag"; depends=[]; }; - mitoODEdata = derive2 { name="mitoODEdata"; version="1.17.0"; sha256="1pabl518xj88hlpfdqsbg2178ac2in11ma3y0syvq7wr2nqdqj6s"; depends=[]; }; - mosaicsExample = derive2 { name="mosaicsExample"; version="1.19.0"; sha256="17xvlaxlw6jn7w81dyg74n84nny6apaxv8b7qbv7gcyil3h2xr7f"; depends=[]; }; - mouse4302barcodevecs = derive2 { name="mouse4302barcodevecs"; version="1.19.0"; sha256="1y7vkiqp4mkf16mpl5yl1jzmh1fv67d6k4i8qfi1lm68q2av9ggv"; depends=[]; }; - msPurityData = derive2 { name="msPurityData"; version="1.9.0"; sha256="0z7gs75bci301mhhp9j8lxpivjns2bmr51vsz04d4k308j19w1wv"; depends=[]; }; - msd16s = derive2 { name="msd16s"; version="1.1.0"; sha256="09zjzad3blq6i1m6fnkfjpllnvjn9vlrlc075gcm2gpwcx4w775a"; depends=[Biobase metagenomeSeq]; }; - msdata = derive2 { name="msdata"; version="0.21.0"; sha256="1srm1djnzfrj6klzxm2s721glk75lakb2428arqn3bm8vzvqw5vy"; depends=[]; }; - msqc1 = derive2 { name="msqc1"; version="1.9.1"; sha256="041fz9md3q95p1cwc7bcqam2z555sin2ib7ryssp79hp8iibx50g"; depends=[lattice]; }; - mtbls2 = derive2 { name="mtbls2"; version="1.11.0"; sha256="1ismd5yp3vgj1cqp4y92gy5z856bs6sy3fgbigjjba2rrb3m4k1z"; depends=[]; }; - mvoutData = derive2 { name="mvoutData"; version="1.17.0"; sha256="13kakn04xrngx9m80m1gqwdx3f75qixy6h9y0jvh16jk49kdnxcd"; depends=[affy Biobase lumi]; }; - pRolocdata = derive2 { name="pRolocdata"; version="1.19.5"; sha256="0gci5k1wxmnwy76nhnpjm9hysxpzjz29xw8j8srp96zn1bskaayi"; depends=[Biobase MSnbase]; }; - parathyroidSE = derive2 { name="parathyroidSE"; version="1.19.0"; sha256="1dmnm348yxa9p6lnia4iiil1s4jkxj1n83frhml06brnqymbb9wn"; depends=[SummarizedExperiment]; }; - pasilla = derive2 { name="pasilla"; version="1.9.0"; sha256="09rzh3w8nki9gqsk3pznk867ipg7s7imz7ma67cl0rh8pz2vg05i"; depends=[]; }; - pasillaBamSubset = derive2 { name="pasillaBamSubset"; version="0.19.0"; sha256="0d2b4qav1m0whr7gwn2h2962qd72i3fc0y9c36k6nxr7jyfmv1jj"; depends=[]; }; - pathprintGEOData = derive2 { name="pathprintGEOData"; version="1.11.0"; sha256="1s5nilgzs1kgdjaqyq7warfg672qvd14m61bdvl0g12bkab61sv8"; depends=[]; }; - pcaGoPromoter_Hs_hg19 = derive2 { name="pcaGoPromoter.Hs.hg19"; version="1.17.0"; sha256="0wwd5cc8ywi5181q8hrxw6jx6pxyrfayfdpw7jzp3nkj8x222d31"; depends=[]; }; - pcaGoPromoter_Mm_mm9 = derive2 { name="pcaGoPromoter.Mm.mm9"; version="1.17.0"; sha256="0g5y5nsi99dsx6n1zfjlc6vi4ikmv2l1ba6sbdid9019k79v4495"; depends=[]; }; - pcaGoPromoter_Rn_rn4 = derive2 { name="pcaGoPromoter.Rn.rn4"; version="1.17.0"; sha256="1qz6saflpsa9naj536k7ciqks95hb6l1z2v6srclqq7b45465h1b"; depends=[]; }; - pcxnData = derive2 { name="pcxnData"; version="2.3.0"; sha256="1whw0wrfq1dfbxpfcz9z749dh27fadxmwp3dln945qh0nrjli6zc"; depends=[]; }; - pd_atdschip_tiling = derive2 { name="pd.atdschip.tiling"; version="0.19.0"; sha256="1rfp34332p0fbx9yfb87rlhwwzjy1pm3zf372pvhv1r7qm8w3dyh"; depends=[Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; - pepDat = derive2 { name="pepDat"; version="1.1.0"; sha256="0yqlsdzjqwdvjfy7p6rls2xy5bph75pivkvizj575pmagdviv882"; depends=[GenomicRanges]; }; - plasFIA = derive2 { name="plasFIA"; version="1.9.0"; sha256="0ivyvrx2wmr9wsi852h3fdkbc8qrxhx1gf21aiazlygz3x796fml"; depends=[proFIA]; }; - ppiData = derive2 { name="ppiData"; version="0.19.0"; sha256="0hglfcyzlz7j090qylilqxx9jhivk3ipkq6q0zn2grydrj0g0xib"; depends=[AnnotationDbi graph]; }; - prebsdata = derive2 { name="prebsdata"; version="1.17.0"; sha256="1jccx76j7xqbl4660f0akh6bnvhcvpn1wkn2hchbv9w1s9ywy9pi"; depends=[]; }; - prostateCancerCamcap = derive2 { name="prostateCancerCamcap"; version="1.9.0"; sha256="0wqm9wbqz15ls55mzvd6kfssix02pn2qaymin6s0b6w2imji85np"; depends=[Biobase]; }; - prostateCancerGrasso = derive2 { name="prostateCancerGrasso"; version="1.9.0"; sha256="19r3gb718gll5fx03q1q0471r7fx25iix7ncff6v54pp4lvnjk9q"; depends=[Biobase]; }; - prostateCancerStockholm = derive2 { name="prostateCancerStockholm"; version="1.9.0"; sha256="1y9pzi3w2k3fj6lnmlhzh5dvazb7vkqvchm1a6fi3lj3wdqv12lw"; depends=[Biobase]; }; - prostateCancerTaylor = derive2 { name="prostateCancerTaylor"; version="1.9.0"; sha256="0pclqc7qzypwd4jvld3dmy43fc5hram1lzcfbdnp4vj8r86mw7il"; depends=[Biobase]; }; - prostateCancerVarambally = derive2 { name="prostateCancerVarambally"; version="1.9.0"; sha256="02vg37vllda3yvw6lq7xggil6l3n7v4y37s2cqixqrrmnczzqb2z"; depends=[Biobase]; }; - pumadata = derive2 { name="pumadata"; version="2.17.0"; sha256="0ag7kv1k9jaj943l0szxlk2qfx5mlpspwsrnnyxxcpi3s8r8nyn4"; depends=[affy Biobase oligo puma]; }; - qPLEXdata = derive2 { name="qPLEXdata"; version="0.99.1"; sha256="05v19rlbskvy15504ys8x3s2hhbdzwnyz3dwjas6h0b7rs3d51p7"; depends=[dplyr knitr MSnbase qPLEXanalyzer]; }; - rRDPData = derive2 { name="rRDPData"; version="1.1.0"; sha256="16xk33bry0203sr79lzs89pwzbqds29894fc2hjr9qs624wrzvnk"; depends=[rRDP]; }; - rcellminerData = derive2 { name="rcellminerData"; version="2.3.1"; sha256="1i149vpfm873nzykbxf93rkrmyjshri5xi7awmxf60yiwacbafkk"; depends=[Biobase]; }; - restfulSEData = derive2 { name="restfulSEData"; version="1.3.0"; sha256="01vbzdx354qpl58lznn9938jn93rf9nikwjfmy1w33z5cmirc7ad"; depends=[ExperimentHub SummarizedExperiment]; }; - rheumaticConditionWOLLBOLD = derive2 { name="rheumaticConditionWOLLBOLD"; version="1.19.0"; sha256="1bcn3s36w3asb2di8851wg67dpx3rwalw9php1sklzrbh2f7jazs"; depends=[]; }; - sampleClassifierData = derive2 { name="sampleClassifierData"; version="1.5.0"; sha256="06p4cq30diwx5flxc31lw3k6z66y6villf99qq99f4ab5x3gad94"; depends=[SummarizedExperiment]; }; - scRNAseq = derive2 { name="scRNAseq"; version="1.7.0"; sha256="15cxr52qakxhsbjnm8vl33qlwbvl3lghkrk4l2v0dih4mw4g65nb"; depends=[SummarizedExperiment]; }; - seq2pathway_data = derive2 { name="seq2pathway.data"; version="1.13.0"; sha256="0z9dspkjvjn20q542bjq7xyc7fpy76y3ic01h14cvql42m0vhl53"; depends=[]; }; - seqCNA_annot = derive2 { name="seqCNA.annot"; version="1.17.0"; sha256="0hz9vf8fplqm3gfrfiiirm0w6g9x6bjq7l96275aizbx3g6a80kb"; depends=[]; }; - seqc = derive2 { name="seqc"; version="1.15.2"; sha256="1bc4ibhb7wr08c794m1ljy3hz4fy0vikavg7g7y6l3rjfvlns7lk"; depends=[Biobase]; }; - serumStimulation = derive2 { name="serumStimulation"; version="1.17.0"; sha256="153zq6qpk02mkk31v5sl129j50wiw9n8c7n28f39w0mzg93yjyv5"; depends=[]; }; - sesameData = derive2 { name="sesameData"; version="0.99.5"; sha256="0y2xkxrbj5fla75rq4iysa5ckmvv6fnbi06nk372n0gyvi0v5w8d"; depends=[AnnotationHub curl ExperimentHub]; }; - seventyGeneData = derive2 { name="seventyGeneData"; version="1.17.3"; sha256="1aq5pzj70alv4kmi79kdyc9v0441gvfgibzf5j06zh6b2bc409x6"; depends=[]; }; - shinyMethylData = derive2 { name="shinyMethylData"; version="1.1.0"; sha256="1qd8193vvs22x8hfy70ih2m5gx4s46hd0fas9ann198vv4rhygxz"; depends=[]; }; - simpIntLists = derive2 { name="simpIntLists"; version="1.17.0"; sha256="1cgr86ibyz4xmhsrmrr0qx8f1xhclw7q4mrrbr5znvy4nvhbzpz6"; depends=[]; }; - stemHypoxia = derive2 { name="stemHypoxia"; version="1.17.0"; sha256="076h70m11z178q1v58rbb1731nskck64sr4w29x1jby8h87rqkvk"; depends=[]; }; - stjudem = derive2 { name="stjudem"; version="1.21.0"; sha256="1ccr0zcqwffizqbd624j980kn40hmic2497mj2ws19chwqxaz24j"; depends=[]; }; - synapterdata = derive2 { name="synapterdata"; version="1.19.0"; sha256="1yppixbw3pxsaag1zfsd39p78d5l8702ysxxjgnmi50ak0lrwb2w"; depends=[synapter]; }; - systemPipeRdata = derive2 { name="systemPipeRdata"; version="1.9.4"; sha256="0k8nybycswz78l0v61nidnirw3i9k41f1150ssglxyhqsvxpn8xd"; depends=[BiocGenerics]; }; - tcgaWGBSData_hg19 = derive2 { name="tcgaWGBSData.hg19"; version="0.99.3"; sha256="16p36sailxw14f051c3k89gz2i9blky0vx961s36mmnd5sqn6skn"; depends=[bsseq ExperimentHub knitr]; }; - tinesath1cdf = derive2 { name="tinesath1cdf"; version="1.19.0"; sha256="0mpj8j8s9380lf830b862k2rj1mpfa3vflkai5bacwnx9i3dbmnz"; depends=[]; }; - tinesath1probe = derive2 { name="tinesath1probe"; version="1.19.0"; sha256="07fyj1vdpzkz8iw6d9bqxgi4482rvq0r945p3rxa5a0cvwcsh1xi"; depends=[AnnotationDbi]; }; - tissueTreg = derive2 { name="tissueTreg"; version="1.1.0"; sha256="1whm1a9r5bmrdzqchv7qzgnxnclq1qbzqjv0p6f6d6y7mw3rr6f6"; depends=[]; }; - tofsimsData = derive2 { name="tofsimsData"; version="1.9.0"; sha256="17pwxdik4phg1cc10ycp2j38n63l1rfna8pzz16j05858ig24lif"; depends=[]; }; - topdownrdata = derive2 { name="topdownrdata"; version="1.3.0"; sha256="095mhjpni166p351k50y0605gb3ydsrhdnf8i92w6q84qnl9dapw"; depends=[topdownr]; }; - tweeDEseqCountData = derive2 { name="tweeDEseqCountData"; version="1.19.0"; sha256="1gby12vp7b88h3g86r5r01lj86chs30q505qijv3zq769px7fd2g"; depends=[Biobase]; }; - tximportData = derive2 { name="tximportData"; version="1.9.2"; sha256="0j7nwkfrvli8wx3jvrfn1qygvzyzvmzlp5vq529ssqf6mka8i2r3"; depends=[]; }; - vulcandata = derive2 { name="vulcandata"; version="1.3.1"; sha256="1jgiryn6cpmbipaif5d5yhwrl692hc6nac5abjip31l0rqmf4qig"; depends=[]; }; - waveTilingData = derive2 { name="waveTilingData"; version="1.17.0"; sha256="1w0wvnk4r7vvg9xvqmpmwzbp1sr7plg214d6wgdwgmp9bm785vxf"; depends=[]; }; - yeastCC = derive2 { name="yeastCC"; version="1.21.0"; sha256="1kbhbqcab7p3p160xvgwka8gfhxnjl05p9hxb7jjixi4yr30dzvj"; depends=[Biobase]; }; - yeastExpData = derive2 { name="yeastExpData"; version="0.27.0"; sha256="13vz99brk9bb10swlrisiiwilyjn6pl1z3arw47sahm7grw4sgpc"; depends=[graph]; }; - yeastGSData = derive2 { name="yeastGSData"; version="0.19.0"; sha256="06gnrh6kll5rmdvhigrf7blyyap6dz517gkhx2ljvlbwwz1hd35l"; depends=[]; }; - yeastNagalakshmi = derive2 { name="yeastNagalakshmi"; version="1.17.0"; sha256="0xq65383vmh1jnfxnfhrzfdhr5s0qzy0xb844d8lvmsn77mq7jpr"; depends=[]; }; - yeastRNASeq = derive2 { name="yeastRNASeq"; version="0.19.0"; sha256="0sy72a0dvqq75hg599nfq6rv9frjwmvzqyissksa4dpbm8n3q086"; depends=[]; }; - yri1kgv = derive2 { name="yri1kgv"; version="0.23.0"; sha256="08i7iz0shrhh3pnn88x3fnkpqrics4nq43fcwzkk1582j1spg8yr"; depends=[Biobase GGBase]; }; - yriMulti = derive2 { name="yriMulti"; version="0.11.0"; sha256="0gsr2y94hfmjmpz37y7q80wnkhlz8q028qn7dwm15a5rvzvs8ccv"; depends=[dsQTL GenomeInfoDb GenomicFiles GenomicRanges geuvPack gQTLBase Homo_sapiens MultiAssayExperiment SummarizedExperiment VariantAnnotation]; }; - zebrafishRNASeq = derive2 { name="zebrafishRNASeq"; version="1.1.0"; sha256="1sfdzs0s0jjrm36v016zf4xbw2rl2gfibzbzvgj7vark30f8w960"; depends=[]; }; + ABAData = derive2 { name="ABAData"; version="1.16.0"; sha256="1mv8xvpb2086rnrzclpmb6wjfj68hyilx5k3mcwbkvgnhfn4j454"; depends=[]; }; + ALL = derive2 { name="ALL"; version="1.28.0"; sha256="16fq2bgp9c56mmc5a7y1wrfdak6fympmfr6yi7dzqsinigf1m17g"; depends=[Biobase]; }; + ALLMLL = derive2 { name="ALLMLL"; version="1.26.0"; sha256="0yv9wyq5q0dmwl9cj0rkncklsqa4il3a1vd2mvi9sr8rn4nrvkmi"; depends=[affy]; }; + ARRmData = derive2 { name="ARRmData"; version="1.22.0"; sha256="1s8cy24gjawi01x84lliir5101p49s6dbx5gnhl5ymsz60jpbpix"; depends=[]; }; + ASICSdata = derive2 { name="ASICSdata"; version="1.6.0"; sha256="1b14w929z75q4ihavj642sa176cj96m629yd9ga1733m8gj8hsg2"; depends=[]; }; + Affyhgu133A2Expr = derive2 { name="Affyhgu133A2Expr"; version="1.22.0"; sha256="18n2gchvpaspdgpzdr9b06y96zmhkyprn3s4xr2pa140z2518sgx"; depends=[]; }; + Affyhgu133Plus2Expr = derive2 { name="Affyhgu133Plus2Expr"; version="1.20.0"; sha256="0f4gqdhwn2n2gchwfxxylajps4ghj0s0q72schzxjvrd3p10rik4"; depends=[]; }; + Affyhgu133aExpr = derive2 { name="Affyhgu133aExpr"; version="1.24.0"; sha256="1qy0p6ndva9j3lbfnpn3619x6kyyjbnbyw7qb4bdk6nfq63ddbk6"; depends=[]; }; + AffymetrixDataTestFiles = derive2 { name="AffymetrixDataTestFiles"; version="0.24.0"; sha256="07i5ww735ixwiyahqx2r09xymvs23ni0vvbjmj0vryy0g247ix9s"; depends=[]; }; + Affymoe4302Expr = derive2 { name="Affymoe4302Expr"; version="1.24.0"; sha256="0zzrx1bzg684hz7hvvf3dlvrc1jp2yi3jqy4yp3z4jn6vz6fnzb5"; depends=[]; }; + AmpAffyExample = derive2 { name="AmpAffyExample"; version="1.26.0"; sha256="03gwffv5xjcm4zyp3rmfzqix6si5pyjwqxg4bq7w4pn7ayvn2ls4"; depends=[affy]; }; + AneuFinderData = derive2 { name="AneuFinderData"; version="1.14.0"; sha256="1ar2n45bhns0m651p6xlff5ja56s2a906c01qsyza348pjh5fmi7"; depends=[]; }; + AshkenazimSonChr21 = derive2 { name="AshkenazimSonChr21"; version="1.16.0"; sha256="11gz0wwbfk5v3kksw1bgl3vvqna4qcys9bs6x3sp4gffgm794lz7"; depends=[]; }; + AssessORFData = derive2 { name="AssessORFData"; version="1.4.0"; sha256="1wcgkn20iw2i914zyyndhan65biwcj2a9maqkx0w94h99fzdrjh7"; depends=[DECIPHER]; }; + BeadArrayUseCases = derive2 { name="BeadArrayUseCases"; version="1.24.0"; sha256="1ykfm4w5dgdq5f6k807ma2fhchnqfrm1z35wvm8v0203amqbgmd2"; depends=[beadarray GEOquery limma]; }; + BloodCancerMultiOmics2017 = derive2 { name="BloodCancerMultiOmics2017"; version="1.6.2"; sha256="1ylbywkf20mgprbijxvxx2dfs0y8h3h10kg05xv0f7dkbaq6wlnw"; depends=[beeswarm Biobase DESeq2 devtools dplyr ggdendro ggplot2 glmnet gtable ipflasso RColorBrewer reshape2 scales SummarizedExperiment survival tibble]; }; + CCl4 = derive2 { name="CCl4"; version="1.24.0"; sha256="1bsrk06hbfh1fp5vqjzcn91y5bjj726040809hql61z2iz9r7269"; depends=[Biobase limma]; }; + CLL = derive2 { name="CLL"; version="1.26.0"; sha256="02h018zwkf357fa7rj94dz5lf8vl2synv4ngwf03q6gh7yggr479"; depends=[affy Biobase]; }; + CLLmethylation = derive2 { name="CLLmethylation"; version="1.6.1"; sha256="07fjzchdh4rf4dbqx54x2gq0a4jhikifqq498asv5ld0cjpvvljx"; depends=[ExperimentHub SummarizedExperiment]; }; + COHCAPanno = derive2 { name="COHCAPanno"; version="1.22.0"; sha256="07afc6cvbn3445ib68968wm9dqby1imwg8s30n2l91y94ak9ny2c"; depends=[]; }; + CONFESSdata = derive2 { name="CONFESSdata"; version="1.14.0"; sha256="04nzyv424fnwgr658yvwm80q1vmn66sqm0c2bf8dppdx86xm12xx"; depends=[]; }; + COPDSexualDimorphism_data = derive2 { name="COPDSexualDimorphism.data"; version="1.22.0"; sha256="0ahifads1fird2rjvar8xqwfsn6rlq42p7dpa60ybhiyn4wl054w"; depends=[]; }; + COSMIC_67 = derive2 { name="COSMIC.67"; version="1.22.0"; sha256="0sick7wgv241bdp6f7828psfbzfdig2rqzdwf2qhmmflkdxd81cb"; depends=[GenomicRanges SummarizedExperiment VariantAnnotation]; }; + CRCL18 = derive2 { name="CRCL18"; version="1.6.0"; sha256="0m3bpivjl1lgj7fpkqlg05cj9mvwpqrmd806jr9hfjh6xksd5c4q"; depends=[Biobase]; }; + CardinalWorkflows = derive2 { name="CardinalWorkflows"; version="1.18.0"; sha256="0lzlxynbi66vnz8nisag88mcjfhmxwbaj2ghj65xf7lkb3cfr8rj"; depends=[Cardinal]; }; + CellMapperData = derive2 { name="CellMapperData"; version="1.12.0"; sha256="00yr36qv4mz0rbsdw9zfll8g915w5d41ys1kydpgax52cl0s68ip"; depends=[CellMapper ExperimentHub]; }; + ChAMPdata = derive2 { name="ChAMPdata"; version="2.18.0"; sha256="1p0i8a1akx6jmlk7a23f0hyzmlfychm6lkqzm5j2ygvdn20ylq2v"; depends=[BiocGenerics GenomicRanges]; }; + ChIC_data = derive2 { name="ChIC.data"; version="1.6.0"; sha256="05lqwv54032css4q4qigfi9bbq0vzkxd8hq41bk3sg0xcxiz7wwh"; depends=[caret]; }; + ChIPXpressData = derive2 { name="ChIPXpressData"; version="1.24.0"; sha256="039wqv3qnsycw7zicf2ab03bgld8n0543iwc48hx90ybkwzpla5m"; depends=[bigmemory]; }; + ChIPexoQualExample = derive2 { name="ChIPexoQualExample"; version="1.10.0"; sha256="1g4lhhprd5453q6q2m56x6ry8isx3rw08xdmvlq8mbxp0f86jwii"; depends=[]; }; + ChimpHumanBrainData = derive2 { name="ChimpHumanBrainData"; version="1.24.0"; sha256="0frnrihjfmmks0vz30ynz8iq02sb40v6ncwc7hd9a1mhdlw2azb8"; depends=[affy hexbin limma qvalue statmod]; }; + CluMSIDdata = derive2 { name="CluMSIDdata"; version="1.2.0"; sha256="0k4gdr9xgljb7ksbzyypdlagn2bs7v3znr053pd3zzlsc1wnrzj3"; depends=[]; }; + ConnectivityMap = derive2 { name="ConnectivityMap"; version="1.22.0"; sha256="1jk85r0k4bn2l8sg6p5l3id4n559hkd1pyfdy2qw5x3jqz9m3bc2"; depends=[]; }; + CopyNeutralIMA = derive2 { name="CopyNeutralIMA"; version="1.4.0"; sha256="01vb8f9ady8lnzhxg39nf1xgsjsv096bp3jdzb3q4ymw6qh8v95w"; depends=[ExperimentHub Rdpack]; }; + CopyhelpeR = derive2 { name="CopyhelpeR"; version="1.18.0"; sha256="1da58cyfgpvdsysharn2d8xmjjvsgb757q89hasajwqn1fnf5bcd"; depends=[]; }; + DAPARdata = derive2 { name="DAPARdata"; version="1.16.0"; sha256="0r2dzhzdsfnxalq9g6gd126vavjcs30jddpv8yczqpz3rzg8ly1a"; depends=[knitr MSnbase]; }; + DLBCL = derive2 { name="DLBCL"; version="1.26.0"; sha256="04wjzzmjjh0f8idhj7hpr9vld04ilsa17iy70k5gqyv3fq9188z2"; depends=[Biobase]; }; + DMRcatedata = derive2 { name="DMRcatedata"; version="2.2.1"; sha256="1z5vyaj7vv0adsb2bjx0mrpi1wdkx7jsbgsahvvf37g895blibsy"; depends=[ExperimentHub GenomicFeatures Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 plyr readxl rtracklayer]; }; + DREAM4 = derive2 { name="DREAM4"; version="1.22.0"; sha256="0bcby3wcwvqigldnv3kcgkds6a79f1qw18r080a9ajazmqi1fs0d"; depends=[SummarizedExperiment]; }; + DeSousa2013 = derive2 { name="DeSousa2013"; version="1.22.0"; sha256="1v4plygbdja5rnzavikbi3ks60zannkv3ld7w286n41dc9kwdmkp"; depends=[affy AnnotationDbi Biobase cluster ConsensusClusterPlus frma frmaTools gplots hgu133plus2_db hgu133plus2frmavecs pamr rgl ROCR siggenes survival sva]; }; + DmelSGI = derive2 { name="DmelSGI"; version="1.18.0"; sha256="016q7n5xqyz8iawajgjng750drrddnz7y76k5bs76k8g7k1krwnb"; depends=[abind gplots igraph knitr limma rhdf5 TSP]; }; + DonaPLLP2013 = derive2 { name="DonaPLLP2013"; version="1.24.0"; sha256="1bc6mipbzpbjfd3r5ll62903avmwm4vc7s2nzx23a8xg15agmnbf"; depends=[EBImage]; }; + DrugVsDiseasedata = derive2 { name="DrugVsDiseasedata"; version="1.22.0"; sha256="0g201qrvpxv1b8fx2xl6r3fai2sfv54s3y65n86q6mi8jf49m3lx"; depends=[]; }; + DuoClustering2018 = derive2 { name="DuoClustering2018"; version="1.4.0"; sha256="15zs1pinqbmbbwap8qpp1lkp2yva1mks6a1lp8yr8i8g3mkgjgrx"; depends=[dplyr ExperimentHub ggplot2 ggthemes magrittr mclust purrr reshape2 tidyr viridis]; }; + DvDdata = derive2 { name="DvDdata"; version="1.22.0"; sha256="02rr69i3xkal2a551f56703lwzwjqzr50q0i6srlyri7ad2r8bix"; depends=[]; }; + EGSEAdata = derive2 { name="EGSEAdata"; version="1.14.0"; sha256="1vvvnrq58ilzr2rkjqky1n4f87f7k4grzgny58yms9wkz213ly9q"; depends=[]; }; + ELMER_data = derive2 { name="ELMER.data"; version="2.10.0"; sha256="0ffvvmyvyc6lalmwslvgmipjj6kvww459hz63fb047jc9z9m6g1f"; depends=[GenomicRanges]; }; + EatonEtAlChIPseq = derive2 { name="EatonEtAlChIPseq"; version="0.24.0"; sha256="19yqjlh0x5w5590r63ykbpx6vbvcwsjfqq887vcywbzd5ky4w46q"; depends=[GenomicRanges rtracklayer ShortRead]; }; + FANTOM3and4CAGE = derive2 { name="FANTOM3and4CAGE"; version="1.22.0"; sha256="0kb77dmyg1ry5dagrjpwg59icr79kxvn7dw0jm6420pf4axnr99v"; depends=[]; }; + FIs = derive2 { name="FIs"; version="1.14.0"; sha256="0sqdbyp9g5g6craxkbgyrmirr37lr9f3a2gw27m81mad2v3ajia4"; depends=[]; }; + Fletcher2013a = derive2 { name="Fletcher2013a"; version="1.22.0"; sha256="119wab4xf1jldvyqhckkkky9l94hp9192c70mq4wm6mvqx3i11wi"; depends=[Biobase gplots limma VennDiagram]; }; + Fletcher2013b = derive2 { name="Fletcher2013b"; version="1.22.0"; sha256="0j3hwx51rj8alfnwyfzvnbkjswwxj6jiysjq42fwp6z6ggpjn3f7"; depends=[Fletcher2013a igraph RColorBrewer RedeR RTN]; }; + FlowSorted_Blood_450k = derive2 { name="FlowSorted.Blood.450k"; version="1.24.0"; sha256="0i93kgi1y3kppb08zyzpwphldn6j8511ca81lg8bsx4m0v20iihp"; depends=[minfi]; }; + FlowSorted_Blood_EPIC = derive2 { name="FlowSorted.Blood.EPIC"; version="1.4.1"; sha256="0b6823h8j8f72fpf6wj3jdhk6zwz6qk3bmzbkiiqbw9fj6s36gvw"; depends=[ExperimentHub genefilter IlluminaHumanMethylationEPICanno_ilm10b4_hg19 minfi nlme quadprog S4Vectors SummarizedExperiment]; }; + FlowSorted_CordBlood_450k = derive2 { name="FlowSorted.CordBlood.450k"; version="1.14.0"; sha256="1m1r0kb4zk7687mh17aqggv5fidzv2igx20j2bclmwffv64mzw3h"; depends=[minfi]; }; + FlowSorted_CordBloodCombined_450k = derive2 { name="FlowSorted.CordBloodCombined.450k"; version="1.2.1"; sha256="1dzkcsn5lhmhrvi9g5mqlm5zw7w4kcm3vfrzyk61yhdhl4ysxz03"; depends=[ExperimentHub FlowSorted_Blood_EPIC IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 minfi SummarizedExperiment]; }; + FlowSorted_CordBloodNorway_450k = derive2 { name="FlowSorted.CordBloodNorway.450k"; version="1.12.0"; sha256="1swpqi2626j8nyd2iilqx7b6qjjjr1qc9lamjgq46l06jb80gr79"; depends=[minfi]; }; + FlowSorted_DLPFC_450k = derive2 { name="FlowSorted.DLPFC.450k"; version="1.22.0"; sha256="0jbwx5pd8g91qg80sibizpi6cnsv15x5w5675zxgj2l8v00dzqjx"; depends=[minfi]; }; + FunciSNP_data = derive2 { name="FunciSNP.data"; version="1.22.0"; sha256="0hmrazvyh8yfwz9g23pfaf3y0l929h4yv1vmcrs44wbdva2jijwr"; depends=[IRanges rtracklayer]; }; + GGdata = derive2 { name="GGdata"; version="1.24.0"; sha256="03094j1pjjjb5z4qplsxlazca5vmpcifh154nbxp94sc7h5yskyi"; depends=[AnnotationDbi Biobase GGBase illuminaHumanv1_db snpStats]; }; + GIGSEAdata = derive2 { name="GIGSEAdata"; version="1.4.0"; sha256="0d31pn4ra2nr5gk4bszyqakj8v1sya10aj2n044gn5zsspf4dkaw"; depends=[]; }; + GSBenchMark = derive2 { name="GSBenchMark"; version="1.6.0"; sha256="0rhgidjirz9i7n1f60jk1injifm1nacak29qz0wsw6vjwibr47sp"; depends=[]; }; + GSE62944 = derive2 { name="GSE62944"; version="1.14.0"; sha256="1p31cwwa1w01d2hxs2r9gsmsdfi1zr3wa2dsci9jwhxvm79hj5wz"; depends=[Biobase GEOquery]; }; + GSVAdata = derive2 { name="GSVAdata"; version="1.22.0"; sha256="0db7w860i98rrwramw8dp2p1a022a4hxqc71ypdhxcli5718hh7c"; depends=[Biobase GSEABase hgu95a_db]; }; + GWASdata = derive2 { name="GWASdata"; version="1.24.0"; sha256="0743q6ak2ncda0l1p6xd7g11052nz2jp3mjk0h89yklan931q06j"; depends=[GWASTools]; }; + GeuvadisTranscriptExpr = derive2 { name="GeuvadisTranscriptExpr"; version="1.14.0"; sha256="0w44fghds8l2frdn2z2kyzc94ndr2pqd2lashsp4vradfpy5fvcm"; depends=[]; }; + HCAData = derive2 { name="HCAData"; version="1.2.0"; sha256="0gikkfizjh7k3rvk13rkpdf3wshajd9x146awk09syc4mm70p0sb"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; }; + HD2013SGI = derive2 { name="HD2013SGI"; version="1.26.0"; sha256="04wl1yjc5lg5n33a0d9gxigx56g5dks1sh8x3ajkx73579ikwj6j"; depends=[EBImage geneplotter gplots limma LSD RColorBrewer splots vcd]; }; + HDCytoData = derive2 { name="HDCytoData"; version="1.6.6"; sha256="0zy7q8n6nh06y63aav1q5zvd3yhqxpn1rvlz8k3i24qjs192pi3c"; depends=[ExperimentHub flowCore SummarizedExperiment]; }; + HEEBOdata = derive2 { name="HEEBOdata"; version="1.24.0"; sha256="02dff6na4wq5pz7yh6w5bk407ydnlhcmzpxh5pa7gdrhsi94llyy"; depends=[]; }; + HIVcDNAvantWout03 = derive2 { name="HIVcDNAvantWout03"; version="1.26.0"; sha256="0426jz2r1lhn660lvkmqpfkg2yrramwj5kji547rq2c8flnhyjjx"; depends=[]; }; + HMP16SData = derive2 { name="HMP16SData"; version="1.6.0"; sha256="13k7rvnxykapsy5wnwl3k25ivb7hm51cv1hs5yry2jkdp0vpvmjr"; depends=[AnnotationHub assertthat dplyr ExperimentHub kableExtra knitr magrittr readr S4Vectors SummarizedExperiment tibble]; }; + HMP2Data = derive2 { name="HMP2Data"; version="1.0.0"; sha256="15fxfwp0gi2hppk4v2gnk71inlqrw1f9d975gzf41iqcb10wjsax"; depends=[AnnotationHub assertthat data_table dplyr ExperimentHub kableExtra knitr magrittr MultiAssayExperiment phyloseq readr S4Vectors SummarizedExperiment]; }; + HSMMSingleCell = derive2 { name="HSMMSingleCell"; version="1.6.0"; sha256="0mxsa8k4vxiimlpwc3y2p1n05wvp68y05pddb82yy15pdaghs2wj"; depends=[]; }; + HarmanData = derive2 { name="HarmanData"; version="1.14.0"; sha256="0rs7mjyg2mg5pmkl8529x9mwq8xl6fp3ngr6snfh478435lfjg23"; depends=[]; }; + HarmonizedTCGAData = derive2 { name="HarmonizedTCGAData"; version="1.8.0"; sha256="1p1ghmcq5l1gqr8g3bw1n320dn6fv5ii9krp7vnqxx90igww0akn"; depends=[ExperimentHub]; }; + HelloRangesData = derive2 { name="HelloRangesData"; version="1.12.0"; sha256="1qbvj80gz4sbhg4h8r8hsza4jl06kmn9y91n1h48b0fvsxgk0zfn"; depends=[]; }; + HiCDataHumanIMR90 = derive2 { name="HiCDataHumanIMR90"; version="1.6.0"; sha256="0z568y0rqsmc0i2gjfg1fycsdyh1nixyk1cysr2c2714ijqh9ryi"; depends=[]; }; + HiCDataLymphoblast = derive2 { name="HiCDataLymphoblast"; version="1.22.0"; sha256="1vq7q1ih9njvjfp7j1dmydfkdp9ch8adqrrzp17vi0nj0m2j9qdg"; depends=[]; }; + Hiiragi2013 = derive2 { name="Hiiragi2013"; version="1.22.0"; sha256="1n5li9q6s2xzibcl5vnmzx5jbyd2li37k8awm2fbz9jcs0ldw92v"; depends=[affy Biobase boot clue cluster genefilter geneplotter gplots gtools KEGGREST lattice latticeExtra MASS mouse4302_db RColorBrewer xtable]; }; + HumanAffyData = derive2 { name="HumanAffyData"; version="1.12.0"; sha256="1hwl32cp5hvfcq7740g60wzm1b99qrzb5vbmll8mh89dwcsr00n4"; depends=[Biobase ExperimentHub]; }; + IHWpaper = derive2 { name="IHWpaper"; version="1.14.0"; sha256="116kg6pffw5zh7zfmbgg8ar8jwwfxr806fs8kwwh9f0w9qk6s76g"; depends=[Biobase BiocGenerics BiocParallel cowplot DESeq2 dplyr fdrtool genefilter ggplot2 IHW qvalue Rcpp SummarizedExperiment]; }; + ITALICSData = derive2 { name="ITALICSData"; version="2.24.0"; sha256="1w31z51ipcfa7yj8pfcx2ff2rqxsqn17fydy6nmap5zmcbn2cbq3"; depends=[]; }; + Illumina450ProbeVariants_db = derive2 { name="Illumina450ProbeVariants.db"; version="1.22.0"; sha256="1jld5lqb5dmy5yjq64rjymq9n4i4r5zjz230r6vyi1vka26isv1v"; depends=[]; }; + IlluminaDataTestFiles = derive2 { name="IlluminaDataTestFiles"; version="1.24.0"; sha256="1nzzmdv212c83hi8l6swzk9dpq1v6xr5z5721zdckrxcl45zzccw"; depends=[]; }; + Iyer517 = derive2 { name="Iyer517"; version="1.28.0"; sha256="1w7f1j1wh087c4f7ssazybv9mg30vy2cy5ydgdzq0h7n49cpcq1h"; depends=[Biobase]; }; + JASPAR2014 = derive2 { name="JASPAR2014"; version="1.22.0"; sha256="0v6hm0sq2mri1b1ylsqyvffr1b1xadc730v0g1a34madk7ih9lg2"; depends=[Biostrings]; }; + JASPAR2016 = derive2 { name="JASPAR2016"; version="1.14.0"; sha256="1vd7zii62k47av9yqw5zqqzrr79s93xfdvyi4hp9qfbxqlkz2jr0"; depends=[]; }; + JctSeqData = derive2 { name="JctSeqData"; version="1.16.0"; sha256="10kp47cpkw01rnz817av3iz6j8zyjns6k54wd2mni18lhscxwq9f"; depends=[]; }; + KEGGandMetacoreDzPathwaysGEO = derive2 { name="KEGGandMetacoreDzPathwaysGEO"; version="1.6.0"; sha256="1ixx5wvyfcah61acra8g5s16ibl514qasx5yw99asw88v2w58mmi"; depends=[Biobase BiocGenerics]; }; + KEGGdzPathwaysGEO = derive2 { name="KEGGdzPathwaysGEO"; version="1.24.0"; sha256="1mb99j31zf5l0279r1qfayr4wk56ar4q6al55l57lb5rd9x8wlqb"; depends=[Biobase BiocGenerics]; }; + KOdata = derive2 { name="KOdata"; version="1.12.0"; sha256="1zwjxwrh75ymj2ln2nwm82ih2zk8rc0nz3pagcypawmci54fzpxb"; depends=[]; }; + LiebermanAidenHiC2009 = derive2 { name="LiebermanAidenHiC2009"; version="0.24.0"; sha256="1ar4v30a2bhcfcw2f2hpirwpmdiik517gj84j5l1n1wz60xh5xd1"; depends=[IRanges KernSmooth]; }; + ListerEtAlBSseq = derive2 { name="ListerEtAlBSseq"; version="1.18.0"; sha256="09dsm8xwh1lzc65i4ryj928yfispdlzhbxmipkpv18dq07nq21km"; depends=[methylPipe]; }; + LungCancerACvsSCCGEO = derive2 { name="LungCancerACvsSCCGEO"; version="1.22.0"; sha256="0dwf55y41dyv78hkzs3zs2243hh1la98n7dz4iq9jcy2r8gn42d4"; depends=[]; }; + LungCancerLines = derive2 { name="LungCancerLines"; version="0.24.0"; sha256="1l3pp2klcmd0di9myqa18qiyx23wkq0wai452k38ww9phjc15min"; depends=[Rsamtools]; }; + M3DExampleData = derive2 { name="M3DExampleData"; version="1.12.0"; sha256="045pqphqi3zbnibb32c8zwhg29ikvjrvcxrn4jbblp0162kv3v87"; depends=[]; }; + MAQCsubset = derive2 { name="MAQCsubset"; version="1.24.0"; sha256="11xbyj2320x6ng3yai85z6qn1awfpc3zmi0slg0jsfhf9y7bry0h"; depends=[affy Biobase lumi]; }; + MAQCsubsetAFX = derive2 { name="MAQCsubsetAFX"; version="1.24.0"; sha256="0pg14y6p9589s1w82ngm64k0a272mwbqrwmfmfqi05mh1kg72z4f"; depends=[affy Biobase]; }; + MAQCsubsetILM = derive2 { name="MAQCsubsetILM"; version="1.24.0"; sha256="129rfiz1z2wn3xvj0qqvcfwwkji60grdjwx14w11i30rg1waa5vi"; depends=[Biobase lumi]; }; + MEDIPSData = derive2 { name="MEDIPSData"; version="1.22.0"; sha256="08a8zqpkxh0vnw6yywd7m2y4c0crc5kamijjy4mvrcdrn7yvmf07"; depends=[]; }; + MEEBOdata = derive2 { name="MEEBOdata"; version="1.24.0"; sha256="05cp488r69wvqmk3znghrpnwiaq0bsclgffkrl7ab5r57128vb6g"; depends=[]; }; + MIGSAdata = derive2 { name="MIGSAdata"; version="1.10.0"; sha256="0kfy63v20qyfgk9w0ymszak89mmq6fgm91g9lkbqxrhzv36vvw7c"; depends=[]; }; + MMAPPR2data = derive2 { name="MMAPPR2data"; version="1.0.0"; sha256="1pwqgxvkdhc0gk99f0c4kk1ypd3mlcm8z9k1sz6yia139yjz3fq4"; depends=[Rsamtools]; }; + MMDiffBamSubset = derive2 { name="MMDiffBamSubset"; version="1.22.0"; sha256="0kl23870ndd7k6gn3svcgn7hz7ijwpnldhwsa1hza8kxvakqnwir"; depends=[]; }; + MOFAdata = derive2 { name="MOFAdata"; version="1.2.0"; sha256="0zpdwmxhniy7jqxfl1g019kc265ixs43s957l3va00r31hh6pl27"; depends=[]; }; + MSMB = derive2 { name="MSMB"; version="1.4.0"; sha256="0sfrbwsfj659k0426nlcwlf13rds4vj0wpcz3wrhmvzp4gp8y913"; depends=[]; }; + MSstatsBioData = derive2 { name="MSstatsBioData"; version="1.8.0"; sha256="00f25dr1sdxz0s8wdzmjp6sxid587kvxvx24ln1x088381kh2awd"; depends=[]; }; + MTseekerData = derive2 { name="MTseekerData"; version="1.3.0"; sha256="042g0yg4ywpz0a1ajp5n8ns2qjhqaq9xrh1gljdjhs25r6pcybb7"; depends=[GenomeInfoDb GenomicFeatures GenomicRanges Homo_sapiens IRanges MTseeker VariantAnnotation]; }; + MUGAExampleData = derive2 { name="MUGAExampleData"; version="1.6.0"; sha256="0wjjgnab1cm4vbf73lmyx0ybl8z2xrq8106abl88hi2j11vvyqjq"; depends=[]; }; + MetaGxBreast = derive2 { name="MetaGxBreast"; version="1.6.0"; sha256="1v40pjb9bkjj0zhba8mpmikqzdygz6dgy50g2257bzx3vlw2pn6y"; depends=[AnnotationHub Biobase ExperimentHub impute lattice SummarizedExperiment]; }; + MetaGxOvarian = derive2 { name="MetaGxOvarian"; version="1.6.1"; sha256="17p6sxvifla2fp3011cqfaygjkxjb354x1gc99frgqjn03baf96z"; depends=[AnnotationHub Biobase ExperimentHub impute lattice SummarizedExperiment]; }; + MetaGxPancreas = derive2 { name="MetaGxPancreas"; version="1.6.0"; sha256="09s7vqabh1kf51m3fvxbgdvmg9jakrp2x4jsi0lic5399ia7ixn5"; depends=[AnnotationHub Biobase ExperimentHub impute lattice SummarizedExperiment]; }; + MethylAidData = derive2 { name="MethylAidData"; version="1.18.0"; sha256="1qz2x0lzhpg6bag5s387ynw948d3c4vgljizfm1jg5q80nv8rh1p"; depends=[MethylAid]; }; + MouseGastrulationData = derive2 { name="MouseGastrulationData"; version="1.0.0"; sha256="1238n954qbcy381rin127nikqsc4yazv7aix7yfj3ynswrn9zlki"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment]; }; + Mulder2012 = derive2 { name="Mulder2012"; version="0.26.0"; sha256="1i22jkxcv5fi3bhm9ff0gh4flgnvh4qkp8wzn9g5rfjawnawpr36"; depends=[HTSanalyzeR igraph KEGG_db MASS org_Hs_eg_db PANR pvclust RedeR]; }; + NCIgraphData = derive2 { name="NCIgraphData"; version="1.22.0"; sha256="1jkkglhpqhgfmplz4ij410mxvkqgjfsgyn7my10bi7w10shfkqnr"; depends=[]; }; + NGScopyData = derive2 { name="NGScopyData"; version="1.6.0"; sha256="0pdag1wqbhg8rghs71va6rhnzwl2jwjjihlplz14f8i26h4k5cw4"; depends=[]; }; + NestLink = derive2 { name="NestLink"; version="1.2.0"; sha256="1cax1r0hlqh7ir6v716z2dl8rg9h9jh4mdm85hy9g3mwia8blmvz"; depends=[AnnotationHub Biostrings ExperimentHub gplots protViz ShortRead]; }; + Neve2006 = derive2 { name="Neve2006"; version="0.24.0"; sha256="1bycs7n28gj348lxqcbvmp4ckicf7h28wnbly92r2snzkgia8al8"; depends=[annotate Biobase hgu133a_db]; }; + OMICsPCAdata = derive2 { name="OMICsPCAdata"; version="1.4.0"; sha256="0g0p18iss8cnafzzm167sfjxzkryhps8xicfdda0fjjjjal0g5ng"; depends=[MultiAssayExperiment]; }; + OnassisJavaLibs = derive2 { name="OnassisJavaLibs"; version="1.8.0"; sha256="1jq10cfrjjsr1bcj9v6ry2k25j7zyqfzn467k5l8x5dmfw7ix7y3"; depends=[rJava]; }; + PCHiCdata = derive2 { name="PCHiCdata"; version="1.14.0"; sha256="0rfll3i9k4ylxfchp6ah1vvhf39287dkz4hj44bpmxykzyddp740"; depends=[Chicago]; }; + PREDAsampledata = derive2 { name="PREDAsampledata"; version="0.26.0"; sha256="0b5rs9vz7bi4fp0pwr2mxrhvghrgzkvs5fcdy98sb1vzps4gchsy"; depends=[affy annotate Biobase PREDA]; }; + PWMEnrich_Dmelanogaster_background = derive2 { name="PWMEnrich.Dmelanogaster.background"; version="4.20.0"; sha256="0c7cbd9hq59ggw5x4q8x1s372p4nwkrypafcyx9kvlvcsyhcf1bz"; depends=[PWMEnrich]; }; + PWMEnrich_Hsapiens_background = derive2 { name="PWMEnrich.Hsapiens.background"; version="4.20.0"; sha256="111s8wl6crzxbm86h3hlpaqw3x01ywf05c2zh83m0dmjympw88jj"; depends=[PWMEnrich]; }; + PWMEnrich_Mmusculus_background = derive2 { name="PWMEnrich.Mmusculus.background"; version="4.20.0"; sha256="0fhq420zi9qbvpspg44yxsxckhlc43snf8hix85x9vhinmg1j73s"; depends=[PWMEnrich]; }; + PasillaTranscriptExpr = derive2 { name="PasillaTranscriptExpr"; version="1.14.0"; sha256="18r0x2vr1da2rcqjga1i8f45a1afzj5as2ay8mmf3s8v5m7qm5za"; depends=[]; }; + PathNetData = derive2 { name="PathNetData"; version="1.22.0"; sha256="1qchahypywlqf5swwqxwlvhsqagc025pijgsmvm22m73gxzmymif"; depends=[]; }; + PepsNMRData = derive2 { name="PepsNMRData"; version="1.4.0"; sha256="04hws2wcf928sm5i0kxalpbcb0il7c5whssdw2nqnrghrnr7iwaq"; depends=[]; }; + PhyloProfileData = derive2 { name="PhyloProfileData"; version="1.0.0"; sha256="03yljc9k2d26vjvzngalk5jay7pbm06rr1r171rfi7gvg9b3q563"; depends=[Biostrings ExperimentHub]; }; + ProData = derive2 { name="ProData"; version="1.24.0"; sha256="0swgyhc4pggfl1sr7fkr50kr66rzlcqvqmvfayldrw70mzh2682z"; depends=[Biobase]; }; + PtH2O2lipids = derive2 { name="PtH2O2lipids"; version="1.12.0"; sha256="1z4zjqg2l7dvipsl6bz69hl8mkay1462h4vxs0zy372pg7q8can2"; depends=[CAMERA LOBSTAHS xcms]; }; + QDNAseq_hg19 = derive2 { name="QDNAseq.hg19"; version="1.16.0"; sha256="0gzyn1sg7pp8vngrdgz1s7r3dak11z700nx714wmihnj4kgsgsg2"; depends=[QDNAseq]; }; + QDNAseq_mm10 = derive2 { name="QDNAseq.mm10"; version="1.16.0"; sha256="1pyly8p9azjcz1c4rj0r2fdk9brd786mz6faaaviwy64c7ksrsj4"; depends=[QDNAseq]; }; + QUBICdata = derive2 { name="QUBICdata"; version="1.14.0"; sha256="1c44a7gs6v2jqxhafns9rnj7zgf97b0lxsfgxk8idi37nkpcdi4k"; depends=[]; }; + RGMQLlib = derive2 { name="RGMQLlib"; version="1.6.0"; sha256="1bd2zp8fhgf8ymixn7nv0q4i3ydsvls55grw1n7a1axr0lajkz7d"; depends=[]; }; + RIPSeekerData = derive2 { name="RIPSeekerData"; version="1.22.0"; sha256="0d73c15b1kwvns9kblmqhrn07cjiazrl6mnms3cq79yi9jgzcw8v"; depends=[RIPSeeker]; }; + RITANdata = derive2 { name="RITANdata"; version="1.10.0"; sha256="0qyv5lpdjv62ql1wz35xnhms13ipir3ic42p00v78fqnzkyax8fs"; depends=[]; }; + RMassBankData = derive2 { name="RMassBankData"; version="1.24.0"; sha256="1cmmqhj1siff0l1ky6pysx9dlp7bm76wr2pd0x89zaayrrwy49hm"; depends=[]; }; + RNASeqRData = derive2 { name="RNASeqRData"; version="1.4.0"; sha256="1am1glxcg7vgski1fgvw2nnpwdibpjndq110rgwrvigvkbqrg0n5"; depends=[]; }; + RNAinteractMAPK = derive2 { name="RNAinteractMAPK"; version="1.24.0"; sha256="0sijk7dhgkrh01yb2inl067gyiy2f737chwdd7zd7dd5si0vbw4v"; depends=[fields gdata genefilter MASS RNAinteract sparseLDA]; }; + RNAmodR_Data = derive2 { name="RNAmodR.Data"; version="1.0.0"; sha256="15i4srk594sxqwc8a6z7n1m5iqga5spaqvcc51frhsn9yna9wl5h"; depends=[ExperimentHub ExperimentHubData]; }; + RNAseqData_HNRNPC_bam_chr14 = derive2 { name="RNAseqData.HNRNPC.bam.chr14"; version="0.24.0"; sha256="13qx3xiyzf5v74jmqvn0ylr6yd0qwsi96immcszrhjwv3iwqq2xd"; depends=[]; }; + RRBSdata = derive2 { name="RRBSdata"; version="1.6.0"; sha256="0nms1h6hck6l6a742b00xrya1bybj4yqazb531a2hymzljc8g1kw"; depends=[BiSeq]; }; + RTCGA_CNV = derive2 { name="RTCGA.CNV"; version="1.14.0"; sha256="0h8x0kk1cl648s36k57dshka89wrmbz7q7p5khvdrk01nl6s23rr"; depends=[RTCGA]; }; + RTCGA_PANCAN12 = derive2 { name="RTCGA.PANCAN12"; version="1.14.0"; sha256="0jwjax6m9l0m16jidiw3vl7380qwmlqki0b907a6482gby6863mp"; depends=[RTCGA]; }; + RTCGA_RPPA = derive2 { name="RTCGA.RPPA"; version="1.14.0"; sha256="0n0f1cz4p34l59kd0g2xkajljf5bq6xm591kkp5jb24mv0i0g3ha"; depends=[RTCGA]; }; + RTCGA_clinical = derive2 { name="RTCGA.clinical"; version="20151101.16.0"; sha256="1cijm9vqcl4vxahnii8xkckq69s50b53gya7x06v1nfp2614xr02"; depends=[RTCGA]; }; + RTCGA_mRNA = derive2 { name="RTCGA.mRNA"; version="1.14.0"; sha256="1zqn72wvv6iylzqgj00ryj88hmzyw5rkp5sdghj4ivbvq6xjh0kl"; depends=[RTCGA]; }; + RTCGA_methylation = derive2 { name="RTCGA.methylation"; version="1.14.0"; sha256="1idyscwrqs2scjan3hpy134jkzqingclqfjrbfy3ims3il5ll37s"; depends=[RTCGA]; }; + RTCGA_miRNASeq = derive2 { name="RTCGA.miRNASeq"; version="1.14.0"; sha256="194p8zr5jcpfbcgfia32p24lbgz5qk1zlg5axlgxr4ac0fhvjss3"; depends=[RTCGA]; }; + RTCGA_mutations = derive2 { name="RTCGA.mutations"; version="20151101.16.0"; sha256="01pjarhjq1jl0lnzajqvryyvzdz4dpn2gx68g2y4pszi6s3f0gyw"; depends=[RTCGA]; }; + RTCGA_rnaseq = derive2 { name="RTCGA.rnaseq"; version="20151101.16.0"; sha256="1pdd1r18vaanhvqgm1dckcb4vmm3l8l89jsld2jy7sangbavpn13"; depends=[RTCGA]; }; + RUVnormalizeData = derive2 { name="RUVnormalizeData"; version="1.6.0"; sha256="0vw1d4n01kz0lsymbacqm8wvb2ivhnxljx04hfy0sba3p3y9hxhf"; depends=[Biobase]; }; + RcisTarget_hg19_motifDBs_cisbpOnly_500bp = derive2 { name="RcisTarget.hg19.motifDBs.cisbpOnly.500bp"; version="1.6.0"; sha256="0jx8y54c4m8a7i8j8m9r5m9bl3lcdknnwllbkf5njdfy24a20154"; depends=[data_table]; }; + ReactomeGSA_data = derive2 { name="ReactomeGSA.data"; version="1.0.0"; sha256="0nfmh765zkni3qslhs86yyfqf2c5hdva7avndahv7d3yai4g60d5"; depends=[edgeR limma ReactomeGSA]; }; + RegParallel = derive2 { name="RegParallel"; version="1.4.0"; sha256="03rm37wbq4bmi8kmm97qliyqrzyyhkkh70zv2lpclmmw7afcwh4z"; depends=[arm data_table doParallel foreach iterators MASS stringr survival]; }; + RforProteomics = derive2 { name="RforProteomics"; version="1.24.0"; sha256="1cp7vyjccknyd58xwng7pbln4pk0idymrr657va5hbnclv17pqds"; depends=[BiocManager biocViews MSnbase R_utils shiny]; }; + RnBeads_hg19 = derive2 { name="RnBeads.hg19"; version="1.18.0"; sha256="087p4gydzsxp6fnmlxsaxb6542nb2bqvzf0dv098ypms20lvqhn5"; depends=[GenomicRanges]; }; + RnBeads_hg38 = derive2 { name="RnBeads.hg38"; version="1.18.0"; sha256="1p4ppxsgk1041gq49gpqiw7yz5l16qjx3sijvjcxywqasy2ckm71"; depends=[GenomicRanges]; }; + RnBeads_mm10 = derive2 { name="RnBeads.mm10"; version="1.18.0"; sha256="0iq41bi87107pk3qh3z4j15gsyfj5vbbplna71zkvjg2w65jz853"; depends=[GenomicRanges]; }; + RnBeads_mm9 = derive2 { name="RnBeads.mm9"; version="1.18.0"; sha256="0755bfmd30ab0gw1vyzmar1na3xm3j5dafvvw2mpg1b7pz8y9jyg"; depends=[GenomicRanges]; }; + RnBeads_rn5 = derive2 { name="RnBeads.rn5"; version="1.18.0"; sha256="1lg98j24arf104a0hnafmpd6hxbnz0fvq4mh4jb36y8392nrjrag"; depends=[GenomicRanges]; }; + RnaSeqSampleSizeData = derive2 { name="RnaSeqSampleSizeData"; version="1.18.0"; sha256="0c2v1vrwx9ryb6zc37f19rx4blq1dqf5hfqdfsva1k484mny6nh2"; depends=[edgeR]; }; + SBGNview_data = derive2 { name="SBGNview.data"; version="1.0.0"; sha256="1ir98sfcsmsxh8s20z93qwlwv8hqx445s3pnb9bxnsni6zhddp6b"; depends=[knitr rmarkdown]; }; + SCLCBam = derive2 { name="SCLCBam"; version="1.18.0"; sha256="0mlv8lppdfr2l4l4af764q1ckm01x3fvrvp3n29wny691z6h47ym"; depends=[]; }; + SNAData = derive2 { name="SNAData"; version="1.32.0"; sha256="0nhxkdr1hxvp8b6bciqnjch20c5wg072wvcqsdy4qxh93s6kahwv"; depends=[graph]; }; + SNAGEEdata = derive2 { name="SNAGEEdata"; version="1.22.0"; sha256="0rgcmzbbsyqrlxnw2x1aavvlz587x2362sg4db0w2dwc0hpi0v6i"; depends=[]; }; + SNPhoodData = derive2 { name="SNPhoodData"; version="1.16.0"; sha256="16flpjhksfqwjx14129331mjjjkv9rfmzlyddvpfhlqdcsplzgcg"; depends=[]; }; + SVM2CRMdata = derive2 { name="SVM2CRMdata"; version="1.18.0"; sha256="0n421m4zrw50afxal8sa91wahc84mkkfifnf3acw9w9z1dqakm0c"; depends=[]; }; + Single_mTEC_Transcriptomes = derive2 { name="Single.mTEC.Transcriptomes"; version="1.14.0"; sha256="08liqg5i7565j9y1i2pb1zs8i4al57f9mfgjvxjccak6kjy4z8zf"; depends=[]; }; + SomatiCAData = derive2 { name="SomatiCAData"; version="1.24.0"; sha256="0n2symnwiidmc2pw8w2xs3ppaxs1hbqac7gkqcs0j1japmif6nm4"; depends=[]; }; + SomaticCancerAlterations = derive2 { name="SomaticCancerAlterations"; version="1.22.0"; sha256="0a4390vn69bhk29fca2zj3f4j26s5sdsiiai04h2wnvikj2pcmjx"; depends=[exomeCopy GenomicRanges IRanges S4Vectors stringr]; }; + SpikeIn = derive2 { name="SpikeIn"; version="1.28.0"; sha256="08aw67jg6sgwjrv8pjnp139nl9xf0m8fvn7sdpy8cx19ia8l3ris"; depends=[affy]; }; + SpikeInSubset = derive2 { name="SpikeInSubset"; version="1.26.0"; sha256="08ifkqjpqkcfyr8hfi6fz0rnil8qqafk8amps0r7dqha07hsv3pk"; depends=[affy Biobase]; }; + TBX20BamSubset = derive2 { name="TBX20BamSubset"; version="1.22.0"; sha256="0qkw0ax17n9zs3n9gx38dpvwpvg93j4xxcqgpmcc76ajvmp1pa44"; depends=[Rsamtools xtable]; }; + TCGAMethylation450k = derive2 { name="TCGAMethylation450k"; version="1.22.0"; sha256="1v947in2f5f6gp9298yiv194x2i7xhsnwgrvp2y06grgm19xb1z4"; depends=[]; }; + TCGAWorkflowData = derive2 { name="TCGAWorkflowData"; version="1.10.0"; sha256="1sp01x69n05lrknzy30n1ym6hfvj8blwnpnvhlky0z24c8aarj3l"; depends=[SummarizedExperiment]; }; + TCGAbiolinksGUI_data = derive2 { name="TCGAbiolinksGUI.data"; version="1.6.0"; sha256="1dyyr1h4i3v44l86lqsb284gq7vwxy7gvprcsgw29pp35pxpfxx4"; depends=[]; }; + TCGAcrcmRNA = derive2 { name="TCGAcrcmRNA"; version="1.6.0"; sha256="0cqlhnmdzlqhymzfmsvl9f352iywq48i9jbzy3saaviwjnq3yxyw"; depends=[Biobase]; }; + TCGAcrcmiRNA = derive2 { name="TCGAcrcmiRNA"; version="1.6.0"; sha256="1arc3n2bpzjrw2y1p5fj3gi66qysc3w9g7ywdsdsbf1cq3h3sbys"; depends=[Biobase]; }; + TENxBUSData = derive2 { name="TENxBUSData"; version="1.0.0"; sha256="07v2hz26jhrlh2bs1bnrk12cp7ldgq63mnsyvh392z1s9km0yyhg"; depends=[AnnotationHub BiocGenerics ExperimentHub]; }; + TENxBrainData = derive2 { name="TENxBrainData"; version="1.6.0"; sha256="04vrmgp9n1hd1xlx29596d253fwyi4mpalmi1ilqc7khki77pwd3"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; }; + TENxPBMCData = derive2 { name="TENxPBMCData"; version="1.4.0"; sha256="0vwlk46dnwyyy16118rn97311mfllk8jrh05m3p779z670d0va0m"; depends=[AnnotationHub ExperimentHub HDF5Array SingleCellExperiment]; }; + TabulaMurisData = derive2 { name="TabulaMurisData"; version="1.4.0"; sha256="1la7mk4rs0m1ql860rr0gwqpirsb29kwax1633r35z671a6rfgmp"; depends=[ExperimentHub]; }; + TargetScoreData = derive2 { name="TargetScoreData"; version="1.22.0"; sha256="0g0asxfrfky5nq6lr99cppwkg9gj1i6v3zy9v379pb4vmp1r4gkm"; depends=[]; }; + TargetSearchData = derive2 { name="TargetSearchData"; version="1.24.0"; sha256="0fpfqglgd07pdzriz2vhay1i5hkdzkhmn96f12b15jmwrx1y5ipa"; depends=[]; }; + TimerQuant = derive2 { name="TimerQuant"; version="1.16.0"; sha256="0swmnal3ns3n4xr7qsb83ig4sx9ynag6lmhy861njfb9s3ybaphg"; depends=[deSolve dplyr ggplot2 gridExtra locfit shiny]; }; + VariantToolsData = derive2 { name="VariantToolsData"; version="1.10.0"; sha256="00bk19fhxg9fgwfivsn9z7kmqdjbmrawa0m9h6n52hdayyv1645p"; depends=[BiocGenerics GenomicRanges VariantAnnotation]; }; + WES_1KG_WUGSC = derive2 { name="WES.1KG.WUGSC"; version="1.18.0"; sha256="08520csd9lz37m0bn1l9fd14z6gnhrl784lvfr4mxyp1lcnj3s22"; depends=[]; }; + XhybCasneuf = derive2 { name="XhybCasneuf"; version="1.24.0"; sha256="122mh8nwfcq7i2k78asgssf43s4czsqnbl6bqi05dv513z2bwr86"; depends=[affy ath1121501cdf RColorBrewer tinesath1cdf]; }; + adductData = derive2 { name="adductData"; version="1.2.0"; sha256="0vadizqvla3dhc0c5ig97gd0v2spfg0mh27x2rn9nd1k8sadc65j"; depends=[AnnotationHub ExperimentHub]; }; + affycompData = derive2 { name="affycompData"; version="1.24.0"; sha256="1x5ccx0b1mvzd9kr3fg0mkkdqb42c7xp795s1325xyh7zigq1k3b"; depends=[affycomp Biobase]; }; + affydata = derive2 { name="affydata"; version="1.34.0"; sha256="004m8bzayg9sgqc2qi288yb2y52k1bq0bkapsa15zg6fcjqa8ngz"; depends=[affy]; }; + airway = derive2 { name="airway"; version="1.6.0"; sha256="0blyfgwczdbj6c180k45b08pv6lwfbzz6n782lsz7cywx2fqbyhp"; depends=[SummarizedExperiment]; }; + allenpvc = derive2 { name="allenpvc"; version="1.4.0"; sha256="0y1gz4364gzkjdrkqcgszxqzchhyg3ipgs4kwn8mf9x21hnacszz"; depends=[AnnotationHub ExperimentHub SingleCellExperiment]; }; + alpineData = derive2 { name="alpineData"; version="1.12.0"; sha256="1cf5ppmds6yx93z2rmfqa8aybg1rz28rzkxmy38i8kmqc9lv1g4x"; depends=[AnnotationHub ExperimentHub GenomicAlignments]; }; + antiProfilesData = derive2 { name="antiProfilesData"; version="1.22.0"; sha256="1m8db6jgpxa88a10byff6shdfdnw6rcwny8xcf4jbrlisir0cl4w"; depends=[Biobase]; }; + aracne_networks = derive2 { name="aracne.networks"; version="1.12.0"; sha256="0cv6p2pf54g0cc1h0azhh8sb41p635r60zz7af61hnjx645gvq6s"; depends=[viper]; }; + bcellViper = derive2 { name="bcellViper"; version="1.22.0"; sha256="088ym3scwbnm2jlkgvjmxx1y13qa0hh02c773ndz5z08v2b4041k"; depends=[Biobase]; }; + beadarrayExampleData = derive2 { name="beadarrayExampleData"; version="1.24.0"; sha256="11dqhljpr0zgdidxqdpn98ssvz3yhrlgfdwr46nzfyylrdym8m20"; depends=[beadarray Biobase]; }; + benchmarkfdrData2019 = derive2 { name="benchmarkfdrData2019"; version="1.0.0"; sha256="08c8xx97ls1vwipvnsx8apxqhcs0rrlixm07madam7lkk3s12yd8"; depends=[ExperimentHub SummarizedExperiment]; }; + beta7 = derive2 { name="beta7"; version="1.24.0"; sha256="1gdjyxw2ap5il68v94l6vxf75jnzlsp6dyksxhrnckxzspyd0r65"; depends=[marray]; }; + biotmleData = derive2 { name="biotmleData"; version="1.10.0"; sha256="1kf2c3x3s7yyk0wy5p8g8a7h0f33y0648misc7iabiwn0lx7dp84"; depends=[]; }; + biscuiteerData = derive2 { name="biscuiteerData"; version="1.0.0"; sha256="0y6k2vajibjh727ahy6fwvnky8na3bh0dwa0w2rvncr1mnh7qcdl"; depends=[AnnotationHub curl ExperimentHub]; }; + bladderbatch = derive2 { name="bladderbatch"; version="1.24.0"; sha256="1yick6zxsgz8i226ffyxfbi5nlvv19c01ij3dmb81bbj7acn0a2p"; depends=[Biobase]; }; + blimaTestingData = derive2 { name="blimaTestingData"; version="1.6.0"; sha256="0g13p528mpgq6lm03rs7n7di328c2gjfarb4apn7v0hxpf94f5gg"; depends=[]; }; + bodymapRat = derive2 { name="bodymapRat"; version="1.2.0"; sha256="0mlsxa59nq6nswabgi9i2lmzqdz1qw2da1802h8kl18zdiphfsik"; depends=[ExperimentHub SummarizedExperiment]; }; + brainImageRdata = derive2 { name="brainImageRdata"; version="1.4.0"; sha256="0ykldw89j4xl26bnhrkk506q1kxm3g6c0wxsla0ljrd145g1izhz"; depends=[ExperimentHub]; }; + breakpointRdata = derive2 { name="breakpointRdata"; version="1.4.0"; sha256="09h0vmp41ci31pppi86isi398wzdc9nrjqmqrkx82kbz0v1mkh5p"; depends=[]; }; + breastCancerMAINZ = derive2 { name="breastCancerMAINZ"; version="1.24.0"; sha256="143wh4n0hcmv08rpz75vbi3qzbwapnqmi05g8smjgpr7m1nxigjw"; depends=[]; }; + breastCancerNKI = derive2 { name="breastCancerNKI"; version="1.24.0"; sha256="13jch65wiyqj2gjr4xjbhr1jpf8yfgxm05ix14xc4z1bygf9xisx"; depends=[]; }; + breastCancerTRANSBIG = derive2 { name="breastCancerTRANSBIG"; version="1.24.0"; sha256="1nvxrqlwfhx14jj5q1fqwm06vfaxsai4c5ficr32gack9lzf1snc"; depends=[]; }; + breastCancerUNT = derive2 { name="breastCancerUNT"; version="1.24.0"; sha256="19qa9h72drjwcn1pl1d28lnpy6niyf4gpgd9k1vf8mq90y9wynm2"; depends=[]; }; + breastCancerUPP = derive2 { name="breastCancerUPP"; version="1.24.0"; sha256="0i69ynj32xig34b25z3qf2883nbqq0m3r5cls708zf0nh97v5qyn"; depends=[]; }; + breastCancerVDX = derive2 { name="breastCancerVDX"; version="1.24.0"; sha256="1jx30fsflfqvl5psy8mhr0p7vx2dimwm4hmb9l0ar64wr24y6ay4"; depends=[]; }; + brgedata = derive2 { name="brgedata"; version="1.8.0"; sha256="1d4h6a0w325iwjsymywsgibdfamk7gc8cwymbs49cihhnmz0bqdb"; depends=[Biobase SummarizedExperiment]; }; + bronchialIL13 = derive2 { name="bronchialIL13"; version="1.24.0"; sha256="12z8wacqdv31adm898idwzrhh4dlq569ljjxax7m0iihx7yk9j2g"; depends=[affy]; }; + bsseqData = derive2 { name="bsseqData"; version="0.24.0"; sha256="104s1h5s552nyrmbks4z343jxfzshxxddppyhl948f1aly4q22dd"; depends=[bsseq]; }; + cMap2data = derive2 { name="cMap2data"; version="1.22.0"; sha256="0aqhnacyjaixh9brn6vf87yzz99qrbvz8663j712b77c4s97ljsc"; depends=[]; }; + cancerdata = derive2 { name="cancerdata"; version="1.24.0"; sha256="00xkqgly6mlmkqlk4siyi47m6hayyi33sigq99pim7p6baabcz6h"; depends=[Biobase]; }; + ccTutorial = derive2 { name="ccTutorial"; version="1.24.0"; sha256="1ypzf3nsmdaynhr739yhbi7y26sinwnxzm689kdqzsadmkmag0fs"; depends=[affy Biobase Ringo topGO]; }; + ccdata = derive2 { name="ccdata"; version="1.12.0"; sha256="1m2b3aa5chl7kk3ckmpfpirjsnpfrisbd9b79y7kcigqhir8npi8"; depends=[]; }; + celarefData = derive2 { name="celarefData"; version="1.4.0"; sha256="1zrdh5c3q44amqf4b63vnak06ga12dy5wd0j4r3mi1wxg6jl4sp0"; depends=[]; }; + ceu1kg = derive2 { name="ceu1kg"; version="0.24.0"; sha256="042xvgr6vsdfjz86k7gskrlidm2kx2wfndgra0bdicpn0820y00a"; depends=[Biobase GGBase GGtools]; }; + ceu1kgv = derive2 { name="ceu1kgv"; version="0.28.0"; sha256="0r29k3lmzmk4qifzfnaa5slsan8dy4s52r55yldphx53n8q8qpl7"; depends=[Biobase GGBase]; }; + ceuhm3 = derive2 { name="ceuhm3"; version="0.24.0"; sha256="18zsz844qg3qy1if7z15658agbpiyd75h8jbc05mvj0fkqvgdrhb"; depends=[Biobase GGBase GGtools]; }; + cgdv17 = derive2 { name="cgdv17"; version="0.24.0"; sha256="1h3wqdwavxs565y2s4jf2fvirdpqvgghb5lv4szx58b1sbi1baba"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors VariantAnnotation]; }; + charmData = derive2 { name="charmData"; version="1.19.0"; sha256="1df933b5p187vblnv0q12n7l2fy69vdhr38hnj1019zw9vl62fnq"; depends=[pd_charm_hg18_example]; }; + chipenrich_data = derive2 { name="chipenrich.data"; version="2.10.0"; sha256="1vg1dqs7jzwnjm10vbd974bhpxq9533j2gqiyn78jj6pflpbamf5"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicRanges IRanges readr rtracklayer S4Vectors]; }; + chipseqDBData = derive2 { name="chipseqDBData"; version="1.2.0"; sha256="100sj7fw82xs0n5s4hhfdf7g6p4k57yfhyp1xc2fmbfmf0n7z694"; depends=[AnnotationHub ExperimentHub S4Vectors]; }; + chromstaRData = derive2 { name="chromstaRData"; version="1.12.0"; sha256="02dsi4q143hxj04fvywkpx6kdafc3ccw74sqv5n2l5f7dc5v6nzy"; depends=[]; }; + cnvGSAdata = derive2 { name="cnvGSAdata"; version="1.22.0"; sha256="1gv8hw7391nwzfd6cqh4b5ph69wzb9ghq9gq9g4knhrlrykf295x"; depends=[cnvGSA]; }; + colonCA = derive2 { name="colonCA"; version="1.28.0"; sha256="1d4b4wi5v102xw0kv3495zzhm32m6khg9krs6qw8513895law1gk"; depends=[Biobase]; }; + curatedAdipoChIP = derive2 { name="curatedAdipoChIP"; version="1.2.0"; sha256="0nkxljkjxkqkqny0a39nds0gd59kr0qiqvrl9p5mzdpykappi1rl"; depends=[ExperimentHub SummarizedExperiment]; }; + curatedAdipoRNA = derive2 { name="curatedAdipoRNA"; version="1.2.0"; sha256="16592i5w7fh1w5yjmmcwrk71j7yx3m33whjdm6yswfddq9rdy6jb"; depends=[SummarizedExperiment]; }; + curatedBladderData = derive2 { name="curatedBladderData"; version="1.22.0"; sha256="0pn3vsllrxpppzh5sv2nw3bqdhki3mn8iyssdklgghanlibmjdk0"; depends=[affy]; }; + curatedBreastData = derive2 { name="curatedBreastData"; version="2.14.0"; sha256="1mvf2cxvqa68vxiq3wxbq8xpk1yd5x1qyq9n1lrh34chnizmm5zi"; depends=[Biobase BiocStyle ggplot2 impute XML]; }; + curatedCRCData = derive2 { name="curatedCRCData"; version="2.18.0"; sha256="068i4clz4v9frf3f8s42asahl814a73fidsdf53bwfizvmjgqdbs"; depends=[BiocGenerics nlme]; }; + curatedMetagenomicData = derive2 { name="curatedMetagenomicData"; version="1.16.1"; sha256="1kykcm8kz1jw9fybryk7sclsd54gls34b9sm5hb4w9rqzk02v6da"; depends=[AnnotationHub Biobase dplyr ExperimentHub magrittr S4Vectors tidyr]; }; + curatedOvarianData = derive2 { name="curatedOvarianData"; version="1.24.0"; sha256="1gn5p2hd3inafh45bjniskhya6nyja9birg7hgxmr5mi5g95fc4s"; depends=[affy BiocGenerics]; }; + curatedTCGAData = derive2 { name="curatedTCGAData"; version="1.8.1"; sha256="0r579scg4f5hfd99wfpvgv62g0h57sc3w118lqgw8g3xhpbxnhcw"; depends=[AnnotationHub ExperimentHub HDF5Array MultiAssayExperiment S4Vectors SummarizedExperiment]; }; + davidTiling = derive2 { name="davidTiling"; version="1.26.0"; sha256="1qidyhjlkhn67llcmwx1wswyr0dm57ydzgwv9fz21mj8xmsc343l"; depends=[Biobase GO_db tilingArray]; }; + depmap = derive2 { name="depmap"; version="1.0.0"; sha256="1v6hhxfy0l1bw8nbkjjc9y6as5dbjlbq6znxjan5gpkll48a49p3"; depends=[AnnotationHub dplyr ExperimentHub]; }; + derfinderData = derive2 { name="derfinderData"; version="2.4.0"; sha256="18n9fmmq5n18c2blyjfxjrr9md175vkw9ldvldjjsjr4i1mdy2pr"; depends=[]; }; + diffloopdata = derive2 { name="diffloopdata"; version="1.14.0"; sha256="1sklif6b3arp1i2kcg6zfsf9rssn5cksk1p9hi3lygwv4h4x7jm1"; depends=[]; }; + diggitdata = derive2 { name="diggitdata"; version="1.18.0"; sha256="1yddn2zsfqixlp8pmmzm33ain877gvppwlr7imgasgyjc42g5r1q"; depends=[Biobase viper]; }; + dressCheck = derive2 { name="dressCheck"; version="0.24.0"; sha256="15wim7s96lkniyfiilhw7hwsjlaaz8vbi2cnnc42d44nxrfd9649"; depends=[Biobase]; }; + dsQTL = derive2 { name="dsQTL"; version="0.24.0"; sha256="1ygnsyzsqdpnvrxaa874xsj74rzk2117cfd1plajsnxcj3ak79hd"; depends=[Biobase GGBase SummarizedExperiment]; }; + dyebiasexamples = derive2 { name="dyebiasexamples"; version="1.26.0"; sha256="0b2wjq2sw44j2qvyfhi7fc8ari9mj0v8a1cr0kr73b4k6khb47yr"; depends=[GEOquery marray]; }; + ecoliLeucine = derive2 { name="ecoliLeucine"; version="1.26.0"; sha256="06mn8qfkdf9jr1hbadhv16dqv9q8w2q506p8qwy9jnjxx65vrwlg"; depends=[affy ecolicdf]; }; + estrogen = derive2 { name="estrogen"; version="1.32.0"; sha256="08h2f9pvzv7b7kv80yjfilcl77q7plb2bbg9yahadnaiaj4d58ix"; depends=[]; }; + etec16s = derive2 { name="etec16s"; version="1.14.0"; sha256="1m40gv1fi6bk2dj6ysp9dmbblfd06gx4f5gy44gfai696s1ll6xv"; depends=[Biobase metagenomeSeq]; }; + faahKO = derive2 { name="faahKO"; version="1.26.0"; sha256="05bsfr4svjgdsnz3h6x9dp2v4jpdjpxlhsk01izy739x2v5nqfqa"; depends=[xcms]; }; + fabiaData = derive2 { name="fabiaData"; version="1.24.0"; sha256="1g4zgf8v7yqgqakzxdwrlg9awxfz7s9yk0k6zs2mnn6b3r2yd8sf"; depends=[Biobase]; }; + facopy_annot = derive2 { name="facopy.annot"; version="1.6.0"; sha256="084zxksx2ar5h4827wb3w2k1490w1dzfxkzvshcs35z1fm18cjyj"; depends=[]; }; + facsDorit = derive2 { name="facsDorit"; version="1.28.0"; sha256="1xymidx155g97rhyrz9h8gikplkmm52188lzjyfxgvrx75b988h0"; depends=[prada]; }; + ffpeExampleData = derive2 { name="ffpeExampleData"; version="1.24.0"; sha256="05ic4cjz4s4jckc61iciq1h4n4bkgdwvb79cnv2r1xdv3jyswsv4"; depends=[lumi]; }; + fibroEset = derive2 { name="fibroEset"; version="1.28.0"; sha256="0hyzrr05dpkvzhl3s3p2zq8vzlhs6d8rkh2vqrsz19r20vimb1ml"; depends=[Biobase]; }; + fission = derive2 { name="fission"; version="1.6.0"; sha256="0xhg88cypz2rp8m5njgp6ksgdc2hc6jykcikndkx3f88al6p67ap"; depends=[SummarizedExperiment]; }; + flowFitExampleData = derive2 { name="flowFitExampleData"; version="1.22.0"; sha256="1isg55458bvcz6yy73b2iqyjiln34rh259862fiz004v1m2fk0dd"; depends=[flowCore]; }; + flowPloidyData = derive2 { name="flowPloidyData"; version="1.12.0"; sha256="02z5dzw5y5ngd4pi8am7yxxm8xad3za5hslqigvdv8sa51z4plm6"; depends=[]; }; + flowQBData = derive2 { name="flowQBData"; version="1.9.0"; sha256="0i9zgql9c8n45hwg28acvqknvxqfjs24irl2ijimklrdmgyd23gw"; depends=[]; }; + flowWorkspaceData = derive2 { name="flowWorkspaceData"; version="2.22.0"; sha256="13r94xs6l55y9gdskwv2hf6jiz0qci6b5wzh1gp06v2l4rakabvc"; depends=[]; }; + frmaExampleData = derive2 { name="frmaExampleData"; version="1.22.0"; sha256="1ww894x9kbkgh13qysqhxd5awfqrz4pf99w5y4nfixp8w26j2rag"; depends=[]; }; + furrowSeg = derive2 { name="furrowSeg"; version="1.14.0"; sha256="1dvqfb8f4gqfi3jfqfc010z65qbi4nynyds08xa0bdh3kd9paqax"; depends=[abind dplyr EBImage locfit tiff]; }; + gageData = derive2 { name="gageData"; version="2.24.0"; sha256="0qslkcizal3p2d78lwpd46s6hzizhsmfyw3rplzx6r0cq3g05gsx"; depends=[]; }; + gaschYHS = derive2 { name="gaschYHS"; version="1.24.0"; sha256="10l1aqxbjyz7067k1hz09gxcgw0m9c5dxqmzx800s7w74w0jw5ni"; depends=[Biobase]; }; + gatingMLData = derive2 { name="gatingMLData"; version="2.26.0"; sha256="0gpp0ynz4q4pakvjp2gw3fxi7dfj7s96rf8sfzfyivgj37ygmc6q"; depends=[]; }; + gcspikelite = derive2 { name="gcspikelite"; version="1.24.0"; sha256="0k086fzmmrpzzlimy0xsy49l0r7f91a5dz5h3y0b83z4n5v2lb8m"; depends=[]; }; + geneLenDataBase = derive2 { name="geneLenDataBase"; version="1.22.0"; sha256="0pygs8084kx3w4ngdijazfy4gj1fdcjda9jigfc4nmbivfa3bsny"; depends=[GenomicFeatures rtracklayer]; }; + genomationData = derive2 { name="genomationData"; version="1.18.0"; sha256="05ig82568q3zlyksg3izzdv0cpkyhz40jrdlkk4kh4mpfp6y90q2"; depends=[]; }; + geuvPack = derive2 { name="geuvPack"; version="1.18.0"; sha256="0nzj26bsji2pi81clcjbjm9wylsj9zjs2x7my2yjirzpgx5l5ia1"; depends=[SummarizedExperiment]; }; + geuvStore2 = derive2 { name="geuvStore2"; version="1.16.0"; sha256="0j40wasarcxm2x5k6vz892592c1d2wi5l1l61qk4yzyq0140hb0q"; depends=[BatchJobs GenomicRanges gQTLBase]; }; + golubEsets = derive2 { name="golubEsets"; version="1.28.0"; sha256="18w8d9m2li8qxd9bi26c1j7bjk7bzpdpi8znfyz5wqdq6h2yzrkx"; depends=[Biobase]; }; + grndata = derive2 { name="grndata"; version="1.18.0"; sha256="0zikyg5wn7q3bwd70gb4fwdw1ki2qvlkr5jn9rv0cjy2a5c2k97k"; depends=[]; }; + gskb = derive2 { name="gskb"; version="1.18.0"; sha256="02ghsd6jnqfji8rjzx1nz32mlvk1hw0s3ddhfbwirizyndjn4r4c"; depends=[]; }; + h5vcData = derive2 { name="h5vcData"; version="2.6.0"; sha256="0b9jf2qlb8a5xk59sbdjbblsh5psnyanci9r631sbddrc5pvszw2"; depends=[]; }; + hapmap100khind = derive2 { name="hapmap100khind"; version="1.28.0"; sha256="0qjzbp91vip9f1rf5hw8mq22w8fxy8a8gkyw58h03zbl5bqnzpvv"; depends=[]; }; + hapmap100kxba = derive2 { name="hapmap100kxba"; version="1.28.0"; sha256="1gr5qkxfxkcmgdllx6k8znacjpcqx1bjqgpm4phvawarqk3hnbvz"; depends=[]; }; + hapmap500knsp = derive2 { name="hapmap500knsp"; version="1.28.0"; sha256="1083m1zw88br0s8hglxv9lvzvpydyl6silgddh8z9y9h0xc02gv6"; depends=[]; }; + hapmap500ksty = derive2 { name="hapmap500ksty"; version="1.28.0"; sha256="14xwg4gavrjb8b9iyw2dhdsj2xhywnq9d10yd3c1sliv1v5fdhma"; depends=[]; }; + hapmapsnp5 = derive2 { name="hapmapsnp5"; version="1.28.0"; sha256="0zhnmksx5anaa7wmxh8f06fixddrkj59b3m05db5swzbcijfa9zw"; depends=[]; }; + hapmapsnp6 = derive2 { name="hapmapsnp6"; version="1.28.0"; sha256="1ybx99zjy5g6xmwbnyvzms1wk0fm8jjz5f57mpw6m5x2pqj9w5am"; depends=[]; }; + harbChIP = derive2 { name="harbChIP"; version="1.24.0"; sha256="0rm4ai4mnxnmim7gxf0cmxpvrxx0v33wv6k0m3f47fb6barwdx8z"; depends=[Biobase Biostrings IRanges]; }; + healthyFlowData = derive2 { name="healthyFlowData"; version="1.24.0"; sha256="14iix2jzha8yr02qr4lb5x4c0k68jy5w0rps1vnaqx54v4lxvsff"; depends=[flowCore]; }; + hgu133abarcodevecs = derive2 { name="hgu133abarcodevecs"; version="1.24.0"; sha256="0k7f57jvyl3l9n7jwm5mcdsvwn55l0mhjbcjd64hsq67f71942xf"; depends=[]; }; + hgu133plus2CellScore = derive2 { name="hgu133plus2CellScore"; version="1.6.0"; sha256="19m1lyl7c5wfzlrws4cnaya984c69sy720wa96wb2v5syzmazvwb"; depends=[Biobase]; }; + hgu133plus2barcodevecs = derive2 { name="hgu133plus2barcodevecs"; version="1.24.0"; sha256="0qnc220b42ls7193nilbhk0hm1awii8r735l9314d8kr5i0lb5vf"; depends=[]; }; + hgu2beta7 = derive2 { name="hgu2beta7"; version="1.26.0"; sha256="08ix30hrjqzdrjcaxr3x5svcsanxmxrqj4j8cwsbnkhjvb39lc29"; depends=[]; }; + hmyriB36 = derive2 { name="hmyriB36"; version="1.22.0"; sha256="174k3fk9gkrk592f3i1qwl4cdrjikdnywh7mla2yyj4qm187wslf"; depends=[Biobase GGBase]; }; + humanStemCell = derive2 { name="humanStemCell"; version="0.26.0"; sha256="1vg9la7av65rknvbvrhbfb0cjhvsfj7bsf0dxzmp3v5gg0mnmyrh"; depends=[Biobase hgu133plus2_db]; }; + kidpack = derive2 { name="kidpack"; version="1.28.0"; sha256="1v54hd2v25p8l5ly3p8wb7gaj6nw03as7kq9i07jivbmnlbvrvh3"; depends=[Biobase]; }; + leeBamViews = derive2 { name="leeBamViews"; version="1.22.0"; sha256="0fcabcsc1crjsd8m6h2lzzrfrl7pjzksp59v991jaimfs5cp8sgw"; depends=[Biobase BSgenome GenomicAlignments GenomicRanges Rsamtools]; }; + leukemiasEset = derive2 { name="leukemiasEset"; version="1.22.0"; sha256="0hk48p3nw1fasxww5pac9jm3xr3xx1lk7cj9gyvaf63r9qag28d8"; depends=[Biobase]; }; + lumiBarnes = derive2 { name="lumiBarnes"; version="1.26.0"; sha256="0b6i4az6a3nj9c0x68nfprazdkm2qlcw09mggwi888zqqx4iga9c"; depends=[Biobase lumi]; }; + lungExpression = derive2 { name="lungExpression"; version="0.24.0"; sha256="0py7jingivvk9pshvl607lzyvyln3ff4b91j85jb67n4a6bivln4"; depends=[Biobase]; }; + lydata = derive2 { name="lydata"; version="1.12.0"; sha256="1z0nw736lz1f2papciajqdqbblgsrv26lkk6ww2vq7h9gxxjsyhp"; depends=[]; }; + mAPKLData = derive2 { name="mAPKLData"; version="1.18.0"; sha256="04dapbb66qbzy5xdz8c43hbq2phvvw86mghkc2pmqphiyjc9z3ky"; depends=[]; }; + mCSEAdata = derive2 { name="mCSEAdata"; version="1.6.0"; sha256="0a4zjil92fql45np0n6b90j55p2yrz7j2pkb65vgm9s3fqpk8pz1"; depends=[]; }; + macrophage = derive2 { name="macrophage"; version="1.2.0"; sha256="0axlys1i2hpzx7w5q1nf18vwipgqnqcbzrwysjffkj6mb9cs57zr"; depends=[]; }; + mammaPrintData = derive2 { name="mammaPrintData"; version="1.22.0"; sha256="11fjkclzmxjbx91pwpbaah2l2frdn3v5a44d592jbw2pahyd81sg"; depends=[]; }; + maqcExpression4plex = derive2 { name="maqcExpression4plex"; version="1.30.0"; sha256="0lrgr2qzg2mm07xffpqkl4ppkmcwaiay0kjr5jgsl0df1pb3z5pp"; depends=[]; }; + mcsurvdata = derive2 { name="mcsurvdata"; version="1.4.0"; sha256="10b8g3c50hw4jp3rbsmz8smvyf6k3d1hff6w77xhy3ly92s9jgg6"; depends=[AnnotationHub Biobase ExperimentHub]; }; + metaMSdata = derive2 { name="metaMSdata"; version="1.22.0"; sha256="1vsn42xj3xxz854i1yhd77lm16v8z4g9r0f7d9wyvq5pwcak44hd"; depends=[]; }; + methyvimData = derive2 { name="methyvimData"; version="1.8.0"; sha256="08w7vzb28s5x5zlwrlj9l0k8iq45zpf1g6mgzwr6p6b43xva5dg9"; depends=[minfi]; }; + miRNATarget = derive2 { name="miRNATarget"; version="1.24.0"; sha256="1ch761d9sfi890sljardrmjm1h0p6x4ii0lj89jg78jdhprl8xgq"; depends=[Biobase]; }; + miRcompData = derive2 { name="miRcompData"; version="1.16.0"; sha256="1izvvglzbqf291wdd9qg3qh834snhcyzdz7mcqvgi1qgw1ri96fm"; depends=[]; }; + microRNAome = derive2 { name="microRNAome"; version="1.8.0"; sha256="0m2iwpx7qblibqlm207ml41imjixc2jgsiq6zqgsa7zrl56wbnfp"; depends=[SummarizedExperiment]; }; + minfiData = derive2 { name="minfiData"; version="0.32.0"; sha256="01fdw5pi8qg03mbc1skvrlmddazmcihyrv7jw70kvq1pv01zxd6n"; depends=[IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest minfi]; }; + minfiDataEPIC = derive2 { name="minfiDataEPIC"; version="1.12.0"; sha256="1kkymjrj34w7sdq057ngsfjbi3h1f2vcncszarybzh0qabh17agg"; depends=[IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest minfi]; }; + minionSummaryData = derive2 { name="minionSummaryData"; version="1.16.0"; sha256="0bdrrzcrvd7h9cb231hi29b9hrvv5cnmd8h5161sij2mdh3rwbwl"; depends=[]; }; + mitoODEdata = derive2 { name="mitoODEdata"; version="1.22.0"; sha256="0wn118bchr3z679nqk3fa1wrlkqvlh213nh88z1caga7k0vqjsin"; depends=[]; }; + mosaicsExample = derive2 { name="mosaicsExample"; version="1.24.0"; sha256="136kh8r8yh7rfkjszjgxz682r3jhw64ic46jykbdnhhypg8jvj2x"; depends=[]; }; + mouse4302barcodevecs = derive2 { name="mouse4302barcodevecs"; version="1.24.0"; sha256="0g7zsy0j34gbad4ijkj90x1z2w6azvkdgm1q9wqbdypl5gbj0zl4"; depends=[]; }; + msPurityData = derive2 { name="msPurityData"; version="1.14.0"; sha256="19mp4fxjbcw76rwyb1bvkc79qlqda1i1sd41s82m04k5wfwsrvz5"; depends=[]; }; + msd16s = derive2 { name="msd16s"; version="1.6.0"; sha256="1dhnscmc477919ylvzb1qp6bvkrk6yrqi3cwvxhwn650jx5cgyhg"; depends=[Biobase metagenomeSeq]; }; + msdata = derive2 { name="msdata"; version="0.26.0"; sha256="0bb53k29jzx0jwzbnrhjilj8prfrrvniy81x47i4qjpva8aqi71x"; depends=[]; }; + msqc1 = derive2 { name="msqc1"; version="1.14.0"; sha256="0sa27px1nnwnbpmab64xiivvy48dicg3xnkz6adyg0k2wbgb0qza"; depends=[lattice]; }; + mtbls2 = derive2 { name="mtbls2"; version="1.16.0"; sha256="1z0b8dh1acpwnqc8hrnlpzb99qd88pcymnz28nkdar8ww0zjddxv"; depends=[]; }; + muscData = derive2 { name="muscData"; version="1.0.0"; sha256="0x1gsj2hp3cqs6r3x3b4gw3jrw8w5s9wyhfc85sacnzq7r9hbp2x"; depends=[ExperimentHub SingleCellExperiment]; }; + mvoutData = derive2 { name="mvoutData"; version="1.22.0"; sha256="0abd9jv57k52lvckxxhg32hdd9999v24nsnc7il9ynl86prisa1m"; depends=[affy Biobase lumi]; }; + nanotubes = derive2 { name="nanotubes"; version="1.2.0"; sha256="1mxg25wfqh2v5n5vg2z5m26xai6blyh9kh9hlzra5pz02kfazkyx"; depends=[]; }; + oct4 = derive2 { name="oct4"; version="1.2.0"; sha256="02w5ccvx9p4bb3pq7w1y85gn58afl30nw1sakhg302rimmx1109n"; depends=[]; }; + pRolocdata = derive2 { name="pRolocdata"; version="1.24.0"; sha256="1gyd6jmha72qpw4lzmnb51z0c992bj2fxjai3pk12lnhpyyk1qqy"; depends=[Biobase MSnbase]; }; + parathyroidSE = derive2 { name="parathyroidSE"; version="1.24.0"; sha256="06vyxzjdfxn6964sv13c4mhxqgrxm5idjcx3c40v0bwys93cgkxm"; depends=[SummarizedExperiment]; }; + pasilla = derive2 { name="pasilla"; version="1.14.0"; sha256="0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"; depends=[]; }; + pasillaBamSubset = derive2 { name="pasillaBamSubset"; version="0.24.0"; sha256="05simp2qbnpisxwdwl59ydjjyphmhy51w4jaq3iapwmwz5qzkbss"; depends=[]; }; + pathprintGEOData = derive2 { name="pathprintGEOData"; version="1.16.0"; sha256="1iargpnk8calgy24nihgxz04w5w4wx9sr5yrl6kzjzwqvxskkkrq"; depends=[]; }; + pcaGoPromoter_Hs_hg19 = derive2 { name="pcaGoPromoter.Hs.hg19"; version="1.22.0"; sha256="00dkclj6vcwjr3zc0fsfga4lpr4b96v2ilasl9mx6f7z3hmn379x"; depends=[]; }; + pcaGoPromoter_Mm_mm9 = derive2 { name="pcaGoPromoter.Mm.mm9"; version="1.22.0"; sha256="03128h4aq839c9ywaxjpb64pjigz5qcmm0v1cnf6zqyj572qk7a6"; depends=[]; }; + pcaGoPromoter_Rn_rn4 = derive2 { name="pcaGoPromoter.Rn.rn4"; version="1.22.0"; sha256="106jrp8b17d2zdvi6384v16pni1hw3ngn7l8l0vzm1wignr3g41i"; depends=[]; }; + pcxnData = derive2 { name="pcxnData"; version="2.8.0"; sha256="08rpca2v3505r8b8lb2yqrz7736cdkx99ahk161h2fjkyzrl4v27"; depends=[]; }; + pd_atdschip_tiling = derive2 { name="pd.atdschip.tiling"; version="0.24.0"; sha256="0njvki7j1vqnckvqj8xn9lnkw9vnc2z1zr02x3rzvl21slkq2nan"; depends=[Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; + pepDat = derive2 { name="pepDat"; version="1.6.0"; sha256="1zcim2l4qvp6ym8325586r6hv4f69dnqykyv5n2kjpa7rwjwmphr"; depends=[GenomicRanges]; }; + plasFIA = derive2 { name="plasFIA"; version="1.14.0"; sha256="02yga7szrxhz9sbwpd3g0khm3mrpgfd8hzfj0mdrzlcx455kyjgd"; depends=[proFIA]; }; + ppiData = derive2 { name="ppiData"; version="0.24.0"; sha256="0d3j7w8af4q6hf8ggrzh0jgk7ddd6jkp80n9w2mvw8b648b42m5r"; depends=[AnnotationDbi graph]; }; + prebsdata = derive2 { name="prebsdata"; version="1.22.0"; sha256="0sgl74pxpc4mxqyjvj4ghgk9y1vgy5rj75253xpjmhfz4pyimflk"; depends=[]; }; + prostateCancerCamcap = derive2 { name="prostateCancerCamcap"; version="1.14.0"; sha256="1a7rhm6n016zvs0kmy2sr419liq26fjgailmyiwbjc0x556vdww9"; depends=[Biobase]; }; + prostateCancerGrasso = derive2 { name="prostateCancerGrasso"; version="1.14.0"; sha256="1grdrjdznnzq3dfgblfa1d79l2wayhsv9hkzk7cw2pzpyb39ramr"; depends=[Biobase]; }; + prostateCancerStockholm = derive2 { name="prostateCancerStockholm"; version="1.14.0"; sha256="07k2vwrmnhs9c44d6lsslmcajmid55ldsbcwqw1l8073jczmhfab"; depends=[Biobase]; }; + prostateCancerTaylor = derive2 { name="prostateCancerTaylor"; version="1.14.0"; sha256="15kfwdyzwyr2bbi7g98q6khkbkk0bisp602if1dnipbmak9f0jdp"; depends=[Biobase]; }; + prostateCancerVarambally = derive2 { name="prostateCancerVarambally"; version="1.14.0"; sha256="14pz58b1g8kq3sx2fc61zlhy1r25hdzcr8xv179pfjnqslfgqbrp"; depends=[Biobase]; }; + pumadata = derive2 { name="pumadata"; version="2.22.0"; sha256="1pw6j2r23x4r0623c8fdhflgfxy66qf0r8khdgljh86xiyc03scs"; depends=[Biobase oligo puma]; }; + pwrEWAS_data = derive2 { name="pwrEWAS.data"; version="1.0.0"; sha256="08k1p5pn0rhvh4zb9cylqxwk3z3s5cbgn5fi06x8nsgh0xhijn6s"; depends=[ExperimentHub]; }; + qPLEXdata = derive2 { name="qPLEXdata"; version="1.4.0"; sha256="069fpjlkynd6rvqcb4hfg2rh092jz8jl2sdsfr066mbywkv4dj1r"; depends=[dplyr knitr MSnbase qPLEXanalyzer]; }; + rRDPData = derive2 { name="rRDPData"; version="1.6.0"; sha256="12ba30ni912anz10n8hqd7cj6bgn0fpzlgzzyvdrl483dhvswla0"; depends=[rRDP]; }; + rcellminerData = derive2 { name="rcellminerData"; version="2.8.0"; sha256="0w1rvdkbwvva5zhciw68207cci2krkwx0vavrsgcm1dhbl4983f7"; depends=[Biobase]; }; + restfulSEData = derive2 { name="restfulSEData"; version="1.8.0"; sha256="1657mp19f5pgdzyl9iiq4cg6n03zz616qkx01xp6q5yfidhc9wml"; depends=[ExperimentHub SummarizedExperiment]; }; + rheumaticConditionWOLLBOLD = derive2 { name="rheumaticConditionWOLLBOLD"; version="1.24.0"; sha256="1nbnvz89b7620qdb5dmrxr1pwjdpbg53m3bb2lqykqrfg8rlgsnx"; depends=[]; }; + sampleClassifierData = derive2 { name="sampleClassifierData"; version="1.10.0"; sha256="1dpnqh9i0wjwzmhvb990nckasdzj1in1ma5v1rcvkfi8vspwf19f"; depends=[SummarizedExperiment]; }; + scRNAseq = derive2 { name="scRNAseq"; version="2.0.2"; sha256="1fpfpim7fiy2b0n3y5k11z0s6kaqf5x3wk6lw4crhp23pfgx34h7"; depends=[BiocGenerics ExperimentHub S4Vectors SingleCellExperiment SummarizedExperiment]; }; + seq2pathway_data = derive2 { name="seq2pathway.data"; version="1.18.0"; sha256="1qywb8433q0bm1f7c3hfxxnnj721ijjmapanlid87hrh0aqvg68h"; depends=[]; }; + seqCNA_annot = derive2 { name="seqCNA.annot"; version="1.22.0"; sha256="0l180zki5mm2ajapbq7nlivg3287b0i9srgk5r331glh65ly8x6d"; depends=[]; }; + seqc = derive2 { name="seqc"; version="1.20.0"; sha256="1w0ymj9f993mb6380yr40gl56xqhbbcnm5f2ijsjg40bmih4hhv2"; depends=[Biobase]; }; + serumStimulation = derive2 { name="serumStimulation"; version="1.22.0"; sha256="1g0sx594hsivk98a2x9pgrxhffl8nwwbp0k58fbn5vl4fba2f4jv"; depends=[]; }; + sesameData = derive2 { name="sesameData"; version="1.4.0"; sha256="0v9rd407ayvbr8g5b63kh3kc1m90mw25qm8i8k7bpyq4f3lp8aqi"; depends=[AnnotationHub curl ExperimentHub]; }; + seventyGeneData = derive2 { name="seventyGeneData"; version="1.22.0"; sha256="0kp1zp8ncc7w60a961p8r8b27rnmwdzipdjj38bpg110c0p79sz3"; depends=[]; }; + shinyMethylData = derive2 { name="shinyMethylData"; version="1.6.0"; sha256="1lilbg2lh6adyik24d9hv2hazfs9rp1zranb4pjz8mp144qbpc9p"; depends=[]; }; + signatureSearchData = derive2 { name="signatureSearchData"; version="1.0.0"; sha256="1gz3054j796czr98wd38c9xj6lzjpfdpp75kcs9ckfdspaaa5g4m"; depends=[affy Biobase dplyr ExperimentHub limma magrittr R_utils rhdf5 signatureSearch]; }; + simpIntLists = derive2 { name="simpIntLists"; version="1.22.0"; sha256="0lilbk76djq5kfsiwjbzdy1lsws635yp38rijgdr2z9zgj8fh6jr"; depends=[]; }; + stemHypoxia = derive2 { name="stemHypoxia"; version="1.22.0"; sha256="13b533qwr05zs5qqyq6ciaxki5dkl5i1kbvzyhpg1fzyyh3k5bwb"; depends=[]; }; + stjudem = derive2 { name="stjudem"; version="1.26.0"; sha256="0amds4vmd3lzlhbsw9rfd7awx66gwb85g7v0jis40x2dxz8669hr"; depends=[]; }; + synapterdata = derive2 { name="synapterdata"; version="1.24.0"; sha256="1xm3pi0ya8alb7qj57kg0naf981q3hfqp892waql209kf866zchb"; depends=[synapter]; }; + systemPipeRdata = derive2 { name="systemPipeRdata"; version="1.14.2"; sha256="0xrq82hinzxy325r2flrif8c0wn5m0kx7mv0jc95gzy0lvp52y9q"; depends=[BiocGenerics]; }; + tartare = derive2 { name="tartare"; version="1.0.0"; sha256="0cvmy89gbsspp5pl0jp3w8q6raza4w1pmm2cmcp9c5hfbiiszj8b"; depends=[AnnotationHub ExperimentHub]; }; + tcgaWGBSData_hg19 = derive2 { name="tcgaWGBSData.hg19"; version="1.4.0"; sha256="1nsig05z8y7ya81i4siiny6058873n227c5isbjw0fkbgkkpbi8d"; depends=[bsseq ExperimentHub knitr]; }; + tinesath1cdf = derive2 { name="tinesath1cdf"; version="1.24.0"; sha256="0sbs1zl6xgnlkcnw955sgzyfcgc76idvys34fwlps6rbpxischmf"; depends=[]; }; + tinesath1probe = derive2 { name="tinesath1probe"; version="1.24.0"; sha256="1sk219jh25lr5nqgv8qgj75xdljgij1j8m2cykr74sssawg375z1"; depends=[AnnotationDbi]; }; + tissueTreg = derive2 { name="tissueTreg"; version="1.6.0"; sha256="1zpn5w5kawr320s578sa1sm5a7rqp180mpa1rcb74zym0qz9qksj"; depends=[]; }; + tofsimsData = derive2 { name="tofsimsData"; version="1.14.0"; sha256="1ydasd2xw3c2gryvhlj9818i0y49n6njk6m65zn9an3csrhv5dc6"; depends=[]; }; + topdownrdata = derive2 { name="topdownrdata"; version="1.8.0"; sha256="1kwcs06w38s41pp4yl4wqv09ag22vamv13v508261razjg8rbya0"; depends=[topdownr]; }; + tweeDEseqCountData = derive2 { name="tweeDEseqCountData"; version="1.24.0"; sha256="1ik0bxdiliwmpgrwi2075il0spwzql61fhx18axg3k1dy3zjhd6d"; depends=[Biobase]; }; + tximportData = derive2 { name="tximportData"; version="1.14.0"; sha256="1496m83dv4adzw0r62fbj9ydsrni82c7lacfpmzg7jasbma3asvy"; depends=[]; }; + vulcandata = derive2 { name="vulcandata"; version="1.8.0"; sha256="18il2kqzfr472jndyraxx5kcy63chgc96cs2bdb2wjlgkkr1fg9v"; depends=[]; }; + waveTilingData = derive2 { name="waveTilingData"; version="1.22.0"; sha256="1vxbswac7zhlb1yg3n7k89rdbxry4ps8hxn4xr4idl7ydiap6igk"; depends=[]; }; + yeastCC = derive2 { name="yeastCC"; version="1.26.0"; sha256="1nbvkg74qh96akq4h950xx4va2bfmm13ri3p4fzhvw8imh5gg59f"; depends=[Biobase]; }; + yeastExpData = derive2 { name="yeastExpData"; version="0.32.0"; sha256="13g7kffkwazasjgfyw5np3aq9j2hlcxskxpl0lchclpczfrnn9g6"; depends=[graph]; }; + yeastGSData = derive2 { name="yeastGSData"; version="0.24.0"; sha256="0npmsfvxlrfiz27lwnij7y41kj8zc1v3vv8cc4nk58xkwypczjza"; depends=[]; }; + yeastNagalakshmi = derive2 { name="yeastNagalakshmi"; version="1.22.0"; sha256="08byj2pw9sfdkq3bcnzhhxv8ik87wa852as11fsph49h886dgd4h"; depends=[]; }; + yeastRNASeq = derive2 { name="yeastRNASeq"; version="0.24.0"; sha256="0rnlx2qsz5dsx9midfk81avlvjn0bjmybj6278ia8s0l83lbqdgh"; depends=[]; }; + yri1kgv = derive2 { name="yri1kgv"; version="0.28.0"; sha256="1wg086rld5ranrb9wd55pwri95qa323wzp2x4vm3bqa7q4xbbk4v"; depends=[Biobase GGBase]; }; + yriMulti = derive2 { name="yriMulti"; version="0.16.0"; sha256="1j1xll3w2v68xp2gfh0xmdr35w71i4g1g4q3v0a73qn8zw4b17r8"; depends=[dsQTL GenomeInfoDb GenomicFiles GenomicRanges geuvPack gQTLBase Homo_sapiens MultiAssayExperiment SummarizedExperiment VariantAnnotation]; }; + zebrafishRNASeq = derive2 { name="zebrafishRNASeq"; version="1.6.0"; sha256="1dk0ijlc6cg0jwn20z125i2zfiayx3bvgwjq974cfxcbv9l0pl7b"; depends=[]; }; } diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix index c02ea4dda4a2b..9cd93633e8f86 100644 --- a/pkgs/development/r-modules/bioc-packages.nix +++ b/pkgs/development/r-modules/bioc-packages.nix @@ -4,1642 +4,1815 @@ # Rscript generate-r-packages.R bioc >new && mv new bioc-packages.nix { self, derive }: -let derive2 = derive { biocVersion = "3.8"; }; +let derive2 = derive { biocVersion = "3.10"; }; in with self; { - ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.12.0"; sha256="0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; }; - ABSSeq = derive2 { name="ABSSeq"; version="1.36.0"; sha256="0nfz9l6zfnxm7lgq39nyzlhgh55kdnq8rgvjx33rn1ybcn63frsw"; depends=[limma locfit]; }; - ABarray = derive2 { name="ABarray"; version="1.50.0"; sha256="06gy96ppfrix6w9vjfljsj1j0hs7k67j0awzx8hkw301z281akxs"; depends=[Biobase multtest]; }; - ACE = derive2 { name="ACE"; version="1.0.0"; sha256="0ry6yfpzi6g0qnimnpzf3iibhm2bsblhi3604hiy76hl6mz20qg8"; depends=[Biobase ggplot2 QDNAseq]; }; - ACME = derive2 { name="ACME"; version="2.38.0"; sha256="17vr6ifjnmpcclifnzpbz538bmvs4xfym6rq9ndkh9xbjfacfcdm"; depends=[Biobase BiocGenerics]; }; - ADaCGH2 = derive2 { name="ADaCGH2"; version="2.22.0"; sha256="121vjv6xbinkkl6zq7gg3pgqwk1068rh2fpd16w5c7pcslkr7n1q"; depends=[aCGH bit cluster DNAcopy ff ffbase GLAD snapCGH tilingArray waveslim]; }; - AGDEX = derive2 { name="AGDEX"; version="1.30.0"; sha256="0l16sfmm3j9lhyjbl0bcghhkmr77a2rrscfd3ry93z7q0gki0fw8"; depends=[Biobase GSEABase]; }; - AIMS = derive2 { name="AIMS"; version="1.14.1"; sha256="1np7r3982i3l5pwakmjmg7c326f47bsr9sbp5c5b6mhz500s5mrb"; depends=[Biobase e1071]; }; - ALDEx2 = derive2 { name="ALDEx2"; version="1.14.1"; sha256="190kcvfqhh1rg67kggdvp4pd6i3dicnqclrri0y06zrnl1c8cnlw"; depends=[BiocParallel GenomicRanges IRanges multtest S4Vectors SummarizedExperiment]; }; - AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.8.0"; sha256="0w8h7a8skvwd8ass98y8sx733hz23kczpxsbwi7cdmpx8b0wxqaq"; depends=[]; }; - ANF = derive2 { name="ANF"; version="1.4.0"; sha256="08kd394kz7x0hjb8js9xpz8f1b7rg4yzghgys0il0w1z335ivb8c"; depends=[Biobase igraph MASS RColorBrewer survival]; }; - ARRmNormalization = derive2 { name="ARRmNormalization"; version="1.22.0"; sha256="09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd"; depends=[ARRmData]; }; - ASAFE = derive2 { name="ASAFE"; version="1.8.0"; sha256="0fjiz98cr83cjfakqq7q3prqha5gzr2k6741327jgjibmhbzpyz3"; depends=[]; }; - ASEB = derive2 { name="ASEB"; version="1.26.0"; sha256="0hyi0yncxwqydwcdmw265k6zip5ahry5yx4na3fiz1n6ivi7dxq2"; depends=[]; }; - ASGSCA = derive2 { name="ASGSCA"; version="1.16.0"; sha256="0sbyvwmjsfsrlc4gymzjb3aqs1k600w2zwnz7ih1gspgj4h6yi6l"; depends=[MASS Matrix]; }; - ASICS = derive2 { name="ASICS"; version="1.2.0"; sha256="12dq0ydn35zyjfspaxpn6k8wk8443a666v5ql4d4x5nf5vy39sk7"; depends=[BiocParallel ggplot2 gridExtra plyr quadprog ropls speaq SummarizedExperiment zoo]; }; - ASSET = derive2 { name="ASSET"; version="2.0.0"; sha256="05d788w7l6sd63xzay8yv0zxjbibm6dfm9rm8shihzn74c9wk7i9"; depends=[MASS msm rmeta]; }; - ASSIGN = derive2 { name="ASSIGN"; version="1.18.0"; sha256="1mcjz9nksk0a5jgd4wyjpf7af6c883idllkx4z14w651840sd6lr"; depends=[ggplot2 gplots msm Rlab sva yaml]; }; - ASpli = derive2 { name="ASpli"; version="1.8.1"; sha256="1lzfmnhpy94q9rj4qsgd7hy031y62jgfs4650ijs3agzb674z1ji"; depends=[AnnotationDbi BiocGenerics BiocStyle edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rsamtools S4Vectors]; }; - ATACseqQC = derive2 { name="ATACseqQC"; version="1.6.4"; sha256="1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; }; - AUCell = derive2 { name="AUCell"; version="1.4.1"; sha256="1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9"; depends=[data_table GSEABase mixtools R_utils shiny SummarizedExperiment]; }; - AffiXcan = derive2 { name="AffiXcan"; version="1.0.0"; sha256="1y07gf8f94s2i080a3bh0gam2fx2n4hmbznddkcxv7rkqgcq0adx"; depends=[BiocParallel MultiAssayExperiment SummarizedExperiment]; }; - AffyCompatible = derive2 { name="AffyCompatible"; version="1.42.0"; sha256="1vkjlpxpckmpgpf2svz866sa2pjpkhp4nc06vzpjfa8sqj5dl6n4"; depends=[Biostrings RCurl XML]; }; - AffyExpress = derive2 { name="AffyExpress"; version="1.48.0"; sha256="0zkk74dnbihc3xna4hlypyyqg3arhdsjqbc7q3dji8j9kz76kmcw"; depends=[affy limma]; }; - AffyRNADegradation = derive2 { name="AffyRNADegradation"; version="1.28.0"; sha256="04lvkd8m1arzilgs0i9f8f52f3yc7himhv4igbxhvhqmz4fln3xi"; depends=[affy]; }; - AgiMicroRna = derive2 { name="AgiMicroRna"; version="2.32.0"; sha256="0iqns14hihxr2rf4g3x47k9sniy6qsfmqq1r4jd8alcis22pl4gx"; depends=[affy affycoretools Biobase limma preprocessCore]; }; - AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.20.0"; sha256="03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; }; - AnalysisPageServer = derive2 { name="AnalysisPageServer"; version="1.16.0"; sha256="088f4h87bvlckf4s4q8iy9n9d9hw9njj6y4wwr3f62xax264glj0"; depends=[Biobase graph log4r rjson]; }; - Anaquin = derive2 { name="Anaquin"; version="2.6.1"; sha256="1p01bgfx5i82x6541q3479fgwln5ri8pyqrm2hbg0hlgl25w3v4d"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; }; - AneuFinder = derive2 { name="AneuFinder"; version="1.10.2"; sha256="0j25syzlnyq8c8pxc5yfm6k4dzvprpna08gg6117v4k3sdmgcz4p"; depends=[AneuFinderData bamsignals Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust ReorderCluster reshape2 Rsamtools S4Vectors]; }; - AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.44.0"; sha256="1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d"; depends=[Biobase BiocGenerics DBI IRanges RSQLite S4Vectors]; }; - AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.6.0"; sha256="0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x"; depends=[GenomicRanges lazyeval]; }; - AnnotationForge = derive2 { name="AnnotationForge"; version="1.24.0"; sha256="13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; - AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.32.0"; sha256="1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"; depends=[AnnotationDbi DBI]; }; - AnnotationHub = derive2 { name="AnnotationHub"; version="2.14.5"; sha256="0iyrxaijl4614iz5c1j53227xy2g756p3bx7hcwglcybh0k30nki"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; }; - AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.12.0"; sha256="1xim76sxldx70h13fpkhz7fxr5rcq0gp7558w4v1iqjjzd4gp3mh"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; }; - ArrayExpress = derive2 { name="ArrayExpress"; version="1.42.0"; sha256="1a61miwsyqghmqnfnfpd7b0p712mz9cpcrq00p9b7jr8j4jd5vla"; depends=[Biobase limma oligo XML]; }; - ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.32.1"; sha256="0gv3f1ynyl52ab7zvmfi9s34ns6nwqyayh5imv6b31l92rw5ifdm"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; }; - ArrayTV = derive2 { name="ArrayTV"; version="1.20.0"; sha256="00azibnfaa7w9gzlx8l21l9xlkzagwb0zbd70f95wvbr5qiq9w93"; depends=[DNAcopy foreach IRanges oligoClasses S4Vectors]; }; - ArrayTools = derive2 { name="ArrayTools"; version="1.42.0"; sha256="08wklnb3wi0yzxis5nic5g7w8shn9n3j6h7vbvxjv8n92bqmc0y1"; depends=[affy Biobase limma xtable]; }; - AssessORF = derive2 { name="AssessORF"; version="1.0.2"; sha256="1kkdds8mmrnh72j267xhyfn40i5czdfwhy8zlxxlm376mxipxwgj"; depends=[Biostrings DECIPHER GenomicRanges IRanges]; }; - BAC = derive2 { name="BAC"; version="1.42.0"; sha256="02r74rwsn59b1f9l3n51xh6jj5bwjcg9qp63i1jczfnglwga01av"; depends=[]; }; - BADER = derive2 { name="BADER"; version="1.20.1"; sha256="114xy8yynfncnrlsi1v44gsiq2a8jyh9q7ssb3f3rhb7rw8v0k4l"; depends=[]; }; - BAGS = derive2 { name="BAGS"; version="2.22.0"; sha256="13zlmffg8y1vrkpj62wawfzx9h68q1p42bizrwzq0cdh6jyafp3z"; depends=[Biobase breastCancerVDX]; }; - BASiCS = derive2 { name="BASiCS"; version="1.4.7"; sha256="1i0ynbc6grg28w8wsibrcfyncdipacb1lprnw11fvgkd0d429mg2"; depends=[BiocGenerics coda data_table ggplot2 KernSmooth MASS matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; }; - BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.12.0"; sha256="0k49ad1k3szjawsn7s97k7y2j7c03cqjcg8kmx8wmypjivjv1nv0"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; }; - BCRANK = derive2 { name="BCRANK"; version="1.44.0"; sha256="0zrmrc4dsz9jl0n7a0fsnmfws54hpda21sxpdqdq86qhj4ljz2nd"; depends=[Biostrings]; }; - BDMMAcorrect = derive2 { name="BDMMAcorrect"; version="1.0.1"; sha256="1i4d9qk4iw8m1p590fg85qg6w55982mn41zp8bqinygx5vzvq8i2"; depends=[ape ellipse ggplot2 Rcpp RcppArmadillo RcppEigen SummarizedExperiment vegan]; }; - BEARscc = derive2 { name="BEARscc"; version="1.2.1"; sha256="0zhf8l789yhp4fx75s3955r0m809r9lilrd57y5qkcpya9vq8fxb"; depends=[data_table ggplot2 SingleCellExperiment]; }; - BEAT = derive2 { name="BEAT"; version="1.20.1"; sha256="1xrfgfw91fdyx2dpkbc6xvwg266ym623mbmqzlg879lh0pny0400"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; }; - BEclear = derive2 { name="BEclear"; version="1.14.0"; sha256="0xwmq59hbkxki573brhp2rvmn06dyysk64n4fs0vna0h729d8lhj"; depends=[BiocParallel data_table futile_logger Matrix Rdpack]; }; - BGmix = derive2 { name="BGmix"; version="1.42.0"; sha256="19n8cqdfrp8br20g7gw787w2sa3sgs41vfnic6l9gdbqphb702d1"; depends=[KernSmooth]; }; - BHC = derive2 { name="BHC"; version="1.34.0"; sha256="0wsz5ak60fd69mds7f3siv4g3hygbzwdapm6jkldnph2x3sv0f2w"; depends=[]; }; - BLMA = derive2 { name="BLMA"; version="1.6.0"; sha256="12fxafyyffgmbnqqpq15wfawa5s1lmygkjxbh08sl34a9d5g2apf"; depends=[Biobase graph GSA limma PADOG ROntoTools]; }; - BPRMeth = derive2 { name="BPRMeth"; version="1.8.1"; sha256="10dsww7bhad59i3667iy2kq40bxd34ikbl8bhbczgwm2pfp0pq9f"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; }; - BRAIN = derive2 { name="BRAIN"; version="1.28.1"; sha256="0nz3ci9jyckbwpvarjmc5k19qspv5xpkks83ys3zz24j1v828z2d"; depends=[Biostrings lattice PolynomF]; }; - BSgenome = derive2 { name="BSgenome"; version="1.50.0"; sha256="07z4zxx0khrc86qqvc7vxww8df9fh6pyks9ajxkc9gdqr5nn79j7"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; }; - BUMHMM = derive2 { name="BUMHMM"; version="1.6.2"; sha256="0vna27h3g86dba5l94s74vjzswds95vsxaiw51da283436g2c2pn"; depends=[Biostrings devtools gtools IRanges stringi SummarizedExperiment]; }; - BUS = derive2 { name="BUS"; version="1.38.0"; sha256="04lk2rq8cv6hw64ssl1v64gqg7fz2jm7hd4hwkf6q6nhivr7skpi"; depends=[infotheo minet]; }; - BUScorrect = derive2 { name="BUScorrect"; version="1.0.0"; sha256="1z841bjyyqah232dhdpm7j77irjim09h3lpy2659n5llgzr7cdi2"; depends=[gplots SummarizedExperiment]; }; - BaalChIP = derive2 { name="BaalChIP"; version="1.8.0"; sha256="0xscwx5afwcyrg8pcq3fd80m9h8mqiswyvnk3x13r020r1jgxr9l"; depends=[coda doBy doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges reshape2 Rsamtools scales]; }; - BadRegionFinder = derive2 { name="BadRegionFinder"; version="1.10.0"; sha256="1d29hnaxyvlpdbzadnjp3x1jba1d4vis797iak81b217wrq34g1z"; depends=[biomaRt GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; - BaseSpaceR = derive2 { name="BaseSpaceR"; version="1.26.0"; sha256="1w7iz4nhgpx25004s9bd6mw9pm1z8dr8p7nxr6ck8wbdv19j1srp"; depends=[RCurl RJSONIO]; }; - Basic4Cseq = derive2 { name="Basic4Cseq"; version="1.18.1"; sha256="1vn9lwyjmhs09cpagiycvcyync54xfyv7id8y597p4i8p2nk6c26"; depends=[Biostrings BSgenome_Ecoli_NCBI_20080805 caTools GenomicAlignments GenomicRanges RCircos]; }; - BasicSTARRseq = derive2 { name="BasicSTARRseq"; version="1.10.0"; sha256="03micn3sy861i7218vcx7fpzflvlh5rsgx0gnc4irzvi1xh478j9"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges S4Vectors]; }; - BatchQC = derive2 { name="BatchQC"; version="1.10.1"; sha256="1clsabpfnaiy0dlb0m88z72kmwslny9rinrgzcb9ljjma3yarx8q"; depends=[corpcor d3heatmap ggvis gplots knitr limma Matrix matrixStats MCMCpack moments pander reshape2 rmarkdown shiny sva]; }; - BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.8.0"; sha256="0ziaciznv926xq6xjj22afcwpvz6ha0g93fgyw0y6cr4kx8mlphd"; depends=[Biobase]; }; - BayesPeak = derive2 { name="BayesPeak"; version="1.34.0"; sha256="0zj06b8r0hqjczhlryfy8z7jf799gglisv4cxszlzw4wj7byyi9x"; depends=[IRanges]; }; - BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.34.0"; sha256="0scdvj7d6gh78h6l1iv6nrd100i0n51a5dki9nvb7sk76sw06zzk"; depends=[]; }; - BgeeDB = derive2 { name="BgeeDB"; version="2.8.0"; sha256="1bhin7h1bd3wc74af1fms0ha3fy9drij26d1np27knpjs95wygiq"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; }; - BiFET = derive2 { name="BiFET"; version="1.2.1"; sha256="0wxyy5y1i06x6q6s89iq9mx7lz84pxx3s20za5r3gydrwphgkc9i"; depends=[GenomicRanges poibin]; }; - BiGGR = derive2 { name="BiGGR"; version="1.18.0"; sha256="0p42i0j2sqz9kc79nh0wi7hb7r8y01cs5gczanza59q3amhjidqq"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; }; - BiRewire = derive2 { name="BiRewire"; version="3.14.0"; sha256="0zawg7gjywf8bsxmr33dj4x0xxy06rxcmimdmwx6flx0igf8xrx0"; depends=[igraph Matrix slam tsne]; }; - BiSeq = derive2 { name="BiSeq"; version="1.22.0"; sha256="0bvq2qn4pn632x8ppqx99ar44xh1nazn34f2jqzhg3m8mc7q5h7c"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; }; - BicARE = derive2 { name="BicARE"; version="1.40.0"; sha256="1dl1jv927l1ywsccmf662j3dl7m4pnkw8v1lpv47nq49pns0qqsw"; depends=[Biobase GSEABase multtest]; }; - BioCor = derive2 { name="BioCor"; version="1.6.1"; sha256="1zli54qjdywwfjzjkwhldy5ma9k6q5fn52vzzfllhwwkxba6ggn7"; depends=[BiocParallel GSEABase Matrix]; }; - BioMVCClass = derive2 { name="BioMVCClass"; version="1.50.0"; sha256="0kkjj1c0s443agk7kaa1dxda4d1bsmlkxmivz2gvf5bhnbaxjn13"; depends=[Biobase graph MVCClass Rgraphviz]; }; - BioNet = derive2 { name="BioNet"; version="1.42.0"; sha256="1hxlwh3jwgnhs8ma0ky6nk9hm2yphd0g7a7ic32vibmw1xcs8znd"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; - BioNetStat = derive2 { name="BioNetStat"; version="1.2.2"; sha256="0d2kh6bbvbxwd48c9wa6nbaj12mmgikknrsdm13r4va7218d24f5"; depends=[BiocParallel ggplot2 Hmisc igraph knitr pathview pheatmap plyr psych RColorBrewer RJSONIO shiny shinyBS whisker yaml]; }; - BioQC = derive2 { name="BioQC"; version="1.10.0"; sha256="0ip0vvq6ln8ci14g2ynxi2ipz60df6bll3ynk5dchz2zybj9l2c2"; depends=[Biobase Rcpp]; }; - BioSeqClass = derive2 { name="BioSeqClass"; version="1.40.0"; sha256="1wx8pc9xv23w1lh1lz5qgv911yh38dz9h1wa3lp1jwb5hsk1lkzv"; depends=[Biobase Biostrings class e1071 foreign ipred klaR nnet party randomForest rpart scatterplot3d tree]; }; - Biobase = derive2 { name="Biobase"; version="2.42.0"; sha256="10nr6nrkj5vlq8hsgbhbhv669z0dbpz4m3vz9k32rx1czbrrqwin"; depends=[BiocGenerics]; }; - BiocCaseStudies = derive2 { name="BiocCaseStudies"; version="1.44.0"; sha256="0sidi2rynhbxmjwd90nccgximv4c60qdw4lc6yrgfi00928xms8d"; depends=[Biobase]; }; - BiocCheck = derive2 { name="BiocCheck"; version="1.18.0"; sha256="0zamvs5jar38293ff27imvwy0ra25y64ls9z8w3q1y4jcp8p8pg7"; depends=[BiocManager biocViews codetools graph httr knitr optparse stringdist]; }; - BiocFileCache = derive2 { name="BiocFileCache"; version="1.6.0"; sha256="0ykcr9saxs0sd03ng6g6r6dzqx28rc6590vfa2jq5sq84w95lxr0"; depends=[curl DBI dbplyr dplyr httr rappdirs RSQLite]; }; - BiocGenerics = derive2 { name="BiocGenerics"; version="0.28.0"; sha256="0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"; depends=[]; }; - BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.0.0"; sha256="1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"; depends=[BiocParallel Rcpp RcppAnnoy S4Vectors]; }; - BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.2.1"; sha256="0w0hqdyv580j2lxp0ma74swi0cmzf6z6v5zqnhss8qawmm90cc9x"; depends=[bigrquery ComplexHeatmap DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 httr IRanges magrittr rjson S4Vectors shiny SummarizedExperiment]; }; - BiocParallel = derive2 { name="BiocParallel"; version="1.16.6"; sha256="1iv2xzm6lz371z0llhcxl8hmc5jfw0hjwnf1qc8d7jk9djgcaks2"; depends=[BH futile_logger snow]; }; - BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.0.3"; sha256="0mfxcabkdxsbkk1j3kncn5jhm08b0zi1jjsz7ajkhhw7c9w85gvm"; depends=[BiocManager dplyr DT gh htmltools htmlwidgets httr igraph jsonlite readr rex rvest stringr tibble tidyr xml2]; }; - BiocSklearn = derive2 { name="BiocSklearn"; version="1.4.0"; sha256="08a1jaxhqaxqrhbgkm11isi3d83sbpfjh02nki7rbwffcjim3fy0"; depends=[BBmisc knitr reticulate SummarizedExperiment]; }; - BiocStyle = derive2 { name="BiocStyle"; version="2.10.0"; sha256="01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31"; depends=[BiocManager bookdown knitr rmarkdown yaml]; }; - BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.8.0"; sha256="1wpihkd5j3v2qls2n67dwydvxk2mjb6cx27if5vxh7v99x3vph04"; depends=[BiocStyle bookdown devtools git2r httr knitr rmarkdown rstudioapi stringr]; }; - Biostrings = derive2 { name="Biostrings"; version="2.50.2"; sha256="16cqqc8i6gb0jcz0lizfqqxsq7g0yb0ll2s9qzmb45brp07dg8f7"; depends=[BiocGenerics IRanges S4Vectors XVector]; }; - BitSeq = derive2 { name="BitSeq"; version="1.26.1"; sha256="19z785hbgal81vywgvxbyr8k99fvyn434f1pzsh67rm8w47gnmv9"; depends=[IRanges Rsamtools S4Vectors zlibbioc]; }; - BrainStars = derive2 { name="BrainStars"; version="1.26.0"; sha256="0ki6jm4ycm3dzdv5fhv7nflpy4zifx364mlq02fq701hjgm36fwf"; depends=[Biobase RCurl RJSONIO]; }; - BridgeDbR = derive2 { name="BridgeDbR"; version="1.16.1"; sha256="09xfcbf9ix25zm7djp306iz6vyx73giamslsndzzpsgcbmg0wadb"; depends=[RCurl rJava]; }; - BrowserViz = derive2 { name="BrowserViz"; version="2.4.0"; sha256="09rdysgw9dxk5qpg7sxw0w3rpcrqjdibvwj3chcpgk6kv5ysfwgj"; depends=[BiocGenerics httpuv jsonlite]; }; - BubbleTree = derive2 { name="BubbleTree"; version="2.12.0"; sha256="0g40mh7b6awdvhqy70mamb33p2qn93z64p770phr8ccyi91dd93j"; depends=[Biobase BiocGenerics BiocStyle biovizBase dplyr e1071 GenomicRanges ggplot2 gridExtra gtable gtools IRanges limma magrittr plyr RColorBrewer WriteXLS]; }; - BufferedMatrix = derive2 { name="BufferedMatrix"; version="1.46.0"; sha256="0llfqpjbb4q8m6gjx0jq6nxpylqi7r715srkk41rx1bjs0ykbksg"; depends=[]; }; - BufferedMatrixMethods = derive2 { name="BufferedMatrixMethods"; version="1.46.0"; sha256="089wh0rvcvagfx1v3y3r2k8ncm14j9cls2yaywlza8damlz4fbb5"; depends=[BufferedMatrix]; }; - CAFE = derive2 { name="CAFE"; version="1.18.0"; sha256="0x3hn8c7p3p5m215kjbcgxak4c7807ikxs7k4b1immqzz8m5rfqd"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; }; - CAGEfightR = derive2 { name="CAGEfightR"; version="1.2.0"; sha256="1xnsbwjnirhh4dsfpxc8f16wxnvabr07yzbbizxqyna0h3hr61s0"; depends=[assertthat BiocGenerics BiocParallel GenomeInfoDb GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges grr Gviz InteractionSet IRanges Matrix Matrix_utils pryr rtracklayer S4Vectors SummarizedExperiment]; }; - CAGEr = derive2 { name="CAGEr"; version="1.24.0"; sha256="1vin6inq3rlj365bhxpx28rp28isi7967r1plpdyi2lwx2f2d4im"; depends=[beanplot BiocGenerics BiocParallel BSgenome data_table DelayedArray formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; - CALIB = derive2 { name="CALIB"; version="1.48.0"; sha256="118sy35hi5p1nkm7ygh4pn7m3855vhywsj66j0v74iis00blpv1z"; depends=[limma]; }; - CAMERA = derive2 { name="CAMERA"; version="1.38.1"; sha256="0mz6ahdyv3334v8fbqan8i6plkyz20smfq4p7hjphcybjfxxsizv"; depends=[Biobase graph Hmisc igraph RBGL xcms]; }; - CAMTHC = derive2 { name="CAMTHC"; version="1.0.0"; sha256="1n2hn4snmlfrwr5c9di214sqvgmmihyxnbzbf0n2hx99rrjlzvpg"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF pcaPP rJava SummarizedExperiment]; }; - CATALYST = derive2 { name="CATALYST"; version="1.6.7"; sha256="08dfjyay6b2ja9jykpzfycnyd9y20pysmshbw5vd5fb69mcjii8q"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus data_table dplyr drc DT flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra htmltools limma magrittr matrixStats nnls plotly purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater shiny shinyBS shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; }; - CAnD = derive2 { name="CAnD"; version="1.14.0"; sha256="0h1ry4z9g4daga7jqnm2wh631d4yzp738yf1vpxvf2d3f2qci8dv"; depends=[ggplot2 reshape]; }; - CCPROMISE = derive2 { name="CCPROMISE"; version="1.8.0"; sha256="1kpz5cwx0bk55w8paldvmvmgprxsrgyqf8r3vxns136ksv1a1zhx"; depends=[Biobase CCP GSEABase PROMISE]; }; - CEMiTool = derive2 { name="CEMiTool"; version="1.6.11"; sha256="1wypc50kq5y6bnwrfkqz50wckb65bxw294472hnzk4vmaiyymvck"; depends=[clusterProfiler data_table dplyr DT ff ffbase fgsea GeneOverlap ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr limma matrixStats network plyr pracma RColorBrewer rmarkdown scales sna stringr tidyr WGCNA]; }; - CFAssay = derive2 { name="CFAssay"; version="1.16.1"; sha256="1l8l157df163cy4i6qc1q95x1pqc80y7dp5jf9nfssgbkls2dpfv"; depends=[]; }; - CGEN = derive2 { name="CGEN"; version="3.18.0"; sha256="0p0c05axpj94v3gksy065244vlxh9q4g6ifv07jxrvl23ji4bnyi"; depends=[mvtnorm survival]; }; - CGHbase = derive2 { name="CGHbase"; version="1.42.0"; sha256="0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"; depends=[Biobase marray]; }; - CGHcall = derive2 { name="CGHcall"; version="2.44.0"; sha256="1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"; depends=[Biobase CGHbase DNAcopy impute snowfall]; }; - CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.36.0"; sha256="1j92x5dyxp6hjj87g1hgw5q8fd4k2q5rb97ir47xkalkcskg0ddh"; depends=[Biobase CGHbase CGHcall]; }; - CGHregions = derive2 { name="CGHregions"; version="1.40.0"; sha256="04j87bd2ygda6np72vs1bx857y5mbaga19ky6pgyxv9lahi62xyw"; depends=[Biobase CGHbase]; }; - CHARGE = derive2 { name="CHARGE"; version="1.2.0"; sha256="0230pvgsf775lq4n9cpxb95bqq438f4z0wx9mmbj4yir8bljy0mk"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats plyr SummarizedExperiment]; }; - CHRONOS = derive2 { name="CHRONOS"; version="1.10.1"; sha256="03j4qcak7bpgw80gzxb2mj6k134jqp5frzd5ls6b5290lkknj720"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl XML]; }; - CINdex = derive2 { name="CINdex"; version="1.10.0"; sha256="0c4p3v9a0njf28gdhvdbnydlhjgpnwzakhnvkvngs3mhbwpy9ih5"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; }; - CMA = derive2 { name="CMA"; version="1.40.0"; sha256="1v77yiqmvd90pxbs64xfpglwy006w88b4zrb5rk90r0vasnvdl5n"; depends=[Biobase]; }; - CNAnorm = derive2 { name="CNAnorm"; version="1.28.0"; sha256="050yhjqqqm5kqjpw2ar8gf0yjqzmr0xzwa0c10dfry6hml63d6m3"; depends=[DNAcopy]; }; - CNEr = derive2 { name="CNEr"; version="1.18.1"; sha256="1h8p7fibhyn7117qwjrl9f7y5cczv50qihzfd83pj76z5k5ylzry"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; }; - CNORdt = derive2 { name="CNORdt"; version="1.24.1"; sha256="1frvylz88524nac6wk4r9j0wfvywzf8dq998pfnl9km7q4f888i0"; depends=[abind CellNOptR]; }; - CNORfeeder = derive2 { name="CNORfeeder"; version="1.22.1"; sha256="1h6l5lq0xqzh4y7mrq2kvnj3gpv3ni9c8qdn1wnrsa8q0i8xcs9v"; depends=[CellNOptR graph]; }; - CNORfuzzy = derive2 { name="CNORfuzzy"; version="1.24.0"; sha256="140a42s9h7li597y45z3dmb8y1nf53xxl7vnipi8k0rgcix465dl"; depends=[CellNOptR nloptr]; }; - CNORode = derive2 { name="CNORode"; version="1.24.1"; sha256="04zf8cidpw1f7zdyd7ns4x84jpdvbvkg5zifw0w1hri70n8yl8r4"; depends=[CellNOptR genalg]; }; - CNPBayes = derive2 { name="CNPBayes"; version="1.12.0"; sha256="1vlbnlr63vv2s5nyndiqcb3kh737apswqqygwqn5pz6973nvlcl3"; depends=[BiocGenerics coda combinat dplyr GenomeInfoDb GenomicRanges ggplot2 gtools IRanges magrittr matrixStats mclust purrr RColorBrewer Rcpp reshape2 S4Vectors scales SummarizedExperiment tibble tidyr]; }; - CNTools = derive2 { name="CNTools"; version="1.38.0"; sha256="038nbqgjahc9b646s9avxgccxz1qsly8vqj84dzqwgpyvx7hxqpi"; depends=[genefilter]; }; - CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.14.0"; sha256="0fh94iv66li3zsnadxyxwzhs1jcz63vpmc6khp0srac2kzvc1kcs"; depends=[exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; - CNVrd2 = derive2 { name="CNVrd2"; version="1.20.0"; sha256="10141xwwkzrkgkad8x5y1ha779b47vp7b2qk32hgw19ys4lraj79"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; }; - CNVtools = derive2 { name="CNVtools"; version="1.76.0"; sha256="0xmqqq3j3xxm1pnldw6l3vnww9lfjlghvkrfzfbwxmq8gkxmyzji"; depends=[survival]; }; - COCOA = derive2 { name="COCOA"; version="1.0.2"; sha256="1y7y3zjzpljfqdhal87xir9z50xg8p96n0yx98qz1lqairbdkcpj"; depends=[Biobase BiocGenerics ComplexHeatmap data_table GenomicRanges ggplot2 IRanges MIRA S4Vectors tidyr]; }; - CODEX = derive2 { name="CODEX"; version="1.14.1"; sha256="0k8x1k1m11r69dbzrxqx9b1pqi5x3pf1cxyf5j4hz7qsk8fncsnq"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; }; - COHCAP = derive2 { name="COHCAP"; version="1.28.1"; sha256="1zn0skpi7h2nws877bj1van3358cmh88prvj9691kwcwj47h1zny"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; }; - COMPASS = derive2 { name="COMPASS"; version="1.20.1"; sha256="0jhi9dhyfdnc9fmybj2q9vcshkikn9rhcdzfr9hi2jizh7pa4w8z"; depends=[abind BiocStyle clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; }; - CONFESS = derive2 { name="CONFESS"; version="1.10.1"; sha256="0w32gz85balsy88q17g303nbn1c8b2gp7cxqqx9vwsvzvd7d78p1"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; }; - CORREP = derive2 { name="CORREP"; version="1.48.0"; sha256="1jg2j61f3cz7c7xf9wm96gvl5ykc8vbb14vhrbcmibjzxf7zfd1r"; depends=[e1071]; }; - COSNet = derive2 { name="COSNet"; version="1.16.0"; sha256="1bw979xx2g17p3pisvbvskv8xq26pqrn9lcq8jh6av8m592b90gp"; depends=[]; }; - CRISPRseek = derive2 { name="CRISPRseek"; version="1.22.1"; sha256="0lpvq8bjjcqz6zn4dnlxjs7vynqmq0cy7jcg9nypmrgjcn0pgc6l"; depends=[BiocGenerics BiocParallel Biostrings BSgenome data_table hash IRanges S4Vectors seqinr]; }; - CRImage = derive2 { name="CRImage"; version="1.30.0"; sha256="11pzsg1bjsg12ad4vrp8slzr53nynb93i6j9zqgcvzh0dl004ss9"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; }; - CSAR = derive2 { name="CSAR"; version="1.34.0"; sha256="0r8rqgz95bk7piwhgh4ljr8zvnvgxz7w7h7cjwqywsg259sf54sj"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; - CSSP = derive2 { name="CSSP"; version="1.20.0"; sha256="06yzh3kgxwg512ycncxj0ann0m918wyij6xwyz0kskln2vsq84jm"; depends=[]; }; - CTDquerier = derive2 { name="CTDquerier"; version="1.2.0"; sha256="0lpf49gdp5bj83sqv3hnaa4l3lib112m0h4k8zbjvjgkw6inn9wb"; depends=[BiocFileCache ggplot2 gridExtra igraph rappdirs RCurl S4Vectors stringdist stringr]; }; - CVE = derive2 { name="CVE"; version="1.8.0"; sha256="0fjisya8iipc4ghslaw3di62mmi93v34w1c39a57mqk5gng2pzr7"; depends=[ape ConsensusClusterPlus ggplot2 gplots jsonlite plyr RColorBrewer shiny tidyverse WGCNA]; }; - CancerInSilico = derive2 { name="CancerInSilico"; version="2.2.1"; sha256="1irbgmwfpsjyl8an06qs7x0nh4jrljhklkm3ak2sd13fgg88j73s"; depends=[BH Rcpp]; }; - CancerMutationAnalysis = derive2 { name="CancerMutationAnalysis"; version="1.24.0"; sha256="10768i5ijrwr7hcshk60r5w6ckqacqk3f9jhs3qkm2ic0g47vgwb"; depends=[AnnotationDbi limma qvalue]; }; - CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.8.0"; sha256="1cg1im5p53n5afz0pzfg7l7wp6lm8cl0dr5x8di62va71n9qdk77"; depends=[cluster ConsensusClusterPlus iCluster impute limma NMF sigclust SNFtool survival]; }; - Cardinal = derive2 { name="Cardinal"; version="2.0.4"; sha256="1119r8993msnldilkp7qv3mslbbv3bfypidnm52cl9ybznlj757r"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr matter ProtGenerics S4Vectors signal sp]; }; - Category = derive2 { name="Category"; version="2.48.1"; sha256="18rsxlwa1l06i635cnznb9b2zssqcgb71pihky29gl2gwp7a654b"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; }; - CausalR = derive2 { name="CausalR"; version="1.14.1"; sha256="0v4k8nbxjf9q092d029pvpy1f29zby8j60b89x559cr2m78zw870"; depends=[igraph]; }; - CellMapper = derive2 { name="CellMapper"; version="1.8.0"; sha256="0qaw5pf3lgdkfcki0z2hp9g0b07j2khinwh9r0ajvji4j7hiwrw5"; depends=[S4Vectors]; }; - CellNOptR = derive2 { name="CellNOptR"; version="1.28.1"; sha256="0ygpryc9sbj031lznlmhr23vgdqgyyyzjx6zbyv2nx703x9vrj3l"; depends=[ggplot2 graph hash RBGL RCurl Rgraphviz XML]; }; - CellScore = derive2 { name="CellScore"; version="1.2.0"; sha256="0rc77c7z9nsid22yrdny6kd4yg6031njznsdvk6n82mv2sadk51b"; depends=[Biobase gplots lsa RColorBrewer squash]; }; - CellTrails = derive2 { name="CellTrails"; version="1.0.1"; sha256="1x64c4fdwlbf57s4s6zjvpjy8jga7sz790gs6ll1d79smsw3ahql"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; }; - CexoR = derive2 { name="CexoR"; version="1.20.0"; sha256="1pwjq3r7l9hinab38g2v5sjrnbhxva1jfjvh20wh75l2hzfjs62j"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; }; - ChAMP = derive2 { name="ChAMP"; version="2.12.4"; sha256="197b3k61panvxw0vxf8qjj8l86q95mf9al055scpcf7sc6xwz0db"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel FEM GenomicRanges globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva kpmt limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; }; - ChIC = derive2 { name="ChIC"; version="1.2.0"; sha256="190jc1k318bk1xh93h726bxl0711qzn672lri3lwsrbjm76w8m1g"; depends=[BiocGenerics caret caTools ChIC_data GenomicRanges IRanges progress S4Vectors spp]; }; - ChIPComp = derive2 { name="ChIPComp"; version="1.12.0"; sha256="1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; }; - ChIPQC = derive2 { name="ChIPQC"; version="1.18.2"; sha256="0khm2y36f92zpwqcqrd8jkrsbgfcir70dwi8zk7pq0hpbpnpl0bm"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; - ChIPSeqSpike = derive2 { name="ChIPSeqSpike"; version="1.2.1"; sha256="0cy2099pc3vcjw47xigiq7qs8czfgaizlqyb5hy4j1lpr5c8qpia"; depends=[BiocGenerics corrplot GenomicRanges ggplot2 IRanges LSD Rsamtools rtracklayer S4Vectors seqplots stringr]; }; - ChIPXpress = derive2 { name="ChIPXpress"; version="1.26.0"; sha256="1b5ss7s8chjm8zgpxkwmghgf2dh1xn225y1qfad838gs0d2rmd5h"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; }; - ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.4.0"; sha256="115ycr6s5lb9888sz9xxdsip22vnbj1gfavrm61ks12rqf0ch2b6"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; }; - ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.6.0"; sha256="1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; - ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.16.1"; sha256="1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager biomaRt Biostrings BSgenome DBI DelayedArray ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GO_db graph idr IRanges limma matrixStats multtest RBGL regioneR Rsamtools S4Vectors seqinr SummarizedExperiment VennDiagram]; }; - ChIPseeker = derive2 { name="ChIPseeker"; version="1.18.0"; sha256="08d8m4svnyki4pg0mwy17p7wi7anw9ba347ck36x8lzbjb8xcmwg"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene UpSetR]; }; - ChIPseqR = derive2 { name="ChIPseqR"; version="1.36.0"; sha256="0m9xrb1aksmrh0zm6sa0nklwbn0mydz70dydhycfknv96l0rrxqn"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; }; - ChIPsim = derive2 { name="ChIPsim"; version="1.36.0"; sha256="096dlqis3mcbhz837ys0n9yimgrh5fw5cpx16kjg9hfs48253nxs"; depends=[Biostrings IRanges ShortRead XVector]; }; - ChemmineOB = derive2 { name="ChemmineOB"; version="1.20.0"; sha256="037j2hwmrbk0k2abygkrkmdshsh1c434dj0iqdmqsnbyyvv34q2m"; depends=[BH BiocGenerics Rcpp zlibbioc]; }; - ChemmineR = derive2 { name="ChemmineR"; version="3.34.1"; sha256="0pzvwaycvz61156ypqf24a42nhhmlhx2hccyra3g0jm97adm69iw"; depends=[base64enc BH BiocGenerics DBI digest DT ggplot2 gridExtra png Rcpp RCurl rjson rsvg]; }; - Chicago = derive2 { name="Chicago"; version="1.10.1"; sha256="0m3fv8qgxaysnc02ndmk0bx0rk8ly02nivhn0hzgdh6vbrgqgzdr"; depends=[data_table Delaporte Hmisc MASS matrixStats]; }; - ChromHeatMap = derive2 { name="ChromHeatMap"; version="1.36.0"; sha256="0ah133mzrwxdhfazpw41h2h0bz555al9yjlyhahm249d4wbdzr8d"; depends=[annotate AnnotationDbi Biobase BiocGenerics GenomicRanges IRanges rtracklayer]; }; - ClassifyR = derive2 { name="ClassifyR"; version="2.2.6"; sha256="1crw7qn6c4h1gx324wgyzjh1z49zb5c43jrl4kiqva8cmds11h46"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; }; - Clomial = derive2 { name="Clomial"; version="1.18.1"; sha256="0m1s90syqm6ll61ii1zms1phrycfngl7r2s7d9lxck19imdg8svz"; depends=[matrixStats permute]; }; - Clonality = derive2 { name="Clonality"; version="1.30.0"; sha256="0nhlrzy6z8kcfghw3ciy4ymbnmwb7y68bb1ikz7fxi4d5pywzm03"; depends=[DNAcopy]; }; - ClusterJudge = derive2 { name="ClusterJudge"; version="1.4.0"; sha256="1yi3hcbk8ka9krrc2q8jv0sq5szpwp3iw3wnn8x9ibn1qyimzwc5"; depends=[httr infotheo jsonlite lattice latticeExtra]; }; - ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.10.0"; sha256="1jwl2v9qja11rrdllqkc2hlqiirzcav7s6343d66qaajq02iagzj"; depends=[pracma princurve RColorBrewer scatterplot3d]; }; - CoCiteStats = derive2 { name="CoCiteStats"; version="1.54.0"; sha256="0ar66vhlw6zhrrf6bpd82hqwxh4g6apic56mx9xir40302ikc1h4"; depends=[AnnotationDbi org_Hs_eg_db]; }; - CoGAPS = derive2 { name="CoGAPS"; version="3.2.40"; sha256="05d8av4q3nvdyf976i9ninb5h3lxk3nr7b327jj7v9qvg9hlmzqh"; depends=[BiocParallel cluster data_table gplots RColorBrewer Rcpp rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; }; - CoRegNet = derive2 { name="CoRegNet"; version="1.20.0"; sha256="1z8ihzn4i9zzn7cw2376j92cx1b0w543vr9f47xkhnsj871f2v6c"; depends=[arules igraph shiny]; }; - CompGO = derive2 { name="CompGO"; version="1.18.0"; sha256="1hzps1isfpdmcxdlpfqhanl0qafydgsgjc5xqxgd8zvib4zb28za"; depends=[GenomicFeatures ggplot2 pathview pcaMethods RDAVIDWebService reshape2 Rgraphviz rtracklayer TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="1.20.0"; sha256="0s01dzcfj1lmpqfpsbqw7r4858krfzy499lz4cwx4fq3mbyvy2aj"; depends=[circlize colorspace GetoptLong GlobalOptions RColorBrewer]; }; - ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.46.0"; sha256="00q1xbi7znfvvcqb1szqlw7zh4vvpf1si80k5zylys512ixg9sns"; depends=[ALL Biobase cluster]; }; - CopywriteR = derive2 { name="CopywriteR"; version="2.14.1"; sha256="1hbiw0m9hmx4na9v502pxf8y5wvxzr68r4d3fqr2755gxx86qck6"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; }; - CorMut = derive2 { name="CorMut"; version="1.24.0"; sha256="1p4xj8f5hf1z31943s51inc0mc28bphzy5qs4ay2nccwshbypq0l"; depends=[igraph seqinr]; }; - Cormotif = derive2 { name="Cormotif"; version="1.28.0"; sha256="0lb691mvr9zim7z5yplncmlzyr799jym1wvrgfm1diqjz2daixai"; depends=[affy limma]; }; - CountClust = derive2 { name="CountClust"; version="1.10.1"; sha256="1b129r97wv3gm25pk3ccg5bmp2476jyhz1pphapqlrb1im3fixq6"; depends=[cowplot flexmix ggplot2 gtools limma picante plyr reshape2 slam SQUAREM]; }; - CoverageView = derive2 { name="CoverageView"; version="1.20.1"; sha256="164lla4v6ll0kqzapm3kmwz39k5shl0cwwashpbwiixrrxhcy8d2"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; - CrispRVariants = derive2 { name="CrispRVariants"; version="1.10.1"; sha256="0n1mw3ybbdaybbcms12cj4vy21wahq5srny0qnbxjlzyl1zjbpr0"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; }; - CytoDx = derive2 { name="CytoDx"; version="1.2.1"; sha256="05apvaf4dmkdfsp2aary14i7znjyzk0k6rqcbsk6m98fkp3d9r8b"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; - CytoML = derive2 { name="CytoML"; version="1.8.1"; sha256="18isg4kjdn975q8vpziisnyxj1jxm4lkq7hi9jy4imf7bffc234i"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; }; - DAPAR = derive2 { name="DAPAR"; version="1.14.5"; sha256="0s09y5kpivaichzmfchksaayxchdmqgldcba0waxfxzsapwfb9p1"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; }; - DART = derive2 { name="DART"; version="1.30.0"; sha256="0dxwy95p43c0shx30y95sj1pl64kqkh2bsnj680q196zgyg937s6"; depends=[igraph]; }; - DBChIP = derive2 { name="DBChIP"; version="1.26.0"; sha256="1wk8nvfcfhsymhbi6id0kd1jzcykh6hhikl2040g0v6gi252gv2v"; depends=[DESeq edgeR]; }; - DChIPRep = derive2 { name="DChIPRep"; version="1.12.0"; sha256="1avcjr7r54grh3yn5pjbzji3syc8vvah9as7asv3cwmyqzaya4r0"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; }; - DECIPHER = derive2 { name="DECIPHER"; version="2.10.2"; sha256="191s87akdjfqdbq4xvz42s10fpq3w7jm6962ndhcibm8kzgz241r"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; }; - DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.2.0"; sha256="1a4m4xs8dd0459vh5bhi96w6vchmqgap3snrj8x6jjlpvkkhwl8l"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; }; - DEDS = derive2 { name="DEDS"; version="1.56.0"; sha256="1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"; depends=[]; }; - DEFormats = derive2 { name="DEFormats"; version="1.10.1"; sha256="01zhxi2gpbdbfxxh8myq7930rk2zcwdchdj7xa2p4hrl2mzhr7c8"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; }; - DEGraph = derive2 { name="DEGraph"; version="1.34.0"; sha256="1vrv3lkda2dhcb9ig38xv0bvnk68z9bpsxr4846fq31dvxp6b5al"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; }; - DEGreport = derive2 { name="DEGreport"; version="1.18.1"; sha256="0fzxlx1bqcggya5bf7s0w2g368hzcjamq33z8mfj23c1d4dm0jmy"; depends=[Biobase BiocGenerics broom circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr lasso2 logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; }; - DEGseq = derive2 { name="DEGseq"; version="1.36.1"; sha256="1p4ldk2wagsnjbxrq3s6fa3l6phqp77hjwv43gbdsh7ph8rzd33g"; depends=[qvalue]; }; - DEP = derive2 { name="DEP"; version="1.4.1"; sha256="0adwq2lgnqf29p1ylq4mvqx16g45bcs79nhsknkl9ph3i7g2slgj"; depends=[assertthat circlize cluster ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; }; - DEScan2 = derive2 { name="DEScan2"; version="1.2.1"; sha256="0l47x2yrxcyj0mfz972acyw2v9n08ib859jb3v9qasrbw04qnvwk"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; }; - DESeq = derive2 { name="DESeq"; version="1.34.1"; sha256="0bpiixczbhlyaiinpbl6xrpmv72k2bq76bxnw06gl35m4pgs94p2"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; }; - DESeq2 = derive2 { name="DESeq2"; version="1.22.2"; sha256="0n5ah84mxn87p45drzy0wh2yknmzj1q5i6gv0v9vgg1lj7awb91r"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; }; - DEXSeq = derive2 { name="DEXSeq"; version="1.28.3"; sha256="1wsj1kqfrakmjnlplxmrv17r2spzcdkmwdkhggyjbf8mdhqs3w16"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; }; - DEqMS = derive2 { name="DEqMS"; version="1.0.1"; sha256="1869msy07xh9y0yr0mskrkpmzmf4x3vdarvn8wi78hk1scq1zk71"; depends=[ggplot2 limma]; }; - DEsingle = derive2 { name="DEsingle"; version="1.2.1"; sha256="0w3b7pz04l60hrbw4k7rkp4xmf8hzxca7pgrjyalf946z6yvky0s"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; - DEsubs = derive2 { name="DEsubs"; version="1.8.1"; sha256="0whs5q02lgis04zyf6abd9b5phv3bw508k4ngp197ka02pbpvxxz"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; }; - DFP = derive2 { name="DFP"; version="1.40.0"; sha256="12kb7cjsfdscdwanjbzvwgp1ra0kmijrp1qyx87sxsk4hxk236ml"; depends=[Biobase]; }; - DMCHMM = derive2 { name="DMCHMM"; version="1.4.0"; sha256="12jn77dxbcbzbfdsy4l1vycf68bnw2wdhrwnnjc3829arcz2mkph"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; }; - DMRScan = derive2 { name="DMRScan"; version="1.8.0"; sha256="0vwmkw3abs0v8z49qdkrqxia0kn5i3pl7yqzv42l5xz7d2498s7q"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; }; - DMRcaller = derive2 { name="DMRcaller"; version="1.14.2"; sha256="13x59irimrjff2pa9vw9yw341xm13wxfzhrfv4ylw60jpzbz71i1"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; }; - DMRcate = derive2 { name="DMRcate"; version="1.18.0"; sha256="0930rrz2aps91mcqihap9830km9x7if6vgpvjplmacvs1x2k3wyh"; depends=[DMRcatedata DSS GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors]; }; - DMRforPairs = derive2 { name="DMRforPairs"; version="1.18.0"; sha256="11gbnxlkgkx9ynmslxvinfnq39rpg392zbff6g36fd5nsr3dppxd"; depends=[GenomicRanges Gviz R2HTML]; }; - DNABarcodes = derive2 { name="DNABarcodes"; version="1.12.0"; sha256="0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"; depends=[BH Matrix Rcpp]; }; - DNAcopy = derive2 { name="DNAcopy"; version="1.56.0"; sha256="04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"; depends=[]; }; - DNAshapeR = derive2 { name="DNAshapeR"; version="1.10.0"; sha256="1rplgi36jn33npihhmk0vdsiali814y5v1wz5fdna3k9b47id6b6"; depends=[Biostrings fields GenomicRanges Rcpp]; }; - DOQTL = derive2 { name="DOQTL"; version="1.18.0"; sha256="0ligqm4l2x5dz794djapri770j27rhibhdzc48y980768gjpkm8k"; depends=[annotate annotationTools Biobase BiocGenerics biomaRt BSgenome_Mmusculus_UCSC_mm10 corpcor doParallel foreach fpc GenomicRanges hwriter IRanges iterators mclust QTLRel rhdf5 Rsamtools RUnit VariantAnnotation XML]; }; - DOSE = derive2 { name="DOSE"; version="3.8.2"; sha256="1gh7dhvfc71kawxcfx8xqlir7mwvg5mmz4lqrdrvw5knvi2h3mfa"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2 S4Vectors]; }; - DRIMSeq = derive2 { name="DRIMSeq"; version="1.10.1"; sha256="021xzx7ndvjdahi715qvq2xxnnhdsn9h8g6imps5ls3qmk5024d2"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; }; - DSS = derive2 { name="DSS"; version="2.30.1"; sha256="0m18793vqaqamx3rj3pwrirc7ygmmg4774il8d59qmwinlppyxqw"; depends=[Biobase bsseq DelayedArray]; }; - DTA = derive2 { name="DTA"; version="2.28.0"; sha256="1gsc6sbi1awi92w1wnqddybz2n2n8f8pvsg95sp90xp11sjrnvvx"; depends=[LSD scatterplot3d]; }; - DaMiRseq = derive2 { name="DaMiRseq"; version="1.6.2"; sha256="0kllq3wndg7p96lqls4xsqdnhrwryry96qxbz5myvdrzywmfppkv"; depends=[arm caret corrplot DESeq2 e1071 EDASeq edgeR FactoMineR FSelector ggplot2 Hmisc ineq kknn limma lubridate MASS pheatmap pls plsVarSel randomForest RColorBrewer reshape2 RSNNS SummarizedExperiment sva]; }; - DeMAND = derive2 { name="DeMAND"; version="1.12.0"; sha256="06hip99jzi5z89v1mprmqxrziv1zf6lysmg6ixsxaq8f0l9x2m38"; depends=[KernSmooth]; }; - DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.24.0"; sha256="1j5mlnx0n3xn2agnp2wwdbyyf36lh277giapz0sknlnpfdhzc4jn"; depends=[ggplot2 limSolve pcaMethods]; }; - DeepBlueR = derive2 { name="DeepBlueR"; version="1.8.1"; sha256="0vsyndijwax7za0kfp51db73b74blj5hd67jar2icp9fsl02x10a"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; }; - DelayedArray = derive2 { name="DelayedArray"; version="0.8.0"; sha256="0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f"; depends=[BiocGenerics BiocParallel IRanges matrixStats S4Vectors]; }; - DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.4.0"; sha256="03fk2avl1vyjv2wslczkc82qr0zmp1ra8iimd47pbmnnm839ly4w"; depends=[BiocParallel DelayedArray HDF5Array IRanges Matrix matrixStats S4Vectors]; }; - DiffBind = derive2 { name="DiffBind"; version="2.10.0"; sha256="0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"; depends=[amap BiocParallel DESeq2 dplyr edgeR GenomicAlignments GenomicRanges ggplot2 ggrepel gplots IRanges lattice limma locfit RColorBrewer Rcpp Rsamtools S4Vectors SummarizedExperiment systemPipeR zlibbioc]; }; - DiffLogo = derive2 { name="DiffLogo"; version="2.6.0"; sha256="1an8c2h0vsy8x3q90bgy7gfigz11k460gpi4wlyj6gq8h6bd1fmy"; depends=[cba]; }; - Director = derive2 { name="Director"; version="1.8.0"; sha256="0xzds7gi9bp6hp8dpw9c4ls6b1rcfk4w4my1wacf0z9hnwpd60r3"; depends=[htmltools]; }; - DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.24.1"; sha256="0vazfjzqy78p5g7dnv30lbqbj4bhq4zafd2wh6gdwy2il1fd78xa"; depends=[BiocGenerics IRanges S4Vectors]; }; - DominoEffect = derive2 { name="DominoEffect"; version="1.2.1"; sha256="0lb3s9lzscnqvs3vq6ah1fib5day98y0fnh1gdjrf49fl8fkgx3r"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; - Doscheda = derive2 { name="Doscheda"; version="1.4.1"; sha256="01k95cbkwswpnzc53rszsnk55bx6xisdj5i8211h8zgwjsikryik"; depends=[affy calibrate corrgram d3heatmap drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; }; - DriverNet = derive2 { name="DriverNet"; version="1.22.0"; sha256="13yd9inyqkaw363m6apiyclkjpb3f5khbi0vwc90whi8q9wvsl8f"; depends=[]; }; - DropletUtils = derive2 { name="DropletUtils"; version="1.2.2"; sha256="0kxfhd7r2r1p0bmzps0d965l84fk63lc1shqywll5rx0scnhlcsw"; depends=[beachmat BiocParallel edgeR HDF5Array Matrix Rcpp rhdf5 Rhdf5lib S4Vectors SingleCellExperiment]; }; - DrugVsDisease = derive2 { name="DrugVsDisease"; version="2.24.2"; sha256="17x0smsb1kdj87ndw0dakqjb4c2dq2kkv5z8cs3i4x87hz56yrbd"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt cMap2data DrugVsDiseasedata GEOquery hgu133a_db hgu133a2_db hgu133plus2_db limma qvalue RUnit xtable]; }; - DupChecker = derive2 { name="DupChecker"; version="1.20.0"; sha256="114g9qx4v2lz521pndha3gk0cl2pq1jxqw1z9pzijgdj9lyj0jzv"; depends=[R_utils RCurl]; }; - DynDoc = derive2 { name="DynDoc"; version="1.60.0"; sha256="0k18f07mg7hg085l0pi5j6l8c04m5zd6jx3ha6cpjv6nd0m2lljw"; depends=[]; }; - EBImage = derive2 { name="EBImage"; version="4.24.0"; sha256="18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx"; depends=[abind BiocGenerics fftwtools htmltools htmlwidgets jpeg locfit png RCurl tiff]; }; - EBSEA = derive2 { name="EBSEA"; version="1.10.0"; sha256="1cbc21a6habvlslavdpn5v1nxkdhcpqp27fwg5y7hy9c8fqixqq0"; depends=[edgeR limma plyr]; }; - EBSeq = derive2 { name="EBSeq"; version="1.22.1"; sha256="1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"; depends=[blockmodeling gplots testthat]; }; - EBSeqHMM = derive2 { name="EBSeqHMM"; version="1.16.1"; sha256="12ml7qlsf7mnib88lm3q6lb3b34yfj4fgvp9c4vmfj62m88m17xw"; depends=[EBSeq]; }; - EBarrays = derive2 { name="EBarrays"; version="2.46.0"; sha256="1qz1z9v3dc0rdwm33v47avvgvqfxhbzw34idcxa1ap7ynx9c2sqs"; depends=[Biobase cluster lattice]; }; - EBcoexpress = derive2 { name="EBcoexpress"; version="1.26.0"; sha256="12hh2qvv0jfpsd8jz41jvzs605mccj35c5rz54697lgi7pdhwm4l"; depends=[EBarrays mclust minqa]; }; - EDASeq = derive2 { name="EDASeq"; version="2.16.3"; sha256="0559ph606ps2g9bwbl0a2knkcs5w581n9igngpjxvk5p56k24gb5"; depends=[AnnotationDbi aroma_light Biobase BiocGenerics BiocManager biomaRt Biostrings DESeq GenomicFeatures GenomicRanges IRanges Rsamtools ShortRead]; }; - EDDA = derive2 { name="EDDA"; version="1.20.1"; sha256="1psyzqsksmv9w3wwj8h4x1ywkkhk05z71afdxh57lhlh0y4vf6fw"; depends=[baySeq DESeq edgeR Rcpp ROCR snow]; }; - EGAD = derive2 { name="EGAD"; version="1.10.0"; sha256="1krwqspyw63zddgksvjvcidfzcxv9165p5dl3cgh1qsb3s427gla"; depends=[affy arrayQualityMetrics Biobase GEOquery gplots igraph impute limma MASS Matrix plyr RColorBrewer RCurl zoo]; }; - EGSEA = derive2 { name="EGSEA"; version="1.10.1"; sha256="0mimy2k7z3zyxksyax8xbl4yk48986b88x7vnfd2hlhibdcc1wg2"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; - ELBOW = derive2 { name="ELBOW"; version="1.18.1"; sha256="03jk906v6my6xf85ki2af8kd540bjjgn76xq4w38xc4dpfmpypla"; depends=[]; }; - ELMER = derive2 { name="ELMER"; version="2.6.3"; sha256="0x9v0z2b649nwnxaj9fkyrlgqdlxl4cmdm5wmpw8nzn6r432wfmi"; depends=[biomaRt circlize ComplexHeatmap DelayedArray doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr progress purrr readr reshape rmarkdown rtracklayer rvest S4Vectors stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; }; - EMDomics = derive2 { name="EMDomics"; version="2.12.0"; sha256="1savm8vh1cl8s9rw5jy341a6azx1d8pm0935jvl10ai0cs6q1f22"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; - ENCODExplorer = derive2 { name="ENCODExplorer"; version="2.8.0"; sha256="1836v5yj5rr3mvmsakbz5ccqc0h3dngipigszbrzcb2qb9m55gqf"; depends=[data_table dplyr DT jsonlite RCurl shiny shinythemes stringi stringr tidyr]; }; - ENVISIONQuery = derive2 { name="ENVISIONQuery"; version="1.30.0"; sha256="0ciilgg8mw4lzclfqqgfrc6crig15m418qfpcfk9s4ykcnjzzial"; depends=[rJava XML]; }; - ENmix = derive2 { name="ENmix"; version="1.18.2"; sha256="0fw4bwdi9yax34r50xclzxgjvq2g02ynz9pxyack20xycn3vn3zn"; depends=[doParallel foreach geneplotter impute MASS minfi preprocessCore SummarizedExperiment sva wateRmelon]; }; - ERSSA = derive2 { name="ERSSA"; version="1.0.1"; sha256="02g7kp2g3jxk9fy9fv2b1pkzc46067jwzq4p340w9c8ss8hrpqwh"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; - EasyqpcR = derive2 { name="EasyqpcR"; version="1.24.0"; sha256="1znawlhb44j21jhspn703d62pi1zknv1khklmsdlspn5db67wpin"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; }; - EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.10.0"; sha256="05n0984x77kvxjj80vx4sh7sz2v90wzf4vqsgbkn7wm45ly6x3h0"; depends=[]; }; - EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.0.1"; sha256="1z7rv5na9j9s95zx0l61ncxxv5a452p0xqfk7p1bdvl3x8ags4mq"; depends=[ggplot2 ggrepel]; }; - EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.12.0"; sha256="1bg3nrlsbfqvkrmwnwyilaniqzkaf2mirdjq58bwvz2022lwyzyg"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; - EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.12.1"; sha256="1jpmwlhdq99rgfk24pj0q72rnsi216i0yzwfc1v959v3p9132qq7"; depends=[AnnotationDbi BiocFileCache biocGraph BiocManager ComplexHeatmap DESeq2 EDASeq edgeR geneplotter GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma MASS pathview rappdirs ReportingTools Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; }; - EpiDISH = derive2 { name="EpiDISH"; version="1.4.1"; sha256="1qd4sglib4852igc1hxrrxsr108mil4mj4xxmf61fz45cxq0v262"; depends=[e1071 MASS quadprog]; }; - EventPointer = derive2 { name="EventPointer"; version="2.0.1"; sha256="0rx31xj13m340m1jfms4bzb5c6shmnh4rrzlv3qcjf6zfgh3n118"; depends=[affxparser cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges graph igraph IRanges limma MASS Matrix matrixStats nnls prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment]; }; - ExCluster = derive2 { name="ExCluster"; version="1.0.1"; sha256="0msz6fd81gyvix0jmh5mnpp4kfhkj6whl0q5l905abnncn2mfgpr"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; - ExiMiR = derive2 { name="ExiMiR"; version="2.24.0"; sha256="1nyyvznjvp9rrgzdp63klq3gah8w1qvgi4hkjf9icwc5liszr48j"; depends=[affy affyio Biobase limma preprocessCore]; }; - ExperimentHub = derive2 { name="ExperimentHub"; version="1.8.0"; sha256="1cxdkzkb4rkzsxcva9ich7p9ysdhijqrmacq1hvciyjrj0ql69w4"; depends=[AnnotationHub BiocGenerics BiocManager curl S4Vectors]; }; - ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.8.0"; sha256="09b64x0rh6j83cwvv0hbwydlcxyp032c8m3h20k8kylkpiyx3csq"; depends=[AnnotationHubData BiocCheck BiocGenerics BiocManager biocViews curl DBI ExperimentHub graph httr S4Vectors]; }; - ExpressionAtlas = derive2 { name="ExpressionAtlas"; version="1.10.0"; sha256="0ll7nhzqn25jwfkxg7cq156hhaiwdcm3fbbwy4891fb8pl4fj81a"; depends=[Biobase httr limma S4Vectors SummarizedExperiment XML xml2]; }; - ExpressionView = derive2 { name="ExpressionView"; version="1.34.0"; sha256="0rar2h2qfhqbxs4haxfm6gfvhdmlr1wdp8ashkxkpx97svd4pa3x"; depends=[AnnotationDbi bitops caTools eisa GO_db isa2 KEGG_db]; }; - FCBF = derive2 { name="FCBF"; version="1.0.1"; sha256="0j5znaw4v0mcz5jyqfm9v599sn472x73x6b9a2jxgynzhnvkbyiq"; depends=[ggplot2 gridExtra SummarizedExperiment]; }; - FELLA = derive2 { name="FELLA"; version="1.2.0"; sha256="09ljq7wfmm30h93k3ig4iqa7hq13lv961s446wiq0b5yi9s0y72g"; depends=[igraph KEGGREST Matrix plyr]; }; - FEM = derive2 { name="FEM"; version="3.10.0"; sha256="1cqba4j2ajyrjyqwp3q2f89afx74603m5pbsjgflc8zfpf498rgl"; depends=[AnnotationDbi BiocGenerics corrplot graph igraph impute limma marray Matrix org_Hs_eg_db]; }; - FGNet = derive2 { name="FGNet"; version="3.16.0"; sha256="12wv1r60nga4llvrx6blv9s6vlpcy22rz72qbf0ixpf16g16yc1x"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; }; - FISHalyseR = derive2 { name="FISHalyseR"; version="1.16.0"; sha256="0gkghipxbdpb3x55j9n583mi1z9cai8g8xcmyj5337dccx91lfag"; depends=[abind EBImage]; }; - FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.18.0"; sha256="0pw7r0w4ppv7jkjrx88a3bj85d96si1f0hqh7a5gpfb2593fd14k"; depends=[fda MASS]; }; - FamAgg = derive2 { name="FamAgg"; version="1.10.4"; sha256="0fkpcamaav0nlsg0j5dl6l7zfn9z6nrrm8avk8waxnxsghanbc6h"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; }; - FastqCleaner = derive2 { name="FastqCleaner"; version="1.0.0"; sha256="0v18zhzh8xd5b7828nnvlxc8gzwjgc9hnhznjd3w62js2yg9xv4l"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; }; - FindMyFriends = derive2 { name="FindMyFriends"; version="1.12.0"; sha256="1yyzqw9hzyxh2sjw8wj3xi5cvkcr9ssnahhwaqrln5zsiq72kn70"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; }; - FitHiC = derive2 { name="FitHiC"; version="1.8.0"; sha256="15xd8mz7660q4zr9p74mq1pqps4iz7pxp8f9ifn21gwg94aq1avn"; depends=[data_table fdrtool Rcpp]; }; - FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.14.1"; sha256="1j059f4hl41kwi6dcjmk8q0hlas7szlzgrvpjvjjcc466c074jhl"; depends=[jsonlite RCurl XML]; }; - FlowSOM = derive2 { name="FlowSOM"; version="1.14.1"; sha256="1s0yjg3jz4v7h60agwzchxa7xzmxszxawcqip4yhspihjpldiw0q"; depends=[BiocGenerics ConsensusClusterPlus flowCore flowUtils igraph tsne XML]; }; - FoldGO = derive2 { name="FoldGO"; version="1.0.2"; sha256="0wgb2zmn3ag2wj752r7gs066dpfdvwk6h87clz414iwp6gi480hq"; depends=[ggplot2 tidyr topGO]; }; - FourCSeq = derive2 { name="FourCSeq"; version="1.16.0"; sha256="1mknsjif4rv1wg5whv8dvkam2fblm2mnvj4qzv12ypnay0hdj8jq"; depends=[Biobase Biostrings DESeq2 fda GenomicAlignments GenomicRanges ggbio ggplot2 gtools LSD Matrix reshape2 Rsamtools rtracklayer SummarizedExperiment]; }; - FunChIP = derive2 { name="FunChIP"; version="1.8.0"; sha256="1b8a2hd5i4zwq28i7zwz8g3b9w2wgrhdrghr70z5n62cxdrbdwd9"; depends=[doParallel fda foreach GenomeInfoDb GenomicAlignments GenomicRanges RColorBrewer Rcpp Rsamtools shiny]; }; - FunciSNP = derive2 { name="FunciSNP"; version="1.26.0"; sha256="1l3p3s9l56ivgwzkixxr51n86s2p91rqayhz605iqpfpxyywyxzg"; depends=[Biobase BiocGenerics ChIPpeakAnno FunciSNP_data GenomicRanges ggplot2 IRanges plyr reshape Rsamtools rtracklayer S4Vectors scales snpStats TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; - GA4GHclient = derive2 { name="GA4GHclient"; version="1.6.0"; sha256="03jk92nrd8n34z0kb88qsv7pxwwrwy7vjhczxz4a9mqwsb2gv891"; depends=[BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite S4Vectors VariantAnnotation]; }; - GA4GHshiny = derive2 { name="GA4GHshiny"; version="1.4.0"; sha256="18g9bhn9wkmfw4f55lly97hf00f6ngh560b87nxyx0c9ls0a6wyg"; depends=[AnnotationDbi BiocGenerics dplyr DT GA4GHclient GenomeInfoDb GenomicFeatures openxlsx purrr S4Vectors shiny shinyjs shinythemes tidyr]; }; - GARS = derive2 { name="GARS"; version="1.2.0"; sha256="1i9dfh9g4sx40r8jdwiv81609jgpaby38hvrvgcf6bw06hip6da4"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; }; - GAprediction = derive2 { name="GAprediction"; version="1.8.1"; sha256="1aybcbaxbwfd9fd1ivkfmhwsm3w9237bf1kph40kdis4zhvf7g1d"; depends=[glmnet Matrix]; }; - GDCRNATools = derive2 { name="GDCRNATools"; version="1.2.1"; sha256="0gwf534xkdg9ajlmhaicpl51kyk74hy7inp83nq4l6gr238x0q85"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; - GDSArray = derive2 { name="GDSArray"; version="1.2.0"; sha256="1yjrdnkbgxdfs5i2s10idy3szc9p6fcq6mv246hbsibl6zxxlqlh"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; - GEM = derive2 { name="GEM"; version="1.8.0"; sha256="008y135dahsrbk2ik5b7hrsjkhg23cxmsfnbyggm000dap6j4a3w"; depends=[ggplot2]; }; - GENESIS = derive2 { name="GENESIS"; version="2.12.4"; sha256="0ij4cmh01khyqxvv5y5n3h53xhhlm5qj8ijcqqg5mp7byn9nzvvc"; depends=[Biobase BiocGenerics data_table dplyr foreach gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; - GENIE3 = derive2 { name="GENIE3"; version="1.4.3"; sha256="1wbgfmv2266djrl71cnhgs89ariw9fncf0kbmz3ps6rc4cm0cj77"; depends=[reshape2]; }; - GEOmetadb = derive2 { name="GEOmetadb"; version="1.44.0"; sha256="05iwq2qglkc3xdkvc1049m1mzyiw91dmfb41vkqbqkyw7jc4561h"; depends=[GEOquery RSQLite]; }; - GEOquery = derive2 { name="GEOquery"; version="2.50.5"; sha256="074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; }; - GEOsubmission = derive2 { name="GEOsubmission"; version="1.34.0"; sha256="1wiaik74yr84jppvq3hqijha2z4m3jr77q2k9zsr6kw0d82ianvw"; depends=[affy Biobase]; }; - GEWIST = derive2 { name="GEWIST"; version="1.26.0"; sha256="0gdq54rjfwlriv61sn0d9v08cfiz1p80p4asb13r05paa25w7vkm"; depends=[car]; }; - GGBase = derive2 { name="GGBase"; version="3.44.0"; sha256="023yzz4sin86fmkl2d0855mkn7iffhvinnz1hchx88f17rn8ysgz"; depends=[AnnotationDbi Biobase BiocGenerics digest genefilter GenomicRanges IRanges limma Matrix S4Vectors snpStats SummarizedExperiment]; }; - GGtools = derive2 { name="GGtools"; version="5.18.0"; sha256="1iqzqmcz8v4gmbcmxmla60848pmwlsbhrj9g8skxfclg7w21qx1m"; depends=[AnnotationDbi biglm Biobase BiocGenerics Biostrings bit data_table ff GenomeInfoDb GenomicRanges GGBase ggplot2 Gviz hexbin Homo_sapiens IRanges iterators reshape2 ROCR Rsamtools rtracklayer S4Vectors snpStats VariantAnnotation]; }; - GIGSEA = derive2 { name="GIGSEA"; version="1.0.0"; sha256="08q4askg07y6pz4j04rd4l1rralx22z4nfw6r2y8b79lcm6svawl"; depends=[locfdr MASS Matrix]; }; - GISPA = derive2 { name="GISPA"; version="1.6.0"; sha256="0xdqfv6ihn4qm1mv1xixyav921scvi406jz00n92jb7lwqm4aadw"; depends=[Biobase changepoint data_table genefilter GSEABase HH lattice latticeExtra plyr scatterplot3d]; }; - GLAD = derive2 { name="GLAD"; version="2.46.0"; sha256="0mj250k9q78z9s5xy2jra3lazv8nva6ngln8pqxdxhlcnrsrw0nk"; depends=[aws]; }; - GMRP = derive2 { name="GMRP"; version="1.10.1"; sha256="187h6fqy5rcrfb5wnvyg078bzxlb5fhbb4xs34r27pyj8xzbza9r"; depends=[diagram GenomicRanges plotrix]; }; - GOFunction = derive2 { name="GOFunction"; version="1.30.0"; sha256="1rsx1nkxyxd4dv4bn4mm1wyq6l0qn7a1gm60j03y9h4idp3hrgr8"; depends=[AnnotationDbi Biobase DBI GO_db graph Rgraphviz SparseM]; }; - GOSemSim = derive2 { name="GOSemSim"; version="2.8.0"; sha256="0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"; depends=[AnnotationDbi GO_db Rcpp]; }; - GOSim = derive2 { name="GOSim"; version="1.20.0"; sha256="00pl7xhs7mskkkmv45fcr448gbvr92v7xc43y0wyj3zrjh1fdm11"; depends=[annotate AnnotationDbi cluster corpcor flexmix GO_db graph Matrix org_Hs_eg_db RBGL Rcpp topGO]; }; - GOTHiC = derive2 { name="GOTHiC"; version="1.18.1"; sha256="12gagxspz8d0w9yng6bvkckvws428m36589drj4mz7pjv3gyy2j3"; depends=[BiocGenerics Biostrings BSgenome data_table GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors ShortRead]; }; - GOexpress = derive2 { name="GOexpress"; version="1.16.1"; sha256="1fh91vh3q6wzgnc71arpl7ahsk868sc3k4h6y9asch4dlhm9qzvh"; depends=[Biobase biomaRt ggplot2 gplots randomForest RColorBrewer RCurl stringr]; }; - GOfuncR = derive2 { name="GOfuncR"; version="1.2.0"; sha256="021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"; depends=[AnnotationDbi GenomicRanges gtools IRanges mapplots Rcpp vioplot]; }; - GOpro = derive2 { name="GOpro"; version="1.8.0"; sha256="1z2lyhnzqvrqfjzavwriaxxzbvbjhjaciyr9azkq296mj3cdih3v"; depends=[AnnotationDbi BH dendextend doParallel foreach GO_db IRanges MultiAssayExperiment org_Hs_eg_db Rcpp S4Vectors]; }; - GOstats = derive2 { name="GOstats"; version="2.48.0"; sha256="0wlqqgfynwqnqhckhsfjwg9zkj6hkmzwd5y76dhqz720vy21rcln"; depends=[annotate AnnotationDbi AnnotationForge Biobase Category GO_db graph RBGL Rgraphviz]; }; - GOsummaries = derive2 { name="GOsummaries"; version="2.18.0"; sha256="0cmb08w5xjqpdjqjkrwqdfiyf1sfj1xqqlyjq9hv0ynjab6skhvm"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; }; - GRENITS = derive2 { name="GRENITS"; version="1.34.0"; sha256="0a2wdsaga0k5x37qad53fdvpp4smmpkfp9f7vy8r9mvr69j3ji9n"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; }; - GRmetrics = derive2 { name="GRmetrics"; version="1.8.1"; sha256="1ak5n76ig3f1bl60in01dbz07vgs2gd65dq18qgrd07dyd20f6xs"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; }; - GRridge = derive2 { name="GRridge"; version="1.6.0"; sha256="0l6r36kzdmgcamjzzrjchz0q4k9dsxvmdvrrnq1br1xlhgscqc85"; depends=[glmnet graph Iso mvtnorm penalized survival]; }; - GSALightning = derive2 { name="GSALightning"; version="1.10.0"; sha256="0d1zfxzhcgb6h6p8pcfra9ck031n4yb309m17zbql1ld911nv297"; depends=[data_table Matrix]; }; - GSAR = derive2 { name="GSAR"; version="1.16.0"; sha256="1jdjr432i0njpfmymzbv4irf786hrp1wk4vy4sk2x0hcbjigds5z"; depends=[igraph]; }; - GSCA = derive2 { name="GSCA"; version="2.12.0"; sha256="08j8n9hjaf872c1n7ilzhm96d0hb4qa6l30qq516jpynxf326g2w"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; }; - GSEABase = derive2 { name="GSEABase"; version="1.44.0"; sha256="110al7x0ig8plzrprvhwc7xshi1jzpj2n8llhhg2fh6v6k0k6awr"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; }; - GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.2.1"; sha256="142x3mx8cknca82hj93l397566rliqmq9z888v1b4ip0vd87qk4l"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub GEOquery KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO rappdirs S4Vectors SummarizedExperiment]; }; - GSEAlm = derive2 { name="GSEAlm"; version="1.42.0"; sha256="16xflz0ad07qy3cl9r4qvi98hlxs2j9wm7dsbw518qkacynpc29g"; depends=[Biobase]; }; - GSRI = derive2 { name="GSRI"; version="2.30.0"; sha256="16zxia3ksgx14rafkjbxbic2rnskh7hql7ifi45n8gg0mkhw535c"; depends=[Biobase fdrtool genefilter GSEABase les]; }; - GSReg = derive2 { name="GSReg"; version="1.16.0"; sha256="08fasaa8inivgs3li8z0yhs2qaa878lrjymk67f8622wlskvmqcd"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; }; - GSVA = derive2 { name="GSVA"; version="1.30.0"; sha256="0q8jwmxv2w5m7z4i7ggdzm2z627484vn5rm0qfxkkqna3hpjnl4i"; depends=[Biobase BiocGenerics geneplotter GSEABase shiny shinythemes]; }; - GUIDEseq = derive2 { name="GUIDEseq"; version="1.12.1"; sha256="1z6y53z58rmvhaw0qd69xfh45fjcmz0r5m02l3lxkxr7b2ca3vcf"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table GenomeInfoDb GenomicAlignments GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; }; - GWASTools = derive2 { name="GWASTools"; version="1.28.0"; sha256="1g039bg6pcbxnz9zyzknrl9qx6wzncqjw4lpiy1lq4pc91lqzjln"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; }; - GateFinder = derive2 { name="GateFinder"; version="1.2.1"; sha256="1figmf8cpz1mfrcz69jfrxprl88aw01jb30pq3bi2n1r3dyvyxzp"; depends=[diptest flowCore flowFP mvoutlier splancs]; }; - GenRank = derive2 { name="GenRank"; version="1.10.0"; sha256="1fs9kfpm1xcdkyfc52hyysxwdb86aghcgig0jam3cvvfgnpm4xk9"; depends=[matrixStats reshape2 survcomp]; }; - GenVisR = derive2 { name="GenVisR"; version="1.14.2"; sha256="1sidsnzz6hfw072fk5n4i2v7ib9p0fm77p1vf26kgm0xi32ld679"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; }; - GeneAccord = derive2 { name="GeneAccord"; version="1.0.0"; sha256="1g1rjgvqnf3bqa4phj0q4gzrm3y6ijbxzyjz83ilwdmwxd4vs5rw"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; }; - GeneAnswers = derive2 { name="GeneAnswers"; version="2.24.0"; sha256="0cx6k2m3cllj0hvfmznkydwnw96q5a6k4781jiix7n9j97ys1rf5"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; }; - GeneBreak = derive2 { name="GeneBreak"; version="1.12.0"; sha256="049876x0665zv2apxf48hc5yqi7nbh89sqxlgyfqc2vk4knjgkbj"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; }; - GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.28.0"; sha256="12ww6hlgpxchlvrcc0va4x0ayb3119kakmm4yfscbp2xiy1dlinj"; depends=[Biobase PGSEA]; }; - GeneGA = derive2 { name="GeneGA"; version="1.32.0"; sha256="1z83rrlp82q56wp3ywbacrh8ws5rhqn572p94hqj895jb3b2w3km"; depends=[hash seqinr]; }; - GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.8.0"; sha256="12bx94xw3pmsnwqb4ksgz9ydn8581x2pdvbdba8p7cwcwbkp2lfk"; depends=[data_table FactoMineR GenomicRanges GGtools igraph IRanges kernlab mvtnorm plspm rioja Rsamtools snpStats]; }; - GeneMeta = derive2 { name="GeneMeta"; version="1.54.0"; sha256="0cwnhr98sc2xb9y7k4c502r1s1pwlwimpajfp7q34qs3w10sj8my"; depends=[Biobase genefilter]; }; - GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.24.1"; sha256="1hjaqw2zzyszkrp38mki04bljcpsxbdxf93bkcccq9x4yrv0lgas"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; - GeneOverlap = derive2 { name="GeneOverlap"; version="1.18.0"; sha256="1p87ngk0lfbb86hwx63x4xjnw77xslh5a7136l1dwia24r9dccls"; depends=[gplots RColorBrewer]; }; - GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.38.0"; sha256="1f266nq1179gyxqwn0pbbwia04hsshs4653flgm2730cyczq58ki"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; }; - GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.26.0"; sha256="1kv81bn9kr3lf41zhixr56ipsxf2ig1zny742494r3j8d4wi947p"; depends=[Biobase limma MASS survival]; }; - GeneSelector = derive2 { name="GeneSelector"; version="2.32.0"; sha256="0hjrwj7z67j6rmfvcd44j4284v3dq7qjcm24arnfskja5zk8zb6j"; depends=[Biobase limma multtest samr siggenes]; }; - GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.2.1"; sha256="1rqw74rj3x9f4sslsamsz7g1k835qp76qhxz7i7sxvgi3gv21m9g"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; }; - GeneticsDesign = derive2 { name="GeneticsDesign"; version="1.50.0"; sha256="1pzqdrny4hx6sxnc9glhb5plgrahfdckmcr7symykcc8d896payl"; depends=[gmodels gtools mvtnorm]; }; - GeneticsPed = derive2 { name="GeneticsPed"; version="1.44.0"; sha256="00v32167gl0kkglrzl3xm5bw7p8mfc933k074mf9lpbbf9s1liy7"; depends=[gdata genetics MASS]; }; - GenoGAM = derive2 { name="GenoGAM"; version="2.0.3"; sha256="09c7bk6jmfslr5clnrxp8f9s1fkq83w51nbj25akl3b8p5y5nagh"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; }; - GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.42.0"; sha256="0n3nbhgwnd09fnn7pyaa8n46hhjrz1gkvzbjjf7p9clv6p937y18"; depends=[biomaRt]; }; - GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.18.2"; sha256="07bm35jcczpyxap0b3gky4b28z38z423sngzsm19d9krjxr76b5p"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; - GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.18.1"; sha256="1maslav2r34wjyzh2nlwa862in1ir7i5xk57nw2nlfh5gqy112jd"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; - GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.6.0"; sha256="00xlskvrcjmj28mqkdi2d4ksqsb603g6wckqvzqyjr417xyyanrl"; depends=[dplyr GenomicRanges httr IRanges jsonlite lazyeval magrittr rappdirs readr S4Vectors SummarizedExperiment xml2]; }; - GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.34.8"; sha256="1sxp86hdsg32l2c85jgic65gy92d8kxsm01264hrx6yikdhicjax"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; - GenomicFiles = derive2 { name="GenomicFiles"; version="1.18.0"; sha256="0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.16.0"; sha256="0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; - GenomicRanges = derive2 { name="GenomicRanges"; version="1.34.0"; sha256="0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; - GenomicScores = derive2 { name="GenomicScores"; version="1.6.0"; sha256="0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n"; depends=[AnnotationHub Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors XML]; }; - GenomicTuples = derive2 { name="GenomicTuples"; version="1.16.0"; sha256="1d5bdsrs521rxnwiy2xg09d95p45n68dsqq17m4xw3xnfyfzpn3s"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; - Genominator = derive2 { name="Genominator"; version="1.36.0"; sha256="0lv8ar4z086k8hfjl187klv4yqsb2dawp0xvly6bz6pj3prrih50"; depends=[BiocGenerics DBI GenomeGraphs IRanges RSQLite]; }; - Glimma = derive2 { name="Glimma"; version="1.10.1"; sha256="1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"; depends=[edgeR jsonlite S4Vectors]; }; - GlobalAncova = derive2 { name="GlobalAncova"; version="4.0.0"; sha256="1fzd5122z8d68f4brsp2cv8bqcz9yjh5p41pgn6phqkkzjwj9ivg"; depends=[annotate AnnotationDbi Biobase corpcor dendextend globaltest GSEABase VGAM]; }; - GoogleGenomics = derive2 { name="GoogleGenomics"; version="2.4.0"; sha256="0xcj10r85hxh5qy43cjb6ypd849b5wphhhv528simxq4glhgrhxp"; depends=[Biobase Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; }; - GraphAT = derive2 { name="GraphAT"; version="1.54.0"; sha256="1xfd0i0j1fai58c15mc3lrg2jc4iwswyfpyg0ff5hnyhmgr3wnsa"; depends=[graph MCMCpack]; }; - GraphAlignment = derive2 { name="GraphAlignment"; version="1.46.0"; sha256="1qql33ikps9x0dkvc31sxvyf8w119ax7519v5bv35s3i5yxh16i6"; depends=[]; }; - GraphPAC = derive2 { name="GraphPAC"; version="1.24.0"; sha256="0dwh3xshp74isq3rljlivks04mw4r0vgzg74qwyc2ar5b2j96bbg"; depends=[igraph iPAC RMallow TSP]; }; - GreyListChIP = derive2 { name="GreyListChIP"; version="1.14.0"; sha256="1hsjv4r88ldb7pgl5a3im8vdhmbiaj0rrn0clij7jfh5p5r81r1r"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; - Guitar = derive2 { name="Guitar"; version="1.20.1"; sha256="1d4j54jdnsi8gi6p0kk6zxkk6kzd1r1k77mw142xlvh8b6zrl3nq"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer]; }; - Gviz = derive2 { name="Gviz"; version="1.26.5"; sha256="1dpkcaar7qgzg3vgafvkplprhwmhzpb7ph009kr6ajm36hx4z81c"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; - HDF5Array = derive2 { name="HDF5Array"; version="1.10.1"; sha256="1qwdsygcadl58qj598hfyvs8hp0hqcl9ghnhknahrlhmb7k2bd2d"; depends=[BiocGenerics DelayedArray IRanges rhdf5 S4Vectors]; }; - HDTD = derive2 { name="HDTD"; version="1.16.0"; sha256="1girysaq3w4vfmrdb4vx2g0z9f4nb7ly44b72yhvw9fxsdjzbsc5"; depends=[Rcpp RcppArmadillo]; }; - HELP = derive2 { name="HELP"; version="1.40.0"; sha256="0l6ysv1wdivimvn895alshz6v6avvp7y2gmdphg4iqrmvmjzsd36"; depends=[Biobase]; }; - HEM = derive2 { name="HEM"; version="1.54.0"; sha256="0nkxr9kihihmvap24ir3mgzyq5zq2ng484z9byq5yrbm69wrk887"; depends=[Biobase]; }; - HIBAG = derive2 { name="HIBAG"; version="1.18.1"; sha256="0wgkvqkyv526hdq5n3z27qfk1axbpj5ab6rdlrvjf4fw1v54whmv"; depends=[]; }; - HIREewas = derive2 { name="HIREewas"; version="1.0.2"; sha256="1l0q9x8c4fapa3qkcb3ny3bfvlwwmyl1mvv1hmxqw514ch5ylaiy"; depends=[gplots quadprog]; }; - HMMcopy = derive2 { name="HMMcopy"; version="1.24.0"; sha256="0kn9cqslx6hf70r2gr8x7dwcmvgnf9c3hxrwmvr4vbkl4d3xg8ic"; depends=[geneplotter IRanges]; }; - HPAanalyze = derive2 { name="HPAanalyze"; version="1.0.0"; sha256="1z17384m893wyf7a9v31ghcmsfvly8llbzh98kjz91a6mlqj2aqf"; depends=[cowplot dplyr ggplot2 hpar magrittr readr reshape2 tibble tidyr XLConnect xml2]; }; - HTSFilter = derive2 { name="HTSFilter"; version="1.22.1"; sha256="18fb3xl39n4n6n98bw2lbfrncg1m226yyx6v8cmrcgz88k0wqjrc"; depends=[Biobase BiocParallel DESeq DESeq2 edgeR]; }; - HTSanalyzeR = derive2 { name="HTSanalyzeR"; version="2.34.1"; sha256="1c9qajkfnhpn5a2lywn8bh467pwzzqx7gc4f2pns0jr911fq6fyb"; depends=[AnnotationDbi biomaRt BioNet cellHTS2 graph GSEABase igraph RankProd]; }; - HTSeqGenie = derive2 { name="HTSeqGenie"; version="4.12.0"; sha256="1rj81n21y6n4zlh0ck2i5zxani6hryb7xzf8azl03qk6q9yy09c5"; depends=[BiocGenerics BiocParallel Biostrings Cairo chipseq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR hwriter IRanges Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment VariantAnnotation VariantTools]; }; - HTqPCR = derive2 { name="HTqPCR"; version="1.36.0"; sha256="15raybys2fks10a5w1084yy5sx7r4n61rran7xk7yp0cifg9k8ji"; depends=[affy Biobase gplots limma RColorBrewer]; }; - Harman = derive2 { name="Harman"; version="1.10.0"; sha256="0j116k1gkxxbg210y4knc0wdbqjmb2ql72pzsh9r07zcaw2y8fzj"; depends=[Rcpp]; }; - Harshlight = derive2 { name="Harshlight"; version="1.54.0"; sha256="133b98p7b9shxz4nf6qg9qs5bb8yqxdw83cljjblxh5nngpm0s5b"; depends=[affy altcdfenvs Biobase]; }; - Heatplus = derive2 { name="Heatplus"; version="2.28.0"; sha256="0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"; depends=[RColorBrewer]; }; - HelloRanges = derive2 { name="HelloRanges"; version="1.8.0"; sha256="1brx8bj4xxn63iwfv7ys1fzw7aa1ir8k6jhdq26rzpk973nl6cyy"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - HiCBricks = derive2 { name="HiCBricks"; version="1.0.0"; sha256="0w3qw22jln44qxx635miaa807q08w010gad7bnqwr0z0zpwrw769"; depends=[BiocFileCache curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges R6 rappdirs RColorBrewer reshape2 rhdf5 S4Vectors scales stringr viridis]; }; - HiCcompare = derive2 { name="HiCcompare"; version="1.4.0"; sha256="08sk4sgjnjchyl1p3dbgr0yjbxl5qg35k4l5gzs08xa9pypw9jjq"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq S4Vectors]; }; - HiTC = derive2 { name="HiTC"; version="1.26.0"; sha256="11f96k1707g6milpjgnrjf3b5r42hsrxhb5d8znkcr3y3mrskdbj"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; }; - HilbertCurve = derive2 { name="HilbertCurve"; version="1.12.0"; sha256="1yagxajf5paj45a35d1l9aqb5mxwrh06b5jcrw2gldgndmxss9a8"; depends=[circlize GenomicRanges HilbertVis IRanges png]; }; - HilbertVis = derive2 { name="HilbertVis"; version="1.40.0"; sha256="1b6cfzycskklhxp4fw8hyxgnxdrzx047n2igrqdhbh8pv59cdsfa"; depends=[lattice]; }; - HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.40.0"; sha256="1qjfbgzzhj54fvgbvzlk37n1p32bc2vbf2yqkbn5y5ml6hsnmccw"; depends=[HilbertVis]; }; - HybridMTest = derive2 { name="HybridMTest"; version="1.26.0"; sha256="1xjykw1j81bai77nhxhxyib5z118isfr755q700934zh8zmsra61"; depends=[Biobase fdrtool MASS survival]; }; - IHW = derive2 { name="IHW"; version="1.10.1"; sha256="10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; - IMAS = derive2 { name="IMAS"; version="1.6.1"; sha256="0dy56awxbjkqx3xlafdz9p8prh5qk5ivgh1cp1gp69aph99xyrkf"; depends=[AnnotationDbi BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfortify ggplot2 gridExtra IRanges IVAS lattice lme4 Matrix Rsamtools S4Vectors survival]; }; - IMMAN = derive2 { name="IMMAN"; version="1.2.0"; sha256="1z8bxi7szjqzp630yg1hh1jkswy4iqnly325f11bhkaj8d04df21"; depends=[BiocFileCache Biostrings igraph seqinr STRINGdb]; }; - IMPCdata = derive2 { name="IMPCdata"; version="1.18.0"; sha256="0qqdpi4g29kf3y2cj7y3db40myacl368alc72lrv1qbw3qncjyjd"; depends=[rjson]; }; - INDEED = derive2 { name="INDEED"; version="1.0.1"; sha256="0w5h7zjalvz595fgz5ds5y4vxmny00psg60rwhjdjsh3z5rh6hwm"; depends=[devtools glasso]; }; - INPower = derive2 { name="INPower"; version="1.18.0"; sha256="074fylal7rn880vidi10d78s4zcxakq8f4gcxlgpq2hg0ivhd8rk"; depends=[mvtnorm]; }; - INSPEcT = derive2 { name="INSPEcT"; version="1.12.2"; sha256="1ykkr15b4bc2carwppf9yxzpl2n6lqpc6z6i2qy37vc6xffzgdx4"; depends=[Biobase BiocGenerics BiocParallel DESeq2 deSolve GenomicAlignments GenomicFeatures GenomicRanges IRanges plgem preprocessCore pROC rootSolve Rsamtools S4Vectors shiny SummarizedExperiment TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - IONiseR = derive2 { name="IONiseR"; version="2.6.0"; sha256="01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; }; - IPO = derive2 { name="IPO"; version="1.8.1"; sha256="0az0wvbnanaaviv4z91q4qa2zh7rjbmgybh4s78z9426cfk2yz7g"; depends=[BiocParallel CAMERA rsm xcms]; }; - IPPD = derive2 { name="IPPD"; version="1.30.0"; sha256="19g39k2cxfrbfh8hzmwk6hh67mp3na8447kd7jrdshd6zd2raaas"; depends=[bitops digest MASS Matrix XML]; }; - IRanges = derive2 { name="IRanges"; version="2.16.0"; sha256="0ljppsk611xi72gc8mbdx1311b63b1ijd401jz5xmxk5frla1nc1"; depends=[BiocGenerics S4Vectors]; }; - ISoLDE = derive2 { name="ISoLDE"; version="1.10.1"; sha256="1iv32al2z01dgaqfiawx03ga1b380qkhxwi82r9aav3ry42brpmg"; depends=[]; }; - ITALICS = derive2 { name="ITALICS"; version="2.42.0"; sha256="1k55pd3zz9zzwc04m1cjlv1ib3w78n8qzxdhzhpw0pwaw6bzfpmr"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; }; - IVAS = derive2 { name="IVAS"; version="2.2.1"; sha256="1spqlmlgrdcw1679g1j15rycwadnhwkwbaqag9wcn5prnn27xx88"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; }; - IWTomics = derive2 { name="IWTomics"; version="1.6.0"; sha256="0xn12qjac2kxpyvpm8ly58q41cqz0v3q6pl6cn7hb0lvxcplp86s"; depends=[fda GenomicRanges gtable IRanges KernSmooth S4Vectors]; }; - Icens = derive2 { name="Icens"; version="1.54.0"; sha256="0l70vj53cnvgp5ls205ign47zhl12xbaxl5hdkjs73gbdvx2aagk"; depends=[survival]; }; - IdMappingAnalysis = derive2 { name="IdMappingAnalysis"; version="1.26.0"; sha256="0s6s02awa5i86rcp12ijaqb8cga00kpwiap2nj6s2jdg3kh1ady6"; depends=[Biobase boot mclust R_oo rChoiceDialogs RColorBrewer]; }; - IdMappingRetrieval = derive2 { name="IdMappingRetrieval"; version="1.30.0"; sha256="1knaavzdvm1iz6crhqhxsxhvlrpa9k6n6d82q21w6qag8lkvwc2x"; depends=[AffyCompatible biomaRt ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; }; - IdeoViz = derive2 { name="IdeoViz"; version="1.18.0"; sha256="067bd18pb3xyw58xxl0fxa09kcyh4dhdzxbci6i7b82fa17s9hkb"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; }; - Imetagene = derive2 { name="Imetagene"; version="1.12.0"; sha256="0lh15nqjxwgjlhhzrrjj9bpbbkxnq2nlgx3v4fik6q4d5rqx0zbb"; depends=[d3heatmap ggplot2 metagene shiny shinyBS shinyFiles shinythemes]; }; - ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.10.5"; sha256="15j5f8vxl0j135kcc69g9xpkgdcipjhj0slgd52c818hgdbyj4zk"; depends=[Biobase curl data_table digest flowCore flowWorkspace ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; }; - ImpulseDE = derive2 { name="ImpulseDE"; version="1.8.0"; sha256="0jiqclcm0w6nh7j3w5wqv0c6lw0pyn4wczld2fmkqyv71mshmakn"; depends=[amap boot]; }; - ImpulseDE2 = derive2 { name="ImpulseDE2"; version="1.6.1"; sha256="0zbrkwaspwaq9aa9il4ahn5lnhbyz8cair5lx354pr1whm3wn8v3"; depends=[Biobase BiocParallel circlize ComplexHeatmap cowplot DESeq2 ggplot2 knitr Matrix S4Vectors SummarizedExperiment]; }; - InPAS = derive2 { name="InPAS"; version="1.14.2"; sha256="1z0lk2a5wfaykq4r7rmfrc4d4kcg4icygxri4y96i467a3v48m2i"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; }; - InTAD = derive2 { name="InTAD"; version="1.2.3"; sha256="1vahq4rh8icka1qqwnqvw3y5hbrss0nnpyll5bvwnm9514sp030w"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggpubr IRanges mclust MultiAssayExperiment qvalue rtracklayer S4Vectors SummarizedExperiment]; }; - IntEREst = derive2 { name="IntEREst"; version="1.6.2"; sha256="1y9ilxlqi71hy0jzar5bbdn9y9xx7nbfzi6rgkdmf8mpdin5r62f"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; }; - InterMineR = derive2 { name="InterMineR"; version="1.4.1"; sha256="1v11h22nw3chxkscdmbc9z4186x885lpnh537yyijp9429bab44l"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; }; - InteractionSet = derive2 { name="InteractionSet"; version="1.10.0"; sha256="0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; }; - IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.4.0"; sha256="0cv7g8cca447gvzy13xpx7h5sxg2w9n3pmj74rfqpbcpd1m9h2p4"; depends=[FGNet igraph knitr]; }; - IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="1.0.5"; sha256="0qvcck4ky4mlib49xfmmkhmv4ndxnbfn8bssim8m5c7xl5zqxj7a"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; }; - IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.18.0"; sha256="0k7l3h56m4l7l9d7c1vg06dg6a986n4v7v0w6yrmpspajkx302ar"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; }; - IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.4.0"; sha256="1fbrbshan00r8qidz1yran84hj4higf1g4iw1qx58h13laqs1yi0"; depends=[Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer readr reshape2 rtracklayer stringr tximport VennDiagram]; }; - JunctionSeq = derive2 { name="JunctionSeq"; version="1.12.1"; sha256="1azc7sb3yga6v98x4g97g9pj90yk9kzj6m8s4zfaz3ggsrz62m6w"; depends=[Biobase BiocGenerics BiocParallel DESeq2 genefilter geneplotter GenomicRanges Hmisc IRanges locfit plotrix Rcpp RcppArmadillo S4Vectors statmod stringr SummarizedExperiment]; }; - KCsmart = derive2 { name="KCsmart"; version="2.40.0"; sha256="1jhw1w964hvjxcxxzyx03mm5w98a15x4hak9r1bbhi1q38x0vs6p"; depends=[BiocGenerics KernSmooth multtest siggenes]; }; - KEGGREST = derive2 { name="KEGGREST"; version="1.22.0"; sha256="0blpd5a7whd2sswfhqd17h58hg06ymaf80gapdr9ja43hnnlj309"; depends=[Biostrings httr png]; }; - KEGGgraph = derive2 { name="KEGGgraph"; version="1.42.0"; sha256="0ry0pfqc61r0cz98j6zlyhh4qh6568l0w0j61xmysayyp046mgy3"; depends=[graph XML]; }; - KEGGlincs = derive2 { name="KEGGlincs"; version="1.8.0"; sha256="188c5cq2yrcwd991cicgh9ivh5xingdd6d46hahvwmvz3y9qyi7a"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; }; - KEGGprofile = derive2 { name="KEGGprofile"; version="1.24.0"; sha256="140f834dlwry5h6kl3z2zm8ch31syl72l4jkmri4vwy5cyvin5bg"; depends=[AnnotationDbi biomaRt KEGG_db KEGGREST png RCurl TeachingDemos XML]; }; - KinSwingR = derive2 { name="KinSwingR"; version="1.0.3"; sha256="156ins4fqr4kdc5pnikl71pn2ppqknfxf1dcl3ffk82sby1xclkd"; depends=[BiocParallel data_table sqldf]; }; - LBE = derive2 { name="LBE"; version="1.50.0"; sha256="1padaxr7hdqrbwgkma4r64ndxhig7ygl7dvbixziz4qdl7cwi869"; depends=[]; }; - LEA = derive2 { name="LEA"; version="2.4.0"; sha256="1bbcsk6k2w8bbjksbnvd7zi4m1zldmjj5pwspjcciqssk10abwn9"; depends=[]; }; - LINC = derive2 { name="LINC"; version="1.10.0"; sha256="1lbpqdhiyh52m3jrsqlwshaz0ncflx5gpyp7lknw4z1vgyvi4ad5"; depends=[ape Biobase clusterProfiler DOSE ggplot2 ggtree gridExtra org_Hs_eg_db png Rcpp ReactomePA reshape2 sva]; }; - LMGene = derive2 { name="LMGene"; version="2.38.0"; sha256="0ynyknm86lvcimva5krmy3xwi2ni7js6jrvkkjsy7w3q90cr2q6q"; depends=[affy Biobase multtest survival]; }; - LOBSTAHS = derive2 { name="LOBSTAHS"; version="1.8.1"; sha256="0q416vx4frw1dm29yfg06laxkp8ns4mk17p1fw2ir96l44awam7y"; depends=[CAMERA xcms]; }; - LOLA = derive2 { name="LOLA"; version="1.12.0"; sha256="1ysdxkaarwwzw06c9d5xh617g284wk57wpj9lbkfv8rrxkla33d0"; depends=[BiocGenerics data_table GenomicRanges IRanges reshape2 S4Vectors]; }; - LPE = derive2 { name="LPE"; version="1.56.0"; sha256="0ryvbkjx9x394a9za4wyy6rk9avjpwqsgdz6rywp9rr4di551a4h"; depends=[]; }; - LPEadj = derive2 { name="LPEadj"; version="1.42.0"; sha256="11pvvh42idpi7636wrm52whaavl4wnbwki1p82p196m0rvac1jy5"; depends=[LPE]; }; - LRBaseDbi = derive2 { name="LRBaseDbi"; version="1.0.0"; sha256="0idf0gn593b6k0fnpkaphh59cpr6a8582namxrvik1b6zpi5kfzl"; depends=[AnnotationDbi Biobase DBI RSQLite]; }; - LVSmiRNA = derive2 { name="LVSmiRNA"; version="1.32.0"; sha256="14880gimbgw7lmvdq965nm3jgkss1qfakl8xnf66kx4f8mczrvps"; depends=[affy Biobase BiocGenerics limma MASS quantreg SparseM vsn zlibbioc]; }; - LedPred = derive2 { name="LedPred"; version="1.16.0"; sha256="1nimsxm841fnqn0v0x0laq5dcwrp46k9vxaxwd86ayn9sdlgx6fj"; depends=[akima e1071 ggplot2 irr jsonlite plot3D plyr RCurl ROCR testthat]; }; - LineagePulse = derive2 { name="LineagePulse"; version="1.2.1"; sha256="1632g54pyip4dvsq6m08qhfl4xgcfphcw5rix7mr9nf8qh1hrbns"; depends=[BiocParallel circlize ComplexHeatmap ggplot2 gplots knitr Matrix RColorBrewer SingleCellExperiment SummarizedExperiment]; }; - Linnorm = derive2 { name="Linnorm"; version="2.6.1"; sha256="1qgk8m5kc409flqxs3vnf228v3z0112q8py9hgfgyiwvi6yzdbp6"; depends=[amap apcluster ellipse fastcluster fpc ggdendro ggplot2 gmodels igraph limma MASS mclust Rcpp RcppArmadillo Rtsne statmod vegan zoo]; }; - LiquidAssociation = derive2 { name="LiquidAssociation"; version="1.36.0"; sha256="0hz60m9m0098mqwajw83xkraajlbh4q8617d85mfjcbdgmc483a1"; depends=[Biobase geepack org_Sc_sgd_db yeastCC]; }; - Logolas = derive2 { name="Logolas"; version="1.6.0"; sha256="0asi528yb65vwdkxxlsdv9g06fr2y5mzxa3m1669byjb6fjzzs1y"; depends=[Biostrings ggplot2 gridBase LaplacesDemon SQUAREM]; }; - LoomExperiment = derive2 { name="LoomExperiment"; version="1.0.4"; sha256="18pqixrnln5d60g6a5nay2zw4984bnllqzrpylwx2nrxsindp9n1"; depends=[DelayedArray GenomicRanges HDF5Array rhdf5 rtracklayer S4Vectors SingleCellExperiment SummarizedExperiment]; }; - LowMACA = derive2 { name="LowMACA"; version="1.12.1"; sha256="08lh0q88ixad11hgkxs0y1bc7pi3a8f1a70nqxmdwkgghcfziirp"; depends=[BiocParallel Biostrings cgdsr data_table httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; }; - LymphoSeq = derive2 { name="LymphoSeq"; version="1.10.0"; sha256="024d13hrw0s0zmza9bd8nm9s79imwajqvzxiaxj5348pj2d212hr"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; }; - M3C = derive2 { name="M3C"; version="1.4.1"; sha256="0l9063bn0sfcq5qxghaj8f98x0pg91fwsd8l64ga8d7pnlm8i5fm"; depends=[cluster dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust survival]; }; - M3D = derive2 { name="M3D"; version="1.16.0"; sha256="0a7xs3kqvyxswsa4zcdakij4rvpv1pr4fmplnvxyskhh2zps7xyl"; depends=[BiocGenerics BiSeq GenomicRanges IRanges Rcpp S4Vectors SummarizedExperiment]; }; - M3Drop = derive2 { name="M3Drop"; version="1.8.1"; sha256="0bzxv4lnmbz4d7y1c2w7i013rfjscnj1ndb05k9n1i4c9gsknqya"; depends=[bbmle gplots numDeriv RColorBrewer statmod]; }; - MACPET = derive2 { name="MACPET"; version="1.2.0"; sha256="0799d3pr5b6g7xbi75pf693768nspdc73qay72naghyql6g91s96"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; }; - MADSEQ = derive2 { name="MADSEQ"; version="1.8.0"; sha256="1b7d6niz8lhvd17xjl4hy1yyki049cg6wd3g8wp38bm3zs6dzfd1"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; }; - MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.2.3"; sha256="1d2lllsz2jdqma1ifdg7xj9fby85az7bifn0h0hj705m6dyla42z"; depends=[biomaRt bladderbatch clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci gridExtra pathview pheatmap png sva]; }; - MAIT = derive2 { name="MAIT"; version="1.16.1"; sha256="0fg3cah81c4gzm3hw590h4grrja2qgfs8mrpkbifrgsclbybnp95"; depends=[agricolae CAMERA caret class e1071 gplots MASS pls plsgenomics Rcpp xcms]; }; - MANOR = derive2 { name="MANOR"; version="1.54.0"; sha256="102s71adp93n47sz2hcqs5ihykwcvha6sz7v24p409a7rj8ary38"; depends=[GLAD]; }; - MAST = derive2 { name="MAST"; version="1.8.2"; sha256="0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"; depends=[abind Biobase BiocGenerics data_table ggplot2 plyr progress reshape2 S4Vectors SingleCellExperiment stringr SummarizedExperiment]; }; - MBASED = derive2 { name="MBASED"; version="1.16.0"; sha256="0046yjpjdczxjqkpvsdsj8fnah1kmz4m038k49laqlrricyl6f2f"; depends=[BiocGenerics BiocParallel GenomicRanges RUnit SummarizedExperiment]; }; - MBAmethyl = derive2 { name="MBAmethyl"; version="1.16.0"; sha256="05jwqlvmjhcfqjqxv6m5mmc72q8lfv2qqwm0f8j1dddpvvyh8fzd"; depends=[]; }; - MBCB = derive2 { name="MBCB"; version="1.36.0"; sha256="0yizhggn77arg1pnl3qd25xc5awwv1f1hi3mk6p2c5pdk48mz679"; depends=[preprocessCore tcltk2]; }; - MBttest = derive2 { name="MBttest"; version="1.10.0"; sha256="05cwwqj8qjj66ndy2hdx2jxna07xjqg7qv4z1gar6r91p482zsp0"; depends=[gplots gtools]; }; - MCRestimate = derive2 { name="MCRestimate"; version="2.38.0"; sha256="1hl5bqibajwscir94dla23544sg866hqx1h793fj7m38xcjhxlzn"; depends=[Biobase e1071 golubEsets pamr randomForest RColorBrewer]; }; - MCbiclust = derive2 { name="MCbiclust"; version="1.6.1"; sha256="1zjhviz3n0w72kwd0czkxddm23jj8876174lbjc85fd8piqf7x6f"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; }; - MDTS = derive2 { name="MDTS"; version="1.2.0"; sha256="1h0vpbi62j0g1cdp06xkp0y4aymnqqhp7frhwi6f7hsiviaz2c0p"; depends=[Biostrings DNAcopy GenomicAlignments GenomicRanges IRanges Rsamtools stringr]; }; - MEAL = derive2 { name="MEAL"; version="1.12.0"; sha256="05cfyq3fffxj802cyh3bghfn2gg6z0yhy2spii9n8pxmsfcsr7pn"; depends=[Biobase BiocGenerics DMRcate GenomicRanges ggplot2 Gviz IRanges isva limma matrixStats minfi missMethyl MultiDataSet permute S4Vectors SmartSVA SummarizedExperiment vegan]; }; - MEDIPS = derive2 { name="MEDIPS"; version="1.34.0"; sha256="1bb8k0jzxfji79qxb4v6pdp9jyf6hv83g5mmqj74k3x2cglycwia"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; }; - MEDME = derive2 { name="MEDME"; version="1.42.0"; sha256="0yg04lghqc3sfyakf8id3dc5gd0bfhaf9lp903g5jpiai5779byy"; depends=[Biostrings drc MASS]; }; - MEIGOR = derive2 { name="MEIGOR"; version="1.16.0"; sha256="1jxl2bcsbrlab6ss66388l64k5xcjr5g3gpgya2rk4yq237mghl6"; depends=[CNORode deSolve Rsolnp snowfall]; }; - MGFM = derive2 { name="MGFM"; version="1.16.0"; sha256="08ngcr1a979amjdl8x5a7mn1zdvrpa4h35rkhimi9kr0fn68kj34"; depends=[annotate AnnotationDbi]; }; - MGFR = derive2 { name="MGFR"; version="1.8.1"; sha256="1v85b82algx79kbk25inan96kymnpchplbl5r15vyxavvkqzd66a"; depends=[annotate biomaRt]; }; - MIGSA = derive2 { name="MIGSA"; version="1.6.0"; sha256="19gfb98qmb8wbi343lw92sf7d29xliyzb3wz095pd2npsjr69qkl"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; }; - MIMOSA = derive2 { name="MIMOSA"; version="1.20.1"; sha256="0vj7z95pjq62glg1akipydbybxsxc69yjpqrffpc33kqhf46nhfb"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; }; - MIRA = derive2 { name="MIRA"; version="1.4.1"; sha256="0wy4iisp6c0kfns34pr5am055b1x7wdnbdh8lgr5ll91wxz48sg9"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; }; - MLInterfaces = derive2 { name="MLInterfaces"; version="1.62.1"; sha256="1h0x1p2h8x1h276wxx6kcnb4c4s5sglnmd58iigl81a224x8gxwp"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rpart sfsmisc shiny threejs]; }; - MLP = derive2 { name="MLP"; version="1.30.0"; sha256="03h7k5v620x2hw6k3gddaba40fwh6zvpmlnhf6mcml7ldsni95y9"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; }; - MLSeq = derive2 { name="MLSeq"; version="2.0.1"; sha256="1jaw2blnl7jsd2px069af7zqk69d04bma8m5vpqb941vx6yhk095"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; }; - MMDiff2 = derive2 { name="MMDiff2"; version="1.10.0"; sha256="0ljdr6y3plzpf9j70ghw41x3jpb8p52lqb9987gm1mw7lxw9iraf"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; }; - MODA = derive2 { name="MODA"; version="1.8.0"; sha256="0jarqlyfx81pamdl5z1kx96ri6kjq59lv144ifw8ga6kzs5bng58"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; }; - MPFE = derive2 { name="MPFE"; version="1.18.0"; sha256="02lnymmsl1k770jh41sak6dxkzsb0c38934aslbd890dibc2c04i"; depends=[]; }; - MPRAnalyze = derive2 { name="MPRAnalyze"; version="1.0.1"; sha256="0nwd28jcr8dkhi3v71l9dd83dfl4k51sjdnjmml9vbdcznps1ffg"; depends=[BiocParallel progress SummarizedExperiment]; }; - MSGFgui = derive2 { name="MSGFgui"; version="1.16.1"; sha256="0qy7k9l88qna24kmrc2ikg326dk1jwcrl3908p74lh42sr5wxlzj"; depends=[MSGFplus mzID mzR shiny shinyFiles xlsx]; }; - MSGFplus = derive2 { name="MSGFplus"; version="1.16.1"; sha256="0qbyb4wycf6qbkx83rh1n8hc664mw542x6jw658aqhdnfl3gsvxq"; depends=[mzID ProtGenerics]; }; - MSnID = derive2 { name="MSnID"; version="1.16.1"; sha256="077n6ljcnnl7q4w0qj8v46vm4sjk9vzzfqf7wsc6lz0wmyzqdng3"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; }; - MSnbase = derive2 { name="MSnbase"; version="2.8.3"; sha256="1kl1d7byphnfpmbl5fzbgs68dxskhpsdyx7ka51bpfn0nv3pp492"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; }; - MSstats = derive2 { name="MSstats"; version="3.14.1"; sha256="1bgvdq1mfq6rxjf5ag2slrhy4056906wghsirrymf53nw3qz5g6s"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; }; - MSstatsQC = derive2 { name="MSstatsQC"; version="2.0.1"; sha256="1f6gv1fqm5h6xs91wc1bamyri47qggb872qzriwzvff7ydn0q1ag"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; }; - MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.1"; sha256="1k7dhiayf885ax1mg03yg1w4mamk3j1gsm7phszxl3i0j3c2gks7"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; }; - MSstatsTMT = derive2 { name="MSstatsTMT"; version="1.1.2"; sha256="0aaw3qillcfrjczdmd7s21v551hclnq8fn2zvn91wyr4i82q43rr"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; }; - MTseeker = derive2 { name="MTseeker"; version="1.0.6"; sha256="0fsb7k6pkl15q8csygpsjrz4jvy20mfd5rfmhl7q7ffj4d7sprxh"; depends=[Biobase BiocGenerics Biostrings circlize GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR Homo_sapiens IRanges jsonlite Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VariantTools viridis xml2]; }; - MVCClass = derive2 { name="MVCClass"; version="1.56.0"; sha256="1hw36gd1z19dir6fl7j3dzqzi5p1668zbwpcz7l21hbyycv27l0j"; depends=[]; }; - MWASTools = derive2 { name="MWASTools"; version="1.6.0"; sha256="0bkl7vgyac6xhjj636vlmynq75zyp6smvjvzg1ymkgg800wylg4c"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; - MantelCorr = derive2 { name="MantelCorr"; version="1.52.0"; sha256="1z0f6g5zbxl1sqcl6rdx7y6vh637i6209ya9fsan6wi5r8rcsamn"; depends=[]; }; - MassArray = derive2 { name="MassArray"; version="1.34.1"; sha256="0hdydbpg7arsxl0v7zz7w6zrczb44ff2dap4vgwqxdk5jgh1mm4b"; depends=[]; }; - MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.48.1"; sha256="1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz"; depends=[waveslim]; }; - MatrixRider = derive2 { name="MatrixRider"; version="1.14.0"; sha256="17n3s0gdj3jjlf4pangnbdb00ak62j5wvdqd8yhackhs4z9zbchb"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; }; - MaxContrastProjection = derive2 { name="MaxContrastProjection"; version="1.6.1"; sha256="103aqb89g5ca9vp0j3763dypwjqnzvf1dh8s6v03nrisfslwa85s"; depends=[EBImage]; }; - MeSHDbi = derive2 { name="MeSHDbi"; version="1.18.0"; sha256="1if3jrrxlrsrza7404d7banrdfbz5g1v69wydxglldzfim3g9jw3"; depends=[AnnotationDbi Biobase BiocGenerics RSQLite]; }; - MeasurementError_cor = derive2 { name="MeasurementError.cor"; version="1.54.0"; sha256="0s39wlfcqag15y73dapmnz0zrywsnd9flz1n7yl20r9p8dfmhv12"; depends=[]; }; - MergeMaid = derive2 { name="MergeMaid"; version="2.54.0"; sha256="07cgcfvppdvyrb0hhi24126ysdcal8vjyplqxfkqxxyjpv0p8ap8"; depends=[Biobase MASS survival]; }; - Mergeomics = derive2 { name="Mergeomics"; version="1.10.0"; sha256="16xv75q790r0apdb1yb10j6mcjs67a891av1kjf21xyp5g5bgpja"; depends=[]; }; - MetCirc = derive2 { name="MetCirc"; version="1.12.1"; sha256="07y7r4y01v26mxgfivxrhq9r80w228lxicsbxvsbb2xbb8vvjz7j"; depends=[amap circlize scales shiny]; }; - MetID = derive2 { name="MetID"; version="1.0.0"; sha256="12nrbdq4xracd6p7xz3l0dvqp4xlj34jr7wj90wmk09i89h7sfjj"; depends=[ChemmineR devtools igraph Matrix stringr]; }; - MetNet = derive2 { name="MetNet"; version="1.0.1"; sha256="0s45l7y43bhc1sha4wmhch9vfyw7xza95lyyl5ixfz28z99k08vr"; depends=[BiocParallel bnlearn mpmi parmigene ppcor rfPermute sna stabs WGCNA]; }; - MetaCyto = derive2 { name="MetaCyto"; version="1.4.1"; sha256="1yi04zy7kmikac22msynnnm3wqhy9d59qz2v8m54w8h3rn49c1c0"; depends=[cluster fastcluster flowCore FlowSOM ggplot2 metafor tidyr]; }; - MetaNeighbor = derive2 { name="MetaNeighbor"; version="1.2.1"; sha256="007y4dz3mfww6vwmm5d99flgzw372hjkbbv36n8hz1gqrwy52yvp"; depends=[beanplot gplots RColorBrewer SummarizedExperiment]; }; - Metab = derive2 { name="Metab"; version="1.16.1"; sha256="0m7wd4rw0q7y53gpzi0bgn0gwf83kbdx1pjvfblnirkgwyq69f6c"; depends=[pander svDialogs xcms]; }; - MetaboSignal = derive2 { name="MetaboSignal"; version="1.12.0"; sha256="1wgpcn25cpql6dwgwpxw16w8hizny92xfbgs4rjz4dpssg9n1qq3"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; - MethPed = derive2 { name="MethPed"; version="1.10.1"; sha256="1vcy4x7p2bhpyfpj5lxwjzfm09lc3c0rkzam83837b7apz3j9sqn"; depends=[Biobase randomForest]; }; - MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.14.0"; sha256="0by77378lml6ncz53c7xkh29dayach31p3fn0jrf31x947larnzy"; depends=[Biostrings gplots seqinr stringr]; }; - MethylAid = derive2 { name="MethylAid"; version="1.16.0"; sha256="03qf2j12nq6nqfs96lsdk7jny2ak6258j5bq0brp7wmpijlnjrak"; depends=[Biobase BiocGenerics BiocParallel ggplot2 gridBase hexbin matrixStats minfi RColorBrewer shiny SummarizedExperiment]; }; - MethylMix = derive2 { name="MethylMix"; version="2.12.0"; sha256="062jr6qskp3psmpirqn5aiq5mhw3k1ipyb0m16ds2i95n8v3ky5p"; depends=[data_table digest foreach ggplot2 impute limma R_matlab RColorBrewer RCurl RPMM]; }; - MethylSeekR = derive2 { name="MethylSeekR"; version="1.22.0"; sha256="1nqwza5bqkn0k664j1a2p518a3pj27zwlc5pkvjbh09cjvfibyf0"; depends=[BSgenome geneplotter GenomicRanges IRanges mhsmm rtracklayer]; }; - Mfuzz = derive2 { name="Mfuzz"; version="2.42.0"; sha256="105xk52hxc2d5yy0fy4cb0zhrpnansvyb0dzx9jc1dfjvxzq4vjg"; depends=[Biobase e1071 tkWidgets]; }; - MiChip = derive2 { name="MiChip"; version="1.36.0"; sha256="10v9vvyr4bs7l0x6cb6frhni8sa16sdllykjsbnjxd3jynvzrpy9"; depends=[Biobase]; }; - MiPP = derive2 { name="MiPP"; version="1.54.0"; sha256="08g19yw9hbrwsm630rz907dqlfs7qg2xvaby9bx3mjiwlr7d15wx"; depends=[Biobase e1071 MASS]; }; - MiRaGE = derive2 { name="MiRaGE"; version="1.24.1"; sha256="1jak07j4kfnyjhcdik4a4ihbb87sqx7mh3yajjbrm13zpvh9vyf3"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; - MineICA = derive2 { name="MineICA"; version="1.22.0"; sha256="1n10x9y5x1h06k1kv2jv3ym5n950dhcd20g34rarx0zyihd2ln4j"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; }; - MinimumDistance = derive2 { name="MinimumDistance"; version="1.26.0"; sha256="0rv7pgzbrscc8raa49x1nbvbp3ivr8kwdr8rf6hvfw8y1xk3rnba"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; - Mirsynergy = derive2 { name="Mirsynergy"; version="1.18.0"; sha256="19nw7yapcxvidzzdbhjzplajfmss65drqq5xrsz1ycr87jgh8h5b"; depends=[ggplot2 gridExtra igraph Matrix RColorBrewer reshape scales]; }; - MmPalateMiRNA = derive2 { name="MmPalateMiRNA"; version="1.32.0"; sha256="045089yfj5aakabxhpjld9fa62sfr48xqb88j8m3xm7561ml20ql"; depends=[Biobase lattice limma statmod vsn xtable]; }; - MoPS = derive2 { name="MoPS"; version="1.16.0"; sha256="0wypkl5kdjmwf78pwbgdsin8fxiycfwkf3kwrbqxc7r27lplgwyj"; depends=[Biobase]; }; - MoonlightR = derive2 { name="MoonlightR"; version="1.8.0"; sha256="16jhqygppfy82h3jnldigf1mgirbh6wcrqd61nn335kgj1d016p0"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; - MotIV = derive2 { name="MotIV"; version="1.38.0"; sha256="1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"; depends=[BiocGenerics Biostrings IRanges lattice rGADEM S4Vectors]; }; - MotifDb = derive2 { name="MotifDb"; version="1.24.1"; sha256="1q454k3p4ib2z79rcgwyx9s9s7gg5j0vlhca1b579qzi3692m8xi"; depends=[BiocGenerics Biostrings IRanges rtracklayer S4Vectors splitstackshape]; }; - Mulcom = derive2 { name="Mulcom"; version="1.32.0"; sha256="0k3illh3dchd5nwa4y87v1n0lkil7p5yiqzg9v65nxv35mhkg0vv"; depends=[Biobase fields]; }; - MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.8.3"; sha256="04q1y3gkmf6s6ksd3jvxr0r13gzacrxcdgr1zd3ign0zq2ab5bli"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; }; - MultiDataSet = derive2 { name="MultiDataSet"; version="1.10.0"; sha256="1sr93zdirjqgsffmkv9plaqbg3rfsz8lh96mqv7xrnc3nmhmm65y"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; }; - MultiMed = derive2 { name="MultiMed"; version="2.4.0"; sha256="1dfcqh7px0zzgrg96r3930jxzcgvc91xlfm4q9fnn3w85nzgdnrb"; depends=[]; }; - MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.8.0"; sha256="0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; }; - NADfinder = derive2 { name="NADfinder"; version="1.6.1"; sha256="0kz7dz95kdz5dz05bh7x6czrwdr1imaq1mv6bncxxhv1mffhmb9v"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; - NBSplice = derive2 { name="NBSplice"; version="1.0.6"; sha256="1nalcpj7n4qghmkrfq65xd4i0aack2yq4l2wwsy4z0sfi7gh6m49"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; }; - NCIgraph = derive2 { name="NCIgraph"; version="1.30.0"; sha256="16mxxrq6g4szig29cah2a13qp1ybsh8ci37izlq6gpxn0h00maym"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; }; - NGScopy = derive2 { name="NGScopy"; version="1.16.1"; sha256="1zfasfbzzay402igag1ynffz2v9ad70wdy5vs02q0api3rkkn406"; depends=[changepoint Xmisc]; }; - NOISeq = derive2 { name="NOISeq"; version="2.26.1"; sha256="1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"; depends=[Biobase Matrix]; }; - NTW = derive2 { name="NTW"; version="1.32.0"; sha256="10ndg6mina5wz3w87wpv4mnbxdyj6rhvc9jqf954wmh6gj04vyin"; depends=[mvtnorm]; }; - NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.12.0"; sha256="1927ry931ckjrci6yfk3fh774bizh4yb5f7p7x1ra1yxzfizq7k3"; depends=[Biobase matrixStats Rcpp]; }; - NanoStringQCPro = derive2 { name="NanoStringQCPro"; version="1.14.0"; sha256="1kisr7j27iwyxjxsylnlrqz9ac5kbwr4indg0qkc3ycdlqqxbqvl"; depends=[AnnotationDbi Biobase knitr NMF org_Hs_eg_db png RColorBrewer]; }; - NarrowPeaks = derive2 { name="NarrowPeaks"; version="1.26.0"; sha256="06lppn4pbp0f3yb3lbpqmk7fqw6i754h9c8v1akvhg22wgb8428x"; depends=[BiocGenerics CSAR fda GenomeInfoDb GenomicRanges ICSNP IRanges S4Vectors]; }; - NeighborNet = derive2 { name="NeighborNet"; version="1.0.0"; sha256="16fmsh71sx65g505mwbhkv9sf1y7niy24zpygxv3aqklqqrnk97r"; depends=[graph]; }; - NetPathMiner = derive2 { name="NetPathMiner"; version="1.18.0"; sha256="1pyqplxzmdd3sjwlr3dzhb39gfhkbd5a550inrvxh4gqnw9r2lpl"; depends=[igraph]; }; - NetSAM = derive2 { name="NetSAM"; version="1.22.0"; sha256="10wmq1vgzdsp6iyia7gqh1d685cj1nikgvygpl69hgciabn3kzz5"; depends=[graph igraph seriation]; }; - NormalyzerDE = derive2 { name="NormalyzerDE"; version="1.0.0"; sha256="1ql62i9mgnr3vafz0yfi8zxxlkccjlrjkb4lnrxv0sshhs5kw4di"; depends=[ape Biobase car ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; }; - NormqPCR = derive2 { name="NormqPCR"; version="1.28.0"; sha256="1b4j0ngqlkpc1fhfnkmk6h917has6ldi1876rsincl28yfvghz25"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; }; - NuPoP = derive2 { name="NuPoP"; version="1.32.0"; sha256="0p1v7v5shvcbiwgi6fy1fkh55ikks6svh17f2h7biw5j29zwg878"; depends=[]; }; - OCplus = derive2 { name="OCplus"; version="1.56.0"; sha256="0brkcx3vapi7gnw8v6023j56pi6mgki26hx71fq4ldwchwrg4pxr"; depends=[akima multtest]; }; - OGSA = derive2 { name="OGSA"; version="1.12.0"; sha256="0qcnc6658ggv4is9a0s9lid41ns9845qbwd5m0l8r9qjzgmix2s7"; depends=[Biobase gplots limma]; }; - OLIN = derive2 { name="OLIN"; version="1.60.0"; sha256="0vmmxx74i3ch00xsaw60b82h7nbh8rgv6xzbzmcnpa79anaamv3l"; depends=[limma locfit marray]; }; - OLINgui = derive2 { name="OLINgui"; version="1.56.0"; sha256="03n5xlh6fhcw7mvsdaihxn0b39zyhf3f2fayql40nkcinfmbmr50"; depends=[marray OLIN tkWidgets widgetTools]; }; - OMICsPCA = derive2 { name="OMICsPCA"; version="1.0.1"; sha256="17sm8vk96z25q1mdybq6al82yrbb28sjrr40lpwc1syzjabhns2b"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; }; - OPWeight = derive2 { name="OPWeight"; version="1.4.1"; sha256="00xwam4vpa7jpdqz8jy66kckl92sawd2m60qwlp96l8dpm5f7kxv"; depends=[MASS qvalue tibble]; }; - ORFik = derive2 { name="ORFik"; version="1.2.1"; sha256="0x8pj6j3g8gq3i6fqgnd85s60kadq4shjr4hykf00f9zzkj3gnv9"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp Rsamtools rtracklayer S4Vectors]; }; - OSAT = derive2 { name="OSAT"; version="1.30.0"; sha256="12cswkscavbkx8cxj0kzk6gz1h8xwp24mwy53dgyr771sch76k7j"; depends=[]; }; - OTUbase = derive2 { name="OTUbase"; version="1.32.0"; sha256="0xhwa9yd0qd86j03190riff5z64h93pn7q0b6qb2awwf5zrda8fs"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; - OUTRIDER = derive2 { name="OUTRIDER"; version="1.0.4"; sha256="0wivnc4dd8zlz7305jjps3iid5sjcy3z1q6sb5yj56i81hz5734j"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; }; - OmaDB = derive2 { name="OmaDB"; version="1.2.2"; sha256="16qy6p36mkw4fkyp9yis56zyn88x780767ahnqhnyzqlm9g5kv5w"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; }; - OmicCircos = derive2 { name="OmicCircos"; version="1.20.0"; sha256="1akb3djkq0waq1f81zi3nnv8svqf2i8w9agaac732vbdr4cf821d"; depends=[GenomicRanges]; }; - OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.14.0"; sha256="00a8wwk0z73ipdhjlwkwz4nqpjpyylafds88g8dhz0imk8f24gnj"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; }; - Onassis = derive2 { name="Onassis"; version="1.4.5"; sha256="17s3d2wb6mnckpxaq4ppll6fwc6fag4mg9921bf3islkb7vrbxfz"; depends=[AnnotationDbi data_table DT GEOmetadb knitr OnassisJavaLibs RCurl rJava RSQLite]; }; - OncoScore = derive2 { name="OncoScore"; version="1.10.0"; sha256="1q5xirwr184fn3fbkldp5v4cwmkkpggp2xnnh3s3prl4masdf6pk"; depends=[biomaRt]; }; - OncoSimulR = derive2 { name="OncoSimulR"; version="2.12.0"; sha256="0pbq9qbxx35zzpzsc3b18qhcdwskkg5xk6pf4kgbzisa8jkjyxfd"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph nem RColorBrewer Rcpp Rgraphviz smatr]; }; - OrderedList = derive2 { name="OrderedList"; version="1.54.0"; sha256="1hvw6lc39gq867gvz426qyj79yz85k2shwlw4mnk6xaib652gqwf"; depends=[Biobase twilight]; }; - Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.10.0"; sha256="1s2rqzdmzmbif92466x2mgmbjism68c62590pj8swx853f9x668s"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges RSQLite S4Vectors]; }; - OrganismDbi = derive2 { name="OrganismDbi"; version="1.24.0"; sha256="11pyv56cy4iy095h40k6k0mpjdlh6gsb4ld3s57nfa9nd4ypx3yi"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; }; - Oscope = derive2 { name="Oscope"; version="1.12.1"; sha256="0dxdif1zw8vw6p8ci1nlgr6pwh6gf27r6c9q1lng79gi6x2ipv75"; depends=[BiocParallel cluster EBSeq testthat]; }; - OutlierD = derive2 { name="OutlierD"; version="1.46.0"; sha256="1xbkasaf47qmfqqrm1k3mgnjj63rv30094r0f968q7rxfpdmq90f"; depends=[Biobase quantreg]; }; - PAA = derive2 { name="PAA"; version="1.16.0"; sha256="03hd7vvkqfr369wp8r0i9y29li9q91s76wzvbh9scvqd0ngmh9cv"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; }; - PADOG = derive2 { name="PADOG"; version="1.24.0"; sha256="0xia09m11j70n2gfmka620pk66vjvzr1376y2lb0g18k5n6k2zxv"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGG_db KEGGdzPathwaysGEO limma nlme]; }; - PANR = derive2 { name="PANR"; version="1.28.1"; sha256="00ymf82kdgc4pqnmz9hgi9b4pk8cidg8n6icx40rcs5dmlkhl24d"; depends=[igraph MASS pvclust RedeR]; }; - PAPi = derive2 { name="PAPi"; version="1.22.1"; sha256="12hv5cf0mc243w7a95hlbgfvll7qs6wcc3vqkpg7k5giy24n8i1q"; depends=[KEGGREST svDialogs]; }; - PCAN = derive2 { name="PCAN"; version="1.10.0"; sha256="08im6jwzbnnb4z01ayiv1jk8yqna8ncg6z65bfh0ba4jjvjwywfi"; depends=[BiocParallel]; }; - PCpheno = derive2 { name="PCpheno"; version="1.44.0"; sha256="1svdqnfp7ggi29rm5la35p96vmr7nzcfy5a458f1ra0kd4a6nd5l"; depends=[annotate AnnotationDbi Biobase Category GO_db graph GSEABase KEGG_db ppiData ppiStats ScISI SLGI]; }; - PECA = derive2 { name="PECA"; version="1.18.0"; sha256="10hhwvlr5gzcal0g62zimr79a3v2cpp95cb7nafnlq8v3ndg69hd"; depends=[affy aroma_affymetrix aroma_core genefilter limma preprocessCore ROTS]; }; - PGA = derive2 { name="PGA"; version="1.12.1"; sha256="0ss057198960hig0kdc9hgn850830cmjx48n3lbq4nk2y887grcf"; depends=[AnnotationDbi biomaRt Biostrings customProDB data_table GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap RCurl Rsamtools RSQLite rTANDEM rtracklayer S4Vectors stringr VariantAnnotation]; }; - PGSEA = derive2 { name="PGSEA"; version="1.56.0"; sha256="0nmgjfw32flc42qj0vih8r4nsc01qv01cnqrr2nxv30zdwbnfk7w"; depends=[annaffy AnnotationDbi Biobase GO_db KEGG_db]; }; - PICS = derive2 { name="PICS"; version="2.26.0"; sha256="10djnd38jdbyk18yqsypkpxqwnfiy8441zpmx1bhzzn8p5q2jpsv"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; }; - PING = derive2 { name="PING"; version="2.26.0"; sha256="16iygwjsk8n40jp4giik0d4ypd8i4dmd8xdl7dhh81jmjpmycd92"; depends=[BiocGenerics BSgenome chipseq fda GenomicRanges Gviz IRanges PICS S4Vectors]; }; - PLPE = derive2 { name="PLPE"; version="1.42.0"; sha256="1i5a9nzravs4qzlxz4byvrcg0jnhcfd56ir4bm33056l4ymbia9r"; depends=[Biobase LPE MASS]; }; - POST = derive2 { name="POST"; version="1.6.0"; sha256="1grwyy2lisix5iv7brw85vii04yyhqhfkp8srirb0wh6i4q07wwf"; depends=[Biobase CompQuadForm GSEABase Matrix survival]; }; - PPInfer = derive2 { name="PPInfer"; version="1.8.1"; sha256="1ifp7gxvdlvn7wh6aizjfkaj53bcg4hbq2m54ksk2a7n86fympr5"; depends=[biomaRt fgsea ggplot2 igraph kernlab STRINGdb yeastExpData]; }; - PREDA = derive2 { name="PREDA"; version="1.28.0"; sha256="1bm08y242hikgxh8icld6mvnydq2hg4wh6m3km5j3hw3hzv5qmv5"; depends=[annotate Biobase lokern multtest]; }; - PROMISE = derive2 { name="PROMISE"; version="1.34.0"; sha256="0g4qkk7yc7b4idhy78xnwplfwg5ng7y9qwhap90hhw7nnxdvvb3i"; depends=[Biobase GSEABase]; }; - PROPER = derive2 { name="PROPER"; version="1.14.1"; sha256="1wcvpfvj9c1g4yqj02lia3kchf080y81nvl9rb9mls5h6117dmbi"; depends=[edgeR]; }; - PROPS = derive2 { name="PROPS"; version="1.4.0"; sha256="150apwa4c80741kavf2ilz62575pbmjqkwnbgb095ddfqb2wp4ly"; depends=[Biobase bnlearn reshape2 sva]; }; - PROcess = derive2 { name="PROcess"; version="1.58.1"; sha256="0b8simjv3g1dn0dsxa11fzif24z9cmlvczzxzm354m6bkfanl1f0"; depends=[Icens]; }; - PSEA = derive2 { name="PSEA"; version="1.16.0"; sha256="0zw1jrrdl17fmdn3z18rdr86lb9lmpqrsdf9ilm172cxhjbq7iba"; depends=[Biobase MASS]; }; - PSICQUIC = derive2 { name="PSICQUIC"; version="1.20.0"; sha256="0h42hsvh2n0hib9gw4fqpri9lqdnaz6ivzcf406x54zdsgwalyzd"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; }; - PWMEnrich = derive2 { name="PWMEnrich"; version="4.18.0"; sha256="1v8yqczf5784w7a9d21jp3p2dcirrkg6ydccd8k8i0355x8yxxc9"; depends=[BiocGenerics Biostrings evd gdata seqLogo]; }; - PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.10.0"; sha256="0rkkrriik0l010vzn46zm2zm87k38aihz6l5llp1wawwkyac8cla"; depends=[FindMyFriends igraph jsonlite pcaMethods shiny]; }; - Path2PPI = derive2 { name="Path2PPI"; version="1.12.0"; sha256="1yc4hqycjd2zc87wiq9rrswb5f0x33vsd6d23gckn1sqvam2clqj"; depends=[igraph]; }; - PathNet = derive2 { name="PathNet"; version="1.22.0"; sha256="1n4g960m0j38snignsahaq7nr6bahln0cbqhgx530vwzsdv2xzx3"; depends=[]; }; - PathoStat = derive2 { name="PathoStat"; version="1.8.4"; sha256="15n8lmv9vgwh1ain21gfgyl5bfnkfs7rnjdjbz69bvy1k2nmgl3y"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; }; - PathwaySplice = derive2 { name="PathwaySplice"; version="1.6.1"; sha256="09glsv0hj8yzg79hjjpnfn59w12i7l0n2fpwzg98wiqx7yyza5pk"; depends=[annotate AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr EnrichmentBrowser ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq KEGGREST mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; }; - Pbase = derive2 { name="Pbase"; version="0.22.1"; sha256="0z5g2wbjzzqfw0sjb537j84d4l8bvf8pjav5z39ypzx2inq2zzb5"; depends=[AnnotationFilter Biobase BiocGenerics BiocParallel biomaRt Biostrings cleaver ensembldb GenomicRanges Gviz IRanges MSnbase mzID mzR Pviz Rcpp rtracklayer S4Vectors]; }; - PepsNMR = derive2 { name="PepsNMR"; version="1.0.2"; sha256="0x7n8faxrczqwn1kkcp22vwag905pswvr2q198kqbh4fjkxgkmrx"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; }; - PharmacoGx = derive2 { name="PharmacoGx"; version="1.12.0"; sha256="1ddh6bmrddbdmqdpmyy5mlkqvhrk39c19lzybrirfclq6cydfh5g"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; }; - PhenStat = derive2 { name="PhenStat"; version="2.18.1"; sha256="1fq01k4cb4gyzh9knbidcqds2qm1wvlz114s6nldzhl3h0x5h6x5"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; }; - Pi = derive2 { name="Pi"; version="1.10.0"; sha256="03wzmcz57kdflicjb2wmnxg0fvfmbgizvql5164cf24fsi2lvbgi"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex]; }; - Pigengene = derive2 { name="Pigengene"; version="1.8.1"; sha256="13pmw7nf8fvn9bnnh7fwqgrlg589796nqv83snanqwqsp4fcklid"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; }; - Polyfit = derive2 { name="Polyfit"; version="1.16.1"; sha256="0nlclhj5ni09blwf5prpcp2iiflqk17ca3gqjl5shvl9y9v8nbqb"; depends=[DESeq]; }; - PowerExplorer = derive2 { name="PowerExplorer"; version="1.2.2"; sha256="14dzv3p79x95w6185r2srnmw1i8n6x2b1fd2chbx42b3xa65xliy"; depends=[Biobase BiocParallel data_table DESeq2 ggplot2 gridExtra MASS ROTS S4Vectors SummarizedExperiment vsn]; }; - Prize = derive2 { name="Prize"; version="1.12.1"; sha256="046wvhjqyyc79q88lzcx1jfg73f4sr83japiapzgm5gqnri1hs8r"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; }; - Prostar = derive2 { name="Prostar"; version="1.14.12"; sha256="0700nkpjmlw7540qms407mm94nsch1jzk8sf30k4qk7fn5rfl1wb"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets webshot XML]; }; - ProtGenerics = derive2 { name="ProtGenerics"; version="1.14.0"; sha256="053mmxhzncqgigl2iqjlq56qzimlw2zzw31wpzw19rf7rld1vi3b"; depends=[]; }; - ProteoMM = derive2 { name="ProteoMM"; version="1.0.1"; sha256="0gyx7pfswxa7p6whyi2d10341vgc9yr3vvi7a2wj1padas9cm0m1"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; - ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.12.0"; sha256="049c0g20kbf12hs3r4il3gpr9chi2w2d2l0s7pkgc1sxyb0aydvs"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDb MSnbase mzR RCurl]; }; - PureCN = derive2 { name="PureCN"; version="1.12.2"; sha256="109riqxc46f7x2psy096rhhpjzpk75j5i00x2842c4drps86bzy3"; depends=[BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; - Pviz = derive2 { name="Pviz"; version="1.16.0"; sha256="1qgavdwqp2zvixbvpm2mjqcbwcz2gw8kfj6zk9064m7zmh4qg3iz"; depends=[Biostrings biovizBase data_table GenomicRanges Gviz IRanges]; }; - QDNAseq = derive2 { name="QDNAseq"; version="1.18.0"; sha256="04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"; depends=[Biobase BiocParallel CGHbase CGHcall DNAcopy GenomicRanges IRanges matrixStats R_utils Rsamtools]; }; - QSutils = derive2 { name="QSutils"; version="1.0.0"; sha256="1z06c7f2jgr60j9rbarjx310mhy4n91chb3azvw0050z01rgxi02"; depends=[ape BiocGenerics Biostrings psych]; }; - QUALIFIER = derive2 { name="QUALIFIER"; version="1.26.1"; sha256="0656ffwvaiapj4jyksfmqrmwwjs5s9av8lpmy8d31x7iins2kps6"; depends=[Biobase data_table flowCore flowViz flowWorkspace hwriter lattice latticeExtra MASS ncdfFlow reshape XML]; }; - QUBIC = derive2 { name="QUBIC"; version="1.10.0"; sha256="08yp8y6rcggrx69326f8gpx3arg9b6hq9fh1f2ngnd409lhlfxdn"; depends=[biclust Matrix Rcpp RcppArmadillo]; }; - QuartPAC = derive2 { name="QuartPAC"; version="1.14.0"; sha256="0bm18r4yfz3z8dr8hhb1a9issggbrw3x3galvmar0wdr1is5mcfk"; depends=[data_table GraphPAC iPAC SpacePAC]; }; - QuasR = derive2 { name="QuasR"; version="1.22.1"; sha256="15lnrj8m8p1ns7iv5f2j0xshma3gpjp3lwry1s0axsxsk9khzrl0"; depends=[Biobase BiocGenerics BiocManager BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges IRanges Rbowtie Rsamtools rtracklayer S4Vectors ShortRead zlibbioc]; }; - QuaternaryProd = derive2 { name="QuaternaryProd"; version="1.16.0"; sha256="0ww0k2akcpzfxq454g3lcr34270pq6kxxngx23lyanbfqqffhzmr"; depends=[dplyr Rcpp yaml]; }; - R3CPET = derive2 { name="R3CPET"; version="1.14.0"; sha256="0ifvifwilpski32pp1z904s97f5g109b8d4l5yds6alpl9663hls"; depends=[BiocGenerics clues clValid data_table GenomeInfoDb GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp RCurl reshape2 S4Vectors]; }; - R453Plus1Toolbox = derive2 { name="R453Plus1Toolbox"; version="1.32.0"; sha256="15a9jfb5c9mnpas3qvq7ca90y8y1yfqbvhgz7k51rzyynzh5nkx8"; depends=[Biobase BiocGenerics biomaRt Biostrings BSgenome GenomicRanges IRanges R2HTML Rsamtools S4Vectors ShortRead SummarizedExperiment TeachingDemos VariantAnnotation xtable XVector]; }; - R4RNA = derive2 { name="R4RNA"; version="1.10.0"; sha256="1n6fhlj0rmk67gdzknx3fysyg46r5lcqrilqq5rhdzrr4gacwx3j"; depends=[Biostrings]; }; - RBGL = derive2 { name="RBGL"; version="1.58.2"; sha256="0vhnh47pswnp27c0zqcbnnsayfmq3cxcgrs9g860555ldqfl4cyl"; depends=[graph]; }; - RBM = derive2 { name="RBM"; version="1.14.0"; sha256="1yr1qjc7flgxxjngd55i9xjjc8r7gdhn8j8hwyhd4p5358z2qaqg"; depends=[limma marray]; }; - RBioinf = derive2 { name="RBioinf"; version="1.42.0"; sha256="1l2vqnrc6ilsi50zn9f1p174hwc63qhbn05z1ng3d2va3x3qb9hm"; depends=[graph]; }; - RCAS = derive2 { name="RCAS"; version="1.8.0"; sha256="0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; }; - RCASPAR = derive2 { name="RCASPAR"; version="1.28.0"; sha256="1d5mr6j7yfv9amdjyyysw79n4yr57ryxybbccc97jbkmqhijp806"; depends=[]; }; - RCy3 = derive2 { name="RCy3"; version="2.2.9"; sha256="04n73hgh2brfrl9rqmiq1afg7hpvq0l6zbl2h1yqzrgmxgzrx0cv"; depends=[BiocGenerics graph httr igraph R_utils RJSONIO XML]; }; - RCyjs = derive2 { name="RCyjs"; version="2.4.0"; sha256="1m5zxa5r9kjcfacgv8ny6pa2a5xd94kajmb054074r7av4ymig5z"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; }; - RDAVIDWebService = derive2 { name="RDAVIDWebService"; version="1.20.0"; sha256="0agdz7r7qcrxmvcm3d6zs36p239ldhc01qa4c4b4dxvlsq5gh6wk"; depends=[Category ggplot2 GO_db GOstats graph RBGL rJava]; }; - RDRToolbox = derive2 { name="RDRToolbox"; version="1.32.0"; sha256="01dpaniy2chd7kim6q9lqq65pfs3y1z05jrhgjmrmc7hg0yp1zb1"; depends=[MASS rgl]; }; - REBET = derive2 { name="REBET"; version="1.0.0"; sha256="1m2czya7af35xqy9cgrdwwwvfqdq2g8s02jbwv5wl6r6lwhcgid2"; depends=[ASSET]; }; - REDseq = derive2 { name="REDseq"; version="1.28.0"; sha256="1kp7nl3z1w27vmcqkvwbyi6d7dsd125zih8zbzlh96axankcqsck"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome BSgenome_Celegans_UCSC_ce2 ChIPpeakAnno IRanges multtest]; }; - REMP = derive2 { name="REMP"; version="1.6.1"; sha256="1q3011zbglgy2wrsampwslaf5wiz03ly62qf47mhi5pdngnsb6cn"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 caret doParallel foreach GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 impute IRanges iterators kernlab minfi org_Hs_eg_db ranger S4Vectors settings SummarizedExperiment]; }; - RGMQL = derive2 { name="RGMQL"; version="1.2.0"; sha256="0rvlsl9acjkpva4x1wxg7pyscr3pzdr9mw2k7yzy429ad0lpk81s"; depends=[BiocGenerics data_table dplyr GenomicRanges glue httr plyr RGMQLlib rJava rtracklayer S4Vectors xml2]; }; - RGSEA = derive2 { name="RGSEA"; version="1.16.0"; sha256="02df90fjqynw4r9jx55na6ky1g814463ipb4ag1f4605hhdnbhmq"; depends=[BiocGenerics]; }; - RGalaxy = derive2 { name="RGalaxy"; version="1.26.0"; sha256="1a0bswfqdv2z7kml32c42h7zv5ayam96ka9frndvkba36zlzysrw"; depends=[Biobase BiocGenerics optparse roxygen2 XML]; }; - RGraph2js = derive2 { name="RGraph2js"; version="1.10.0"; sha256="0c53c4rrpqyna8yxcc0cgyx6b2fhd6fkwi2g7a4a8hsspja1qhcv"; depends=[digest graph rjson whisker]; }; - RIPSeeker = derive2 { name="RIPSeeker"; version="1.22.0"; sha256="1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - RITAN = derive2 { name="RITAN"; version="1.6.0"; sha256="16w7ypvchhl6ljaq2hga790ycg3hznvr7pc5mf0bah8kk524z6a6"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png RColorBrewer reshape2 RITANdata sqldf STRINGdb]; }; - RIVER = derive2 { name="RIVER"; version="1.6.0"; sha256="1a7i2zdin9znp9z48wnlj4g9y0bmm6anaphhrihkfqmf0s9lcqwy"; depends=[Biobase ggplot2 glmnet pROC]; }; - RImmPort = derive2 { name="RImmPort"; version="1.10.0"; sha256="1gws1zkh5gzw0drw7c21wp2g8wskaagw0f3g1p41z91sffv8vvrm"; depends=[data_table DBI dplyr plyr reshape2 RSQLite sqldf]; }; - RJMCMCNucleosomes = derive2 { name="RJMCMCNucleosomes"; version="1.6.0"; sha256="1kzsmglxq7lriz5vblprj7g1kbwzgcxjd2l1w12npb6j7vw8s598"; depends=[BiocGenerics BiocParallel consensusSeekeR GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; - RLMM = derive2 { name="RLMM"; version="1.44.0"; sha256="17lmjhb0c5w4pp68z4h5ij93n9f31dy7aic40xd958zwxm5gnwyq"; depends=[MASS]; }; - RMassBank = derive2 { name="RMassBank"; version="2.10.1"; sha256="020ilicbbn9rs5pb5mc3dva862jsx1arxbpq45vxig9bbvk2gq73"; depends=[Biobase digest httr MSnbase mzR rcdk Rcpp RCurl rjson S4Vectors XML yaml]; }; - RNASeqPower = derive2 { name="RNASeqPower"; version="1.22.1"; sha256="15x78z3a6j462h4cp93qzrvajnq71p81bn9y6qj4kjv94wdx9v02"; depends=[]; }; - RNASeqR = derive2 { name="RNASeqR"; version="1.0.3"; sha256="07nj0iz25czfvywgl8pp1isd5vnskwnhw9w1mjjkn71sk8q5vxdc"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; }; - RNAdecay = derive2 { name="RNAdecay"; version="1.2.1"; sha256="1hpmr9nip3immkhdzq5qfxf00cdghyhhv8a7bvnan4m7l5c0q509"; depends=[ggplot2 gplots nloptr TMB]; }; - RNAinteract = derive2 { name="RNAinteract"; version="1.30.1"; sha256="14c9h9jqn4h6y28bacvhaib27cr64fljyiw8h7anrlfgqmn9v7hd"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; }; - RNAither = derive2 { name="RNAither"; version="2.30.1"; sha256="0n2wj8gldiiqpyl7i8i8ys6z4kcv076wyhsc5kirmvrzy031g7ls"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; }; - RNAprobR = derive2 { name="RNAprobR"; version="1.14.0"; sha256="0p2cs5ybkj2yjqkcpmrxggm874y05nnz85milx8hix2vdsx6snc7"; depends=[BiocGenerics Biostrings GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr Rsamtools rtracklayer S4Vectors]; }; - ROC = derive2 { name="ROC"; version="1.58.0"; sha256="1qxmxhx5dqnrvp2076512p64rdanaa7cd95zrs783255ifq5jb0v"; depends=[]; }; - ROTS = derive2 { name="ROTS"; version="1.10.1"; sha256="1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"; depends=[Biobase Rcpp]; }; - ROntoTools = derive2 { name="ROntoTools"; version="2.10.0"; sha256="0v0g4kpz3sc1aikwn59vjy75g0vdblw1nz0qrcwz48glh11qpzdz"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; }; - RPA = derive2 { name="RPA"; version="1.38.0"; sha256="04spiv0wp7wm6yx0c4qra148n381k9488j79i91by1qi79zm746z"; depends=[affy BiocGenerics phyloseq]; }; - RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.4.0"; sha256="12r2i9dla3ids1ycfdm670qz61fkf9h5mdzq0q65jaw311dbnspq"; depends=[]; }; - RRHO = derive2 { name="RRHO"; version="1.22.0"; sha256="1p84kgin1vf6vy7la5v0d10l3kv2mnhbjxjykw7yk9faf8xnmsah"; depends=[VennDiagram]; }; - RSVSim = derive2 { name="RSVSim"; version="1.22.0"; sha256="0d99cmazqlsqy58hjs2x9ziyqs7qg084rrp05vnq7ncki7a6bfm1"; depends=[Biostrings GenomicRanges IRanges ShortRead]; }; - RSeqAn = derive2 { name="RSeqAn"; version="1.2.0"; sha256="0jphw3yadhgg0c93sywb7fblv2z54nq6lqrb4p7qx9v2rsv5dvqz"; depends=[]; }; - RTCA = derive2 { name="RTCA"; version="1.34.1"; sha256="0hhk3py6d1r4rl8xim2z3j266dx1bnxk1pxc24k61k5ni05nxjpw"; depends=[Biobase gtools RColorBrewer]; }; - RTCGA = derive2 { name="RTCGA"; version="1.12.1"; sha256="15ibhz60z2fgvpji8kdmpvsdprzqnc0wk4gd6kdrkr4m2s0jgw4j"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; }; - RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.12.1"; sha256="05gmj49hz4mdpsmp1brzha3swybgm1sqf6jyhnj8w2arwc0bh72y"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges IRanges limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; }; - RTN = derive2 { name="RTN"; version="2.6.3"; sha256="1g0xpm31h9yj68cl0pqhlr386hjg0781gp4wcr4hcf52s812wvw5"; depends=[data_table igraph IRanges limma minet mixtools RedeR S4Vectors snow SummarizedExperiment viper]; }; - RTNduals = derive2 { name="RTNduals"; version="1.6.2"; sha256="13f9gw0nrmcznyjcixgk615c1zfyf8w8j30psq66fnsiyjr45p8x"; depends=[RTN]; }; - RTNsurvival = derive2 { name="RTNsurvival"; version="1.6.2"; sha256="0npmn1x5w8g15m14br44zc9vivxlbvgfa74gsa07gbsvlsm466dn"; depends=[RColorBrewer RTN RTNduals scales survival viper]; }; - RTopper = derive2 { name="RTopper"; version="1.28.0"; sha256="0blpza1kq7qh9yb15hrmkfrc7awljafwxkr5kq368yk2gkvjny91"; depends=[Biobase limma multtest]; }; - RUVSeq = derive2 { name="RUVSeq"; version="1.16.1"; sha256="0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"; depends=[Biobase EDASeq edgeR MASS]; }; - RUVcorr = derive2 { name="RUVcorr"; version="1.14.0"; sha256="05lg37rmf9skqcpnd08v6wnh7sfs449hwwq6nw2hkgy9faip14lz"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; }; - RUVnormalize = derive2 { name="RUVnormalize"; version="1.16.0"; sha256="1habqdv35v9ypvfmfaxjqpka67bs6hzf4ph9b0gqd67mbfnb49dv"; depends=[Biobase RUVnormalizeData]; }; - RVS = derive2 { name="RVS"; version="1.4.4"; sha256="1zvbin60p81qyk2c0m88dl94ivzyf4cpjdf2hnw8igmvlxszmb8k"; depends=[gRain kinship2 snpStats]; }; - RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.6.0"; sha256="1w02nnxpmx05gn6d9kjnahdn9kynbg1szm96c03gh4961zknn3r3"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; - RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.2.0"; sha256="022vckcc46bkhfhi2fzgawhf54hi6y2p5ia4v3x3lj221d7hcaax"; depends=[dnet igraph Matrix]; }; - RankProd = derive2 { name="RankProd"; version="3.8.0"; sha256="0jmpwpmj3y13ylk7riyicywpring14dhq4862jgalsjjwa22zzd0"; depends=[gmp Rmpfr]; }; - RareVariantVis = derive2 { name="RareVariantVis"; version="2.10.0"; sha256="0fb59a5568h0wz92blr6m3w01jnzh3kkil2p82fh2b8n2rv40s66"; depends=[BiocGenerics BSgenome BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores googleVis gtools IRanges phastCons100way_UCSC_hg19 S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; - Rariant = derive2 { name="Rariant"; version="1.18.0"; sha256="1wzm0qn8ar6k6fgp8hv79qncc0gca9hks3vzzkqq8ac2ml07zl37"; depends=[BiocGenerics dplyr exomeCopy GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges reshape2 Rsamtools S4Vectors shiny SomaticSignatures VariantAnnotation VGAM]; }; - RbcBook1 = derive2 { name="RbcBook1"; version="1.50.0"; sha256="1900prjqspn5zripf9h9jd5zkdrcc5477rsrflal6n5jdf9lqz3v"; depends=[Biobase graph rpart]; }; - Rbowtie = derive2 { name="Rbowtie"; version="1.22.0"; sha256="00vpszsjkvid25sjrpzw1dylwmgv27z67njvg8h1axnb09a7gnjw"; depends=[]; }; - Rbowtie2 = derive2 { name="Rbowtie2"; version="1.4.0"; sha256="045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr"; depends=[]; }; - Rcade = derive2 { name="Rcade"; version="1.24.0"; sha256="0xx19zxrfjawny75cmp75f1aarngmz8p0vy2ryw0v1qdfm1aby87"; depends=[baySeq GenomeInfoDb GenomicAlignments GenomicRanges IRanges plotrix rgl Rsamtools S4Vectors]; }; - Rchemcpp = derive2 { name="Rchemcpp"; version="2.20.1"; sha256="00sb9xaj51vna030c6nkb27r3ymj98a27kl97ksa86di3a8n4162"; depends=[ChemmineR Rcpp]; }; - RchyOptimyx = derive2 { name="RchyOptimyx"; version="2.22.0"; sha256="10kk9h1cknpdgbmn5k7aabrfr60n66i5yjxbj81x7ji6yk1ramcg"; depends=[flowType graph Rgraphviz sfsmisc]; }; - RcisTarget = derive2 { name="RcisTarget"; version="1.2.1"; sha256="0ggwhfm5yl68qapbr3sxz206mpc8vqi9g4x3isxvrcf94q9jb7iq"; depends=[AUCell BiocGenerics data_table feather GSEABase R_utils SummarizedExperiment]; }; - Rcpi = derive2 { name="Rcpi"; version="1.18.2"; sha256="0kd61ajb4lm5b974476204kw9pkavi2l2n7m6zynblpdccpp913f"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; }; - Rdisop = derive2 { name="Rdisop"; version="1.42.1"; sha256="0pir401z19wx433sxr2r01a5ckd4myygyv0jxj4wfq1fkfpmi1kl"; depends=[Rcpp RcppClassic]; }; - ReQON = derive2 { name="ReQON"; version="1.28.0"; sha256="1llklca4bz2plkmwgvpw7xrn8hxh1vnf6sk91z1yzld49w1b6rxc"; depends=[rJava Rsamtools seqbias]; }; - ReactomePA = derive2 { name="ReactomePA"; version="1.26.0"; sha256="1kglvgn1sjnx9rm45lxp0ji19vzb8qlvjs01agsdbvkn19im5nkm"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; }; - ReadqPCR = derive2 { name="ReadqPCR"; version="1.28.0"; sha256="1c1l7nmnv6bcgnamjja423w5lmfsz8wiv4gv0x22ym1mv3293776"; depends=[Biobase]; }; - RedeR = derive2 { name="RedeR"; version="1.30.0"; sha256="1fq3x0sf146pn0ksddachisrd4782d7qyk1vk96dk7h0knvj9jl9"; depends=[igraph]; }; - RefNet = derive2 { name="RefNet"; version="1.18.0"; sha256="0z7k4f38gphmxqjwvwhp2q0l6ljlpzhl69v1yja0c7gfmhr1lq55"; depends=[AnnotationHub BiocGenerics IRanges PSICQUIC RCurl shiny]; }; - RefPlus = derive2 { name="RefPlus"; version="1.52.0"; sha256="1myrgsxh9713hrzzhzln20iabq520xqdmm8narg79wla5rh3vcq7"; depends=[affy affyPLM Biobase preprocessCore]; }; - Repitools = derive2 { name="Repitools"; version="1.28.0"; sha256="1v08fmn4al3rh20zr3afafmxyapdxylbbsf5s8j1wwfz60ysv557"; depends=[aroma_affymetrix BiocGenerics Biostrings BSgenome cluster DNAcopy edgeR GenomeInfoDb GenomicAlignments GenomicRanges gplots gsmoothr IRanges MASS Ringo Rsamtools Rsolnp rtracklayer S4Vectors]; }; - ReportingTools = derive2 { name="ReportingTools"; version="2.22.1"; sha256="1g9pw6gjc6a81758zd1c1ci9q2wy7jcg3kn3iq77cb0kgbqdb5ia"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category DESeq2 edgeR ggbio ggplot2 GOstats GSEABase hwriter IRanges knitr lattice limma PFAM_db R_utils XML]; }; - Rgin = derive2 { name="Rgin"; version="1.2.0"; sha256="0jj8asqp7p45rlag34m0x2lasw6mdj4rdi4ywnm5bk2cim50pji6"; depends=[RcppEigen]; }; - Rgraphviz = derive2 { name="Rgraphviz"; version="2.26.0"; sha256="0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"; depends=[graph]; }; - Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.4.3"; sha256="0hjhjvg2kss71fkmxlbgnyyy1agwzgq57rxkgkm4riw82x2rvw7q"; depends=[]; }; - Rhtslib = derive2 { name="Rhtslib"; version="1.14.1"; sha256="13fv78sk5g0gqfl3ks3rps3zc1k66a4lzxvgn36r7ix43yxk7hnr"; depends=[zlibbioc]; }; - RiboProfiling = derive2 { name="RiboProfiling"; version="1.12.0"; sha256="1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; }; - Ringo = derive2 { name="Ringo"; version="1.46.0"; sha256="1zg8sq4hqq3yldghfs1m2jn15qmdk6i1pr7c3aq73a6k99qyzihd"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; }; - Risa = derive2 { name="Risa"; version="1.24.0"; sha256="1ln68rxv7wx96b3p2fh70jva07j9hj1cfflxyw34i32qkp2840hm"; depends=[affy Biobase biocViews Rcpp xcms]; }; - Rmagpie = derive2 { name="Rmagpie"; version="1.38.0"; sha256="0di8vf3cj7y2srydjq74r7gmksqhjh3r8wmffq1k96knd68nx0sx"; depends=[Biobase e1071 kernlab pamr]; }; - RmiR = derive2 { name="RmiR"; version="1.38.0"; sha256="0gv6cm5mh54xh2n25mpy6ak849rcppnajq04y7nw9hjv1i66g125"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; }; - Rmmquant = derive2 { name="Rmmquant"; version="1.0.4"; sha256="085yn4qg5sn7cbl7gj3b56n7mxiagdj4k8zqqd131dsd5kzwlylc"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - RnBeads = derive2 { name="RnBeads"; version="2.0.1"; sha256="0lfvl0k138dhniffb4c8wdicsihajr6rnrfmmmcgxk2wh6ciibi5"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; - RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="1.14.1"; sha256="1gxsp3nr5ww3xlqyac704lczsa5xxyz748lpfpkghj4mi3h0lwa8"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; }; - Rnits = derive2 { name="Rnits"; version="1.16.0"; sha256="1l96jvyq0afkv2k3gasf0420wbhrs1nv1f5xx0h9f4mhcx81hr7q"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; }; - Roleswitch = derive2 { name="Roleswitch"; version="1.20.0"; sha256="15cb4gbwgkjvidfdlvc2qf62jf3nvddqni9bbymcyi2pnpd1n6lr"; depends=[Biobase biomaRt Biostrings DBI microRNA plotrix pracma reshape]; }; - RpsiXML = derive2 { name="RpsiXML"; version="2.24.0"; sha256="1l9p5mi7b78cwh4pvwqwxx15rr4hms11m5r0vp0d2krfp7ih9m8h"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; }; - Rqc = derive2 { name="Rqc"; version="1.16.2"; sha256="1cxa6c9k9ahcji2c979hr0xz9hv7m8w4l6aiczfdhcnjraa4k2qq"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase digest GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; }; - Rsamtools = derive2 { name="Rsamtools"; version="1.34.1"; sha256="02paq7klabdkaf1b8pmmbpmyqsj3yncnfsz62rgka6r4dpsilwk9"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; }; - Rsubread = derive2 { name="Rsubread"; version="1.32.4"; sha256="1d0gc3pa7zjz2sa4689xxzppikv7xd6k1d8f1x7h973cyiq5iaj3"; depends=[]; }; - Rtreemix = derive2 { name="Rtreemix"; version="1.44.0"; sha256="013x6rdxsxynr8s0x8a1nk7xcanvgkm2lid9bip3v240bg9wwha4"; depends=[Biobase graph Hmisc]; }; - S4Vectors = derive2 { name="S4Vectors"; version="0.20.1"; sha256="18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"; depends=[BiocGenerics]; }; - SAGx = derive2 { name="SAGx"; version="1.56.0"; sha256="0p81jfm7fr907npbl1qrl4yswbz2a2pgmng5ww68xwmkayxkns79"; depends=[Biobase multtest]; }; - SANTA = derive2 { name="SANTA"; version="2.20.0"; sha256="1x4sq1vxvgrngq5aahbc2sgn1vw8l3d4b24fm0lldvn2b8jprzx7"; depends=[igraph Matrix snow]; }; - SBMLR = derive2 { name="SBMLR"; version="1.78.0"; sha256="02xcsaq2zlsvxj1zs2v4syw0k7fsiq826nny8kazvirkzpqmi446"; depends=[deSolve XML]; }; - SC3 = derive2 { name="SC3"; version="1.10.1"; sha256="04hqbw8k3f2nki5c9brkjlqm072cyw1ppgwlr7id3xqmg4w38l6w"; depends=[BiocGenerics cluster doParallel doRNG e1071 foreach ggplot2 pheatmap Rcpp RcppArmadillo robustbase ROCR rrcov S4Vectors shiny SingleCellExperiment SummarizedExperiment WriteXLS]; }; - SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.24.1"; sha256="00sfnc9pdw8j7gbrc6z4v9ji8kwndabr8zxw8agkbf2zz8pmq4jx"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; - SCBN = derive2 { name="SCBN"; version="1.0.0"; sha256="0cfmpwpp9drz13rrrwg030db1jprxfw2nkxlwlwscaj1vb4q69fv"; depends=[]; }; - SCnorm = derive2 { name="SCnorm"; version="1.4.7"; sha256="1jlfxwqy1gm1v0a40dd3p5zicr0wa4m7k4nqnf5ypbkngf31zfv9"; depends=[BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; }; - SDAMS = derive2 { name="SDAMS"; version="1.2.1"; sha256="0cr1mazrbq4hc2gql7bj4pvqd1vdzvpmg6r3dhvybb4prpdl25ys"; depends=[qvalue SummarizedExperiment trust]; }; - SELEX = derive2 { name="SELEX"; version="1.14.0"; sha256="1hcsngnxv4q0ig80nr91x1qlxi2swcx9xlvayng25izzjc6yj1k8"; depends=[Biostrings rJava]; }; - SEPA = derive2 { name="SEPA"; version="1.12.0"; sha256="04dl578fm1zdd30q9d5dxhcm1xvkn19ijda07yxdsxifik4297fp"; depends=[ggplot2 org_Hs_eg_db org_Mm_eg_db reshape2 segmented shiny topGO]; }; - SEPIRA = derive2 { name="SEPIRA"; version="1.2.0"; sha256="1lvbx621kspl3ry8hbqgf2chins420vn26x81x5q1skvhk9s6h03"; depends=[corpcor limma]; }; - SGSeq = derive2 { name="SGSeq"; version="1.16.2"; sha256="1s4pipdzppnixqx4x6xcy5pz1ps9mhjjxy1zj5h5dy2wi13mnsfs"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer RUnit S4Vectors SummarizedExperiment]; }; - SIAMCAT = derive2 { name="SIAMCAT"; version="1.2.1"; sha256="1gpcir6lcfg5q3m2zisvbnva8vx8mq1pml8na9nmkg92rdv42hwk"; depends=[beanplot corrplot glmnet gridBase gridExtra infotheo LiblineaR matrixStats mlr ParamHelpers phyloseq pROC PRROC RColorBrewer scales stringr]; }; - SICtools = derive2 { name="SICtools"; version="1.12.0"; sha256="06ypc7xqn8rpdyp16rlwsaw37gb94z9c980fwadbjvf2bzga5xwd"; depends=[Biostrings doParallel GenomicRanges IRanges matrixStats plyr Rsamtools stringr]; }; - SIM = derive2 { name="SIM"; version="1.52.0"; sha256="16rkh4nnpm1bzq9z85s64fl09ymrwifmdcanwg4q8vnasqdcyp01"; depends=[globaltest quantreg quantsmooth]; }; - SIMAT = derive2 { name="SIMAT"; version="1.14.1"; sha256="096cmj3xbcddyphy5z5ikwm459fqkibdxzqd24815z6yxld8bmf6"; depends=[ggplot2 mzR Rcpp reshape2]; }; - SIMD = derive2 { name="SIMD"; version="1.0.0"; sha256="15ivvgjhsabg9lvdfylqv4640jvmk65kj1lb3z8h7fwc24qhr6aj"; depends=[edgeR methylMnM statmod]; }; - SIMLR = derive2 { name="SIMLR"; version="1.8.1"; sha256="1j6v950dgbxbmwmn0yhb69six4cs1hlzr24dz7rxpdf84r63zsls"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; }; - SISPA = derive2 { name="SISPA"; version="1.12.0"; sha256="1vqgm6wiymvy83zj71anqknvya0h03pwcavc0gn6dfmxc2rhhk85"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; }; - SLGI = derive2 { name="SLGI"; version="1.42.0"; sha256="09665cxx7rl5aai10pcj5wwq90psygwpj5776vp8fjmv1bq8lgx8"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice ScISI]; }; - SLqPCR = derive2 { name="SLqPCR"; version="1.48.0"; sha256="1izzqzn42pzfxx28qj5nviwqd63jicw9gifk1m9w2r3j7asqwpqy"; depends=[]; }; - SMAP = derive2 { name="SMAP"; version="1.46.0"; sha256="0aqlqq0q5f5n9q8xfharzy55gx7p0gzijndbljj656jpy5dq6l9v"; depends=[]; }; - SMITE = derive2 { name="SMITE"; version="1.10.1"; sha256="1hmsv8i1np9m4dgskwjjzmprdixvx9yakx6y2p2icsjsppvqd69l"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGG_db org_Hs_eg_db plyr reactome_db S4Vectors scales]; }; - SNAGEE = derive2 { name="SNAGEE"; version="1.22.0"; sha256="1r9bvjc9l3xs1i9hrfzajhv6yb25qgnjgh1wyxrg0lky0n00z93m"; depends=[SNAGEEdata]; }; - SNPRelate = derive2 { name="SNPRelate"; version="1.16.0"; sha256="0p6lrjj0v63f2y31727my72c4pnqmyb22d6rpi3yk556d21nlbyr"; depends=[gdsfmt]; }; - SNPchip = derive2 { name="SNPchip"; version="2.28.0"; sha256="0vlrgraczyv4si4mrgssh6ijvq02qnb5h186rzqz0ssscjndh111"; depends=[Biobase foreach GenomeInfoDb GenomicRanges IRanges lattice oligoClasses S4Vectors SummarizedExperiment]; }; - SNPediaR = derive2 { name="SNPediaR"; version="1.8.0"; sha256="124nw9ncf2mlkrw11v0azl69hhvj7cc8zyd78i16n8biw8pcphb7"; depends=[jsonlite RCurl]; }; - SNPhood = derive2 { name="SNPhood"; version="1.12.0"; sha256="1f6rhlkisdx8psl7d2anxm03l205aas2iwr2par2q4bl3v10aqky"; depends=[BiocGenerics BiocParallel Biostrings checkmate cluster data_table DESeq2 GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges lattice RColorBrewer reshape2 Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; - SPEM = derive2 { name="SPEM"; version="1.22.0"; sha256="1qy92c8hjlxiji8bwzfmwf2nndnafqfmxpkxxwz3xsa9nvbsy22j"; depends=[Biobase Rsolnp]; }; - SPIA = derive2 { name="SPIA"; version="2.34.0"; sha256="1x9rkhza6wky0wfy5bb4bjlmwlhpap9l7mc2svk15nv6r7dwr0v8"; depends=[KEGGgraph]; }; - SPLINTER = derive2 { name="SPLINTER"; version="1.8.1"; sha256="0s9cr79xarry5g2s1qp0dp0lp6y49asnbc4dcdrm9j7gqmd78s3l"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 googleVis Gviz IRanges plyr S4Vectors seqLogo stringr]; }; - SPONGE = derive2 { name="SPONGE"; version="1.4.0"; sha256="15f7n452nn0avkylvrh49c2s9k2bnfzn4i6d58k8dp71vld0n07i"; depends=[Biobase data_table doRNG expm foreach glmnet gRbase igraph iterators logging MASS ppcor]; }; - SQUADD = derive2 { name="SQUADD"; version="1.32.0"; sha256="02z9mcbwaprjpwbbbyxi50hkhi13zm4sa9qy43bkha98i2r2flkn"; depends=[RColorBrewer]; }; - SRAdb = derive2 { name="SRAdb"; version="1.44.0"; sha256="1d2fbgzz9vrv1z8wj5pgi8f31dbd6zh8kn76qw972b3s3zd9apni"; depends=[GEOquery graph RCurl RSQLite]; }; - SRGnet = derive2 { name="SRGnet"; version="1.8.0"; sha256="0xcnkdnh7ihjay60fig6vq3xs5953m9ar3pysrka8yi1pfk9j4xx"; depends=[DMwR EBcoexpress gbm Hmisc igraph limma MASS matrixStats pvclust]; }; - SSPA = derive2 { name="SSPA"; version="2.22.1"; sha256="0540i0yfpxzyx2cvsfmd6ymsc4shalpvx134fs9rhaw9l9y17c9n"; depends=[lattice limma qvalue]; }; - STAN = derive2 { name="STAN"; version="2.10.1"; sha256="0fm0y4nks74rqn5fwq8mrg687mnikjhf2rg7fk815l2d52zpsqgk"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; }; - STATegRa = derive2 { name="STATegRa"; version="1.18.0"; sha256="0928yjgaqgx0axiwfrff1dhqcqbjh5hqdsf8607da4ncf58qcglk"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; }; - STRINGdb = derive2 { name="STRINGdb"; version="1.22.0"; sha256="0xfcxq1h4c756rfz1pkcq8zigf0lacrskxzid28lzawd047l224h"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; - STROMA4 = derive2 { name="STROMA4"; version="1.6.1"; sha256="1iw5q8mz8fgjx9prgdp5y11gnrz37rjllbb2xmlvvk92xc06s3f3"; depends=[Biobase BiocParallel cluster matrixStats]; }; - SVAPLSseq = derive2 { name="SVAPLSseq"; version="1.8.1"; sha256="0sd2bhx19pynwm2k4811k0l846cc9vdhf9g7h73kjipmh8fq42lg"; depends=[edgeR ggplot2 limma lmtest pls SummarizedExperiment]; }; - SVM2CRM = derive2 { name="SVM2CRM"; version="1.14.0"; sha256="0m8x176kaf7k4zfb7cyxan4if42v4g3w3yr24a35d3a0yhn9lkgb"; depends=[AnnotationDbi GenomicRanges IRanges LiblineaR mclust pls ROCR rtracklayer squash SVM2CRMdata verification zoo]; }; - SWATH2stats = derive2 { name="SWATH2stats"; version="1.12.1"; sha256="1j92121a48lz5bvxa9p3k1h7j1qi0za7z1vqmi683afn15j7cbmb"; depends=[biomaRt data_table ggplot2 reshape2]; }; - SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.36.1"; sha256="19mmpn10m1vr9c13c9s26jmfhi2ha3w8nkldw2r6ci61vwldicrx"; depends=[]; }; - ScISI = derive2 { name="ScISI"; version="1.54.0"; sha256="1xs5vwgvcq72jiir5sl99z9pa4kh28jaidj1h31cvfsz0yjkfsl9"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; }; - Scale4C = derive2 { name="Scale4C"; version="1.4.0"; sha256="12d8l6j57gwnrigzyprfw03rzgsni7n75ws2hi1ldybx7bx3nlag"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; }; - Sconify = derive2 { name="Sconify"; version="1.2.1"; sha256="141iq9k1psyc25vf1i8hh52i3dckas1l928yjr59p25qng0z4hfy"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; }; - SemDist = derive2 { name="SemDist"; version="1.16.0"; sha256="086lparkzxssz78dn67x4f7c3pw45y7gj2ldvhmkfqyynfm57giq"; depends=[annotate AnnotationDbi GO_db]; }; - SeqArray = derive2 { name="SeqArray"; version="1.22.6"; sha256="1aj6k5vr1rcjavm8q65cw93wwb3kjb1hg74r7nwc5rl94sg0gsan"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; - SeqGSEA = derive2 { name="SeqGSEA"; version="1.22.1"; sha256="1c4lfs9bfdmbq732c13fvph5gwp6ac0fxa489al9lghwxnbkjpqf"; depends=[Biobase biomaRt DESeq doParallel]; }; - SeqSQC = derive2 { name="SeqSQC"; version="1.4.0"; sha256="1dg4dm45s7l5dgq2cr6g9a5a65jlpf801z3a1x42h36ybgs7gg3j"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; }; - SeqVarTools = derive2 { name="SeqVarTools"; version="1.20.2"; sha256="03z40cmymq6agbmp061kvk4xm4cgilb3gyls5ymwyn4p56m0ks2a"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix rlang S4Vectors SeqArray tidyr]; }; - ShortRead = derive2 { name="ShortRead"; version="1.40.0"; sha256="0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; }; - SigCheck = derive2 { name="SigCheck"; version="2.14.0"; sha256="0k00lrzpjfdcp3yvjbd1bc3710pa0dd884k4yyq43nv0cv9f4szp"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; }; - SigFuge = derive2 { name="SigFuge"; version="1.20.0"; sha256="0z78yg43wklzrpqawpprgb6nm1wngkd97g09aa9nzv91p05k85dp"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; }; - SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.20.0"; sha256="0n5awvsjz215g6h0kz6mzhzxw3vnhbf16b1n3bkqb7kv4cdrd4vq"; depends=[Biobase limma mclust Ringo]; }; - SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.4.1"; sha256="12139kk9cqgzpm6f3cwdsq31gj5lxamz2q939dy9fa0fa54gdaq4"; depends=[BiocGenerics S4Vectors SummarizedExperiment]; }; - SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.18.0"; sha256="013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; - SpacePAC = derive2 { name="SpacePAC"; version="1.20.0"; sha256="1qm71d11ggwhkfk1rlq8zx2mjz7942ixcda1pgrd9m537zhjy469"; depends=[iPAC]; }; - SparseSignatures = derive2 { name="SparseSignatures"; version="1.2.0"; sha256="0wvlsdr75na5zi92hgj2bnxcxm8z9p8f99nfg6x3jzi39binwfr8"; depends=[Biostrings BSgenome BSgenome_Hsapiens_1000genomes_hs37d5 data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls]; }; - SpeCond = derive2 { name="SpeCond"; version="1.36.0"; sha256="0xx3wdfadw3jgmvvhsd2irdgqdd8pwlprcy07i3j2vja9ji0cx5f"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; - SpidermiR = derive2 { name="SpidermiR"; version="1.12.1"; sha256="1xz6rygpdc6f78dcg56fqblair1dswn2r6afycny94m3kllhc4hb"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra miRNAtap miRNAtap_db networkD3 org_Hs_eg_db TCGAbiolinks visNetwork]; }; - SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.22.2"; sha256="19isf8wxy7lpaqr4zy5319sx9r2bm6mh8djgcbabg6ns198iy0kq"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; }; - StarBioTrek = derive2 { name="StarBioTrek"; version="1.8.5"; sha256="1z79ylbjsy78ziji641h9jyqdv042csqmvr9wwhwz410xvqmh8ri"; depends=[AnnotationDbi e1071 ggplot2 graphite igraph MLmetrics reshape2 ROCR SpidermiR]; }; - Starr = derive2 { name="Starr"; version="1.38.0"; sha256="1rrs366d8yr02077v34l6yr8w361s94zira2gcf935kkmfrclgij"; depends=[affxparser affy MASS pspline Ringo zlibbioc]; }; - Streamer = derive2 { name="Streamer"; version="1.28.1"; sha256="0spqdjmfz1iaa6rcmbzn9d8z60cs1k0smvnnsdjlg7frdh039ra8"; depends=[BiocGenerics graph RBGL]; }; - SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="2.0.1"; sha256="18gmzwxjwg8j63z213x8r0j6jpmgx4yca29495c2hp4r9gv6hbzr"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; }; - SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.12.0"; sha256="07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix S4Vectors]; }; - Sushi = derive2 { name="Sushi"; version="1.20.0"; sha256="0dv5di0hgbvk9cxnqhyf18mdjl50k6bk00a89r6zgp83rbxwr1r8"; depends=[biomaRt zoo]; }; - SwathXtend = derive2 { name="SwathXtend"; version="2.4.0"; sha256="0986srxbi3f7pfnhghh9dznwrl9k5qrcmcf1vqa3lg06bwz7pbsc"; depends=[e1071 lattice openxlsx VennDiagram]; }; - SwimR = derive2 { name="SwimR"; version="1.20.0"; sha256="0sgci3rs4kak79yibcvxw3mjb30y9q8hacqykrpav2sjyqc6fcy1"; depends=[gplots heatmap_plus R2HTML signal]; }; - TCC = derive2 { name="TCC"; version="1.22.1"; sha256="0yfjlr5pgdnkrcv97cqhkm5xdn7dlspbf3fd60ai8zm2iw62x031"; depends=[baySeq DESeq DESeq2 edgeR ROC]; }; - TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.10.5"; sha256="1p73950jyvnbilpr4rzwmxw2bdi3h7lb2qiaqvm4rahmxmymy9nj"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr sesame stringr SummarizedExperiment survival survminer sva tibble tidyr XML xml2]; }; - TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.8.1"; sha256="1bj4pvchg0fj6gifbkg79fi314ssl8zp4rylp2ib0jfliqjx5199"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame sesameData shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; }; - TCGAutils = derive2 { name="TCGAutils"; version="1.2.2"; sha256="00wi93lxq06aczjj9g5drs4jy6c4md550hbqxf6p11f07mh7kqcy"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; - TCseq = derive2 { name="TCseq"; version="1.6.1"; sha256="01lakq59skdivgyb613x4rwxfap9iiccwi2ixd0nl7vw97wsjfc3"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; - TDARACNE = derive2 { name="TDARACNE"; version="1.32.0"; sha256="0b7p7pl9sn2g3f7wv405nwng2xknxqhdwqm2bkr4czxcrmwdal5f"; depends=[Biobase GenKern Rgraphviz]; }; - TEQC = derive2 { name="TEQC"; version="4.4.0"; sha256="16aj8nadcpnv1lqqz7pfss7vc2s5h0k79ahxb4l4405j8yrf16hl"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; }; - TFARM = derive2 { name="TFARM"; version="1.4.0"; sha256="1bi7j7x8libijsf7c144fbf456f5vhaj8b3avdil49qa4k78623w"; depends=[arules fields GenomicRanges stringr]; }; - TFBSTools = derive2 { name="TFBSTools"; version="1.20.0"; sha256="18iqr2xsmgkmm5x4dz1vm9ig13x9vb1kvqxc0gpc4pzanf3w6jrp"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; }; - TFEA_ChIP = derive2 { name="TFEA.ChIP"; version="1.2.3"; sha256="04qhwx6kmgyiasm2kynacwmd0i17b1bxr3ivg7jw3nr2dmg21h4g"; depends=[biomaRt dplyr GenomicFeatures GenomicRanges IRanges org_Hs_eg_db R_utils TxDb_Hsapiens_UCSC_hg19_knownGene]; }; - TFHAZ = derive2 { name="TFHAZ"; version="1.4.0"; sha256="18mfmcbb5vfr2c96gai3hdzvbb3jzfnmmrclcdp9shrpwg6l1ipd"; depends=[GenomicRanges IRanges S4Vectors]; }; - TFutils = derive2 { name="TFutils"; version="1.2.0"; sha256="1gppabscwfbqyvwrnl7mppw9wp528plp3bxq7g73hhgackfwnwkc"; depends=[dplyr magrittr miniUI shiny]; }; - TIN = derive2 { name="TIN"; version="1.14.0"; sha256="0n5lx8pg066z9adjsfnslxw6fv0w0ibv7nk2yz8qaiq6zivvcc1y"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; }; - TMixClust = derive2 { name="TMixClust"; version="1.4.0"; sha256="03i9fgq29xr3h72c2scb4fa6305l7bpwj6hgk0j1v7ark6xz5xqz"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; }; - TPP = derive2 { name="TPP"; version="3.10.1"; sha256="00rfxhzamz45phav239xki8jy9bj7f0r03wrl9d09ir5amis271p"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown stringr tidyr VennDiagram VGAM]; }; - TRONCO = derive2 { name="TRONCO"; version="2.14.2"; sha256="1cqkk6zsfsjpq8iidvmpfvkfak3ryp2bl9p04in0sn8sl9is6nsq"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; }; - TSCAN = derive2 { name="TSCAN"; version="1.20.0"; sha256="1yas32djld4dlsmzi65dflmnrff48m7vb6j7wgr44jip416mh7l1"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; }; - TSRchitect = derive2 { name="TSRchitect"; version="1.8.9"; sha256="0i5i7m2rfqgnr2n39hfdgbvlhm8aqa6c77i7jvp66lapskww4rgb"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - TSSi = derive2 { name="TSSi"; version="1.28.0"; sha256="1i0qcp5nygfny8pq6x70miig8gcf0an91rckci602m8il2x66rmp"; depends=[Biobase BiocGenerics Hmisc IRanges minqa plyr S4Vectors]; }; - TTMap = derive2 { name="TTMap"; version="1.4.0"; sha256="0cwajx9kfgs4dz10j88fbg5jlzj3yr6im23972swab58kl2n30vz"; depends=[Biobase colorRamps rgl SummarizedExperiment]; }; - TVTB = derive2 { name="TVTB"; version="1.8.0"; sha256="058h38x6x69jsp8qsdy7mz9wjjvhw4dwbph14qgqvagbaiaj7v19"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; }; - TarSeqQC = derive2 { name="TarSeqQC"; version="1.12.0"; sha256="1p1fwmkikh6a6sff3hmdxc3z4ypxz2iv1j544gfmsq47pibn8cgp"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; }; - TargetScore = derive2 { name="TargetScore"; version="1.20.0"; sha256="0kxiv5rghq3fw416gg3z7gfram146hjaf5pjd5hbyvy7rydilvbz"; depends=[Matrix pracma]; }; - TargetSearch = derive2 { name="TargetSearch"; version="1.38.2"; sha256="1vad4kxsanmjk78wjqq6lq3mjif01b89f09mhg0rwp902bdqlk35"; depends=[ncdf4]; }; - TimeSeriesExperiment = derive2 { name="TimeSeriesExperiment"; version="1.0.4"; sha256="03ny8w0z29jblph8nsysrqm7l2m2qpij52415vv1an4wpv821pgd"; depends=[DESeq2 dplyr dynamicTreeCut edgeR ggplot2 Hmisc limma magrittr proxy S4Vectors SummarizedExperiment tibble tidyr vegan viridis]; }; - TissueEnrich = derive2 { name="TissueEnrich"; version="1.2.1"; sha256="13nbcrj441wrbjn8xbrb8fn802bimhnaxjb980bn55l0ix7npy1c"; depends=[dplyr ensurer ggplot2 GSEABase SummarizedExperiment tidyr]; }; - TitanCNA = derive2 { name="TitanCNA"; version="1.20.1"; sha256="0vp5i30n3f8kschal06i3v4szl1vl3lvry522csxdax3pram90g8"; depends=[data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges Rsamtools VariantAnnotation]; }; - TnT = derive2 { name="TnT"; version="1.4.0"; sha256="0cza7l550ly35w0c1xjvixgxwdl53v90q0rnb6i7jj6yxgq4ppwq"; depends=[Biobase data_table GenomeInfoDb GenomicRanges htmlwidgets IRanges jsonlite knitr S4Vectors]; }; - ToPASeq = derive2 { name="ToPASeq"; version="1.16.1"; sha256="0j54fvcs7ynd6n81x07r2xra3l1fr1yfv8gf46r77gzmcn1y39vs"; depends=[graph graphite Rcpp]; }; - TransView = derive2 { name="TransView"; version="1.26.1"; sha256="1y2cdyg0hixm3zxasib18ql9917vnf43cjn9wpkx52fqfwa62ly3"; depends=[BiocGenerics GenomicRanges gplots IRanges Rsamtools S4Vectors zlibbioc]; }; - Trendy = derive2 { name="Trendy"; version="1.4.6"; sha256="0xk3xyx9094ymwfxabgqd0pykwhi8izjpck6dfm16chjlq3hik69"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; }; - TurboNorm = derive2 { name="TurboNorm"; version="1.30.0"; sha256="0a3f1zgj914rklrdilcnqfcr4g3mhg1bzfzxr6nn2cqin47hlakp"; depends=[affy convert lattice limma marray]; }; - TxRegInfra = derive2 { name="TxRegInfra"; version="1.2.1"; sha256="1qvc0lb3x3s1hv1qw1yih79kdd7pa5wa9wdd94yd8z4vfasmfvav"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; }; - TypeInfo = derive2 { name="TypeInfo"; version="1.48.0"; sha256="0h2jnshr2sgyay3isiapfagjjh4wnff7nw711j4gxw9wg328w24l"; depends=[]; }; - UNDO = derive2 { name="UNDO"; version="1.24.0"; sha256="0yins1aw7gfp5qxmsai4l59nl5i6diq1h2frvdshsg6dbfxkzy67"; depends=[Biobase BiocGenerics boot MASS nnls]; }; - Ularcirc = derive2 { name="Ularcirc"; version="1.0.0"; sha256="1h4pv78x78wlgq0zmdjgdapjp7bxzdkw078pq9h6xzhkwvmyilz3"; depends=[AnnotationHub Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicFeatures gsubfn httpuv mirbase_db moments shiny shinyFiles Sushi yaml]; }; - UniProt_ws = derive2 { name="UniProt.ws"; version="2.22.0"; sha256="02rb0ygc3pikb8qbi8134n9hjzza4n3bvqbqfl5dqb2n1ibkknmq"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; }; - Uniquorn = derive2 { name="Uniquorn"; version="2.2.1"; sha256="0wh57344icpd84l4gj7lz2n75mhpw6ywsir7zj4ky83p30x066sr"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; - VanillaICE = derive2 { name="VanillaICE"; version="1.44.0"; sha256="0v4bqcwbbzabmq1pcs55j3jlhqssr2jsr9hxh76p1n7d6fw4dgs6"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; }; - VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.28.13"; sha256="1a7b0bg579ynpbfh5dk87fdgl62r9cwk4zmrl61m6zil7881p3gh"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; - VariantFiltering = derive2 { name="VariantFiltering"; version="1.18.0"; sha256="13z1x1v9xbdzsfn9x66b6sd18pla98cwd5zvxkwaiph8rp8bgvic"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores graph Gviz IRanges RBGL Rsamtools S4Vectors shiny shinyjs shinythemes shinyTree SummarizedExperiment VariantAnnotation XVector]; }; - VariantTools = derive2 { name="VariantTools"; version="1.24.0"; sha256="1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; - Vega = derive2 { name="Vega"; version="1.30.0"; sha256="035f2ly3y5i4cirwvfham5kpyawg9scfvfvyn7ys4lyjxx59y4dd"; depends=[]; }; - VegaMC = derive2 { name="VegaMC"; version="3.20.0"; sha256="0cgvfmwxrprrzgp0fxhi944y1z83h4mjv89iax2bshpwp1q5d9xr"; depends=[Biobase biomaRt genoset]; }; - Wrench = derive2 { name="Wrench"; version="1.0.0"; sha256="12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"; depends=[limma locfit matrixStats]; }; - XBSeq = derive2 { name="XBSeq"; version="1.14.1"; sha256="0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; }; - XDE = derive2 { name="XDE"; version="2.28.0"; sha256="034474qsc065z85wjlr8g695cpknh9kwbhzqdkh8fab2j06249sr"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools MergeMaid mvtnorm RColorBrewer siggenes]; }; - XINA = derive2 { name="XINA"; version="1.0.1"; sha256="0gwgcvipr014w96ds13kf3gap3fkvyq0vamdfds3nacd9h1hgmbp"; depends=[alluvial Biobase ggplot2 gridExtra igraph mclust plyr STRINGdb]; }; - XVector = derive2 { name="XVector"; version="0.22.0"; sha256="01fph1ydd6g0rl5mcw54spx22glq2kqv7wyw8bqw0plmabzcwwdm"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; - YAPSA = derive2 { name="YAPSA"; version="1.8.0"; sha256="1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"; depends=[circlize ComplexHeatmap corrplot dendextend GenomeInfoDb GenomicRanges GetoptLong ggplot2 gridExtra gtrellis KEGGREST lsei PMCMR reshape2 SomaticSignatures VariantAnnotation]; }; - a4 = derive2 { name="a4"; version="1.30.0"; sha256="1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; }; - a4Base = derive2 { name="a4Base"; version="1.30.0"; sha256="0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"; depends=[a4Core a4Preproc annaffy AnnotationDbi Biobase genefilter glmnet gplots limma mpm multtest]; }; - a4Classif = derive2 { name="a4Classif"; version="1.30.0"; sha256="02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"; depends=[a4Core a4Preproc glmnet MLInterfaces pamr ROCR varSelRF]; }; - a4Core = derive2 { name="a4Core"; version="1.30.0"; sha256="1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"; depends=[Biobase glmnet]; }; - a4Preproc = derive2 { name="a4Preproc"; version="1.30.0"; sha256="1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"; depends=[AnnotationDbi]; }; - a4Reporting = derive2 { name="a4Reporting"; version="1.30.0"; sha256="124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"; depends=[annaffy xtable]; }; - aCGH = derive2 { name="aCGH"; version="1.60.0"; sha256="0bmcw2pf4g584vjzagi70bxfasgzbi7nbis638aa5aymqgssclh8"; depends=[Biobase cluster multtest survival]; }; - abseqR = derive2 { name="abseqR"; version="1.0.0"; sha256="0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"; depends=[BiocParallel BiocStyle circlize flexdashboard ggcorrplot ggdendro ggplot2 gridExtra knitr plotly plyr png RColorBrewer reshape2 rmarkdown stringr vegan VennDiagram]; }; - acde = derive2 { name="acde"; version="1.12.0"; sha256="1qlas1fkjwx3x7ylhx4xwgwd3xyyijgsaqprfz3zk32cym67igx2"; depends=[boot]; }; - adSplit = derive2 { name="adSplit"; version="1.52.0"; sha256="0q5h0gizdxmpaz946ynzh1kbx51yd98z23y21bh7a3m2cqhr63gi"; depends=[AnnotationDbi Biobase cluster GO_db KEGG_db multtest]; }; - adaptest = derive2 { name="adaptest"; version="1.2.0"; sha256="1ibrzga0jk5rs6a097gn5ar7hkz8zja54l35xznp72jaradprj2i"; depends=[calibrate origami SummarizedExperiment tmle]; }; - affxparser = derive2 { name="affxparser"; version="1.54.0"; sha256="0cfsab3jih4zbrzfpd2cgi4wry2xmp8hmchpp70z33x0shwcxddx"; depends=[]; }; - affy = derive2 { name="affy"; version="1.60.0"; sha256="0x8h4fk2igv7vykqfvf6v9whmx3344v5rf3gyfajd431xkjldz6k"; depends=[affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc]; }; - affyContam = derive2 { name="affyContam"; version="1.40.0"; sha256="1qday3swgrgziymmwl2iyz2f8kd610hgpj9i9dsv8x09nks0jxcm"; depends=[affy affydata Biobase]; }; - affyILM = derive2 { name="affyILM"; version="1.34.0"; sha256="1v5spxwfg5vbca6rh2d3zsnsz1rlji02wfxq45pljwqcjr7pk6zy"; depends=[affxparser affy Biobase gcrma]; }; - affyPLM = derive2 { name="affyPLM"; version="1.58.0"; sha256="0n827mshllqj867w137x8qly992rvls9wcygmr09gmpy8f5hr0d2"; depends=[affy Biobase BiocGenerics gcrma preprocessCore zlibbioc]; }; - affyPara = derive2 { name="affyPara"; version="1.42.0"; sha256="0jk2r1v3yq1p9ny9hj46w42aq34m00bfm62a2n38cvql4zjrp6wz"; depends=[affy affyio aplpack snow vsn]; }; - affyQCReport = derive2 { name="affyQCReport"; version="1.60.0"; sha256="0l9znngszbjdwyyc1kpjszy3mrmwx781ww3wq8hs19jwvczgscyc"; depends=[affy affyPLM Biobase genefilter lattice RColorBrewer simpleaffy xtable]; }; - affycomp = derive2 { name="affycomp"; version="1.58.0"; sha256="1hkaa0g6kzmsnhd5vq8qy856rj7l5hcknhl62j47pqvwigfb1adg"; depends=[Biobase]; }; - affycoretools = derive2 { name="affycoretools"; version="1.54.0"; sha256="022pmik9gxpc0j3fcb2gmi8vchjwg3pwp1yn0cg5qfhy4w8mbyzz"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; }; - affyio = derive2 { name="affyio"; version="1.52.0"; sha256="1s4zp1211vf0krxzch9v3q3r6vs8hihqppq18i2fpvwlknfja7c1"; depends=[zlibbioc]; }; - affylmGUI = derive2 { name="affylmGUI"; version="1.56.0"; sha256="1hpr812jys2d265r6007bh2p1d6hay25dg7ia39xwcycmwjfn9xq"; depends=[affy affyio affyPLM BiocGenerics BiocManager gcrma limma R2HTML tkrplot xtable]; }; - affypdnn = derive2 { name="affypdnn"; version="1.56.0"; sha256="0v8913xw30xf42pvql9m4wk5sqnrvydhn1a13amk7prfr2hhjnjr"; depends=[affy]; }; - agilp = derive2 { name="agilp"; version="3.14.0"; sha256="0jqgd582b9p3dclfs0ps4agj64vxmvqp9a2a9bw12dywschhngq3"; depends=[]; }; - alpine = derive2 { name="alpine"; version="1.8.0"; sha256="1ijh1lxl6w7raw2lvzxf20jx8x20d8p9mci62q3fpkc35i8312m6"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; }; - alsace = derive2 { name="alsace"; version="1.18.0"; sha256="1946iwghbsy0dcdpx7wl284prg5xikr0s7aj8pvv7gcmah8i9i7n"; depends=[ALS ptw]; }; - altcdfenvs = derive2 { name="altcdfenvs"; version="2.44.0"; sha256="1fkly7m4fgah6v7a6fglxqzik2562q6hg6ffq89kbgnzgvab4xsi"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; }; - ampliQueso = derive2 { name="ampliQueso"; version="1.20.0"; sha256="1dwphzsl45g537ic1m2bbg80dcilvhg1w8c02zlsxlihhid5rwy7"; depends=[DESeq doParallel edgeR foreach genefilter ggplot2 gplots knitr rgl rnaSeqMap samr statmod VariantAnnotation xtable]; }; - amplican = derive2 { name="amplican"; version="1.4.1"; sha256="0wshidpdg3pqzmwshq5ics38gfmrwfqm803y83ynd7b0k9fch07h"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggforce ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats rmarkdown S4Vectors ShortRead stringr waffle]; }; - anamiR = derive2 { name="anamiR"; version="1.10.0"; sha256="0yk56vkibnbfwlnixh5r4a9iw9pnmavl7lv4p0jdmv2wnx85gzgz"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; }; - annaffy = derive2 { name="annaffy"; version="1.54.0"; sha256="16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"; depends=[AnnotationDbi Biobase DBI GO_db KEGG_db]; }; - annmap = derive2 { name="annmap"; version="1.24.0"; sha256="12047l7sc3ayvicqnlxc424kbvbiiz1nn4rczd1n50b8kzc25fjs"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; }; - annotate = derive2 { name="annotate"; version="1.60.1"; sha256="0pk6ayr3vyqxk850ljkbyil4i382ngfqcbxlv0qrp62yfqgzcjwp"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; }; - annotationTools = derive2 { name="annotationTools"; version="1.56.0"; sha256="0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"; depends=[Biobase]; }; - annotatr = derive2 { name="annotatr"; version="1.8.0"; sha256="1rknhlndn9fxa68dbkqjphiv50xqp28vf1259k5w7vlm75vvdkdv"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; }; - anota = derive2 { name="anota"; version="1.30.0"; sha256="182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"; depends=[multtest qvalue]; }; - anota2seq = derive2 { name="anota2seq"; version="1.4.2"; sha256="1x2l9c50j8pi8xk85pp4chvfb865zwj4ppaj02bi2lsjgqyda6wm"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; }; - antiProfiles = derive2 { name="antiProfiles"; version="1.22.0"; sha256="1div92hqrri8c0y5g37cc4ysi30gcklf82n6g0p98xwv54ks2y7j"; depends=[locfit matrixStats]; }; - apComplex = derive2 { name="apComplex"; version="2.48.1"; sha256="01vzk1blgwn0zqdgzhr19haa0ixd78gphxrhjab27n9g8s60i3jg"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; }; - apeglm = derive2 { name="apeglm"; version="1.4.2"; sha256="13yhm14cxw2gmckh7sjr1yy8q2x1wggmnbj2qp6zd7raq4l48qrb"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; - appreci8R = derive2 { name="appreci8R"; version="1.0.0"; sha256="1ajk6q40dr5il19ffnsfglbh1rfn8ylwv08mw9wfpvc26x4znwak"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ESP6500SI_V2_SSA137_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_0_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools rsnps S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; }; - aroma_light = derive2 { name="aroma.light"; version="3.12.0"; sha256="0vfifgpqxjjncbiv6gvlk9jmj14j90r9f30bqk3ks9v1csjnjhrb"; depends=[matrixStats R_methodsS3 R_oo R_utils]; }; - arrayMvout = derive2 { name="arrayMvout"; version="1.40.0"; sha256="1m3n2pqm40wsq7x7acspcq268608pnx58mndqfcbv813685b70p5"; depends=[affy affyContam Biobase lumi mdqc parody simpleaffy]; }; - arrayQuality = derive2 { name="arrayQuality"; version="1.60.0"; sha256="0fbvlilz111ahlm50gmwwjydpasbplr0lpj3dz9apawi0jff4f4a"; depends=[gridBase hexbin limma marray RColorBrewer]; }; - arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.38.0"; sha256="0xhzz9ixc5mp49cwpi4smdgdc3mrf1ppzhx8dpjahq1f7r3xnbb5"; depends=[affy affyPLM beadarray Biobase Cairo genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG vsn XML]; }; - artMS = derive2 { name="artMS"; version="1.0.12"; sha256="0px37blc5qhqwd7azgji67x74sh3y34aqr57g41sbaj1x0rh84bs"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; }; - attract = derive2 { name="attract"; version="1.34.1"; sha256="1370w8qvmiv8r48hk29mlh53xs5a78qpz6pbax7fq7q9xip7fbs0"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; }; - bacon = derive2 { name="bacon"; version="1.10.1"; sha256="1pd3p1cfggiy08458vplsy3s1zm5jqqcwrv4fks8ra2kf97j38df"; depends=[BiocParallel ellipse ggplot2]; }; - ballgown = derive2 { name="ballgown"; version="2.14.1"; sha256="073jyv98s05cxx8n83c20chh0k1sbw8rndldcdfq3habahllf8si"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; - bamsignals = derive2 { name="bamsignals"; version="1.14.0"; sha256="19irfx1y1izf903vq59wxsdbf88g143zy9l89gxqawh7jfxds8w8"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; - banocc = derive2 { name="banocc"; version="1.6.1"; sha256="18n273xwc49mr3d7b83nxqivyr5zzgcbv6kajq8ha641f34nasw1"; depends=[coda mvtnorm rstan stringr]; }; - basecallQC = derive2 { name="basecallQC"; version="1.6.0"; sha256="0l2w55lc8aknj3ivma3arp96j46hcfzw20k9js3dgx8k3sgalxmn"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; }; - bayNorm = derive2 { name="bayNorm"; version="1.0.9"; sha256="1jm06y6mv85hpjmn9qqikm3i2x6afzhkcby75r7k9dqg6an5zgra"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; }; - baySeq = derive2 { name="baySeq"; version="2.16.0"; sha256="0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"; depends=[abind edgeR GenomicRanges]; }; - bcSeq = derive2 { name="bcSeq"; version="1.4.1"; sha256="0izmzb341h85ixxdriiavwjjpw96r2pd2y9kwx9zi2rrbxa6wakf"; depends=[Biostrings Matrix Rcpp]; }; - beachmat = derive2 { name="beachmat"; version="1.4.0"; sha256="07zgmms0qg8gw7x0js46965bbhpfj2aa1h5ixdz9r332bxv9cdmr"; depends=[BiocGenerics DelayedArray HDF5Array Rcpp rhdf5 Rhdf5lib]; }; - beadarray = derive2 { name="beadarray"; version="2.32.0"; sha256="0xy75h98xkclsi2hxzz8qj21sm8fp3cy7ikmjsryvdbk7jwl6lgg"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 illuminaio IRanges limma reshape2]; }; - beadarraySNP = derive2 { name="beadarraySNP"; version="1.48.0"; sha256="1s1k5q1mczbnx5gdxa8r1igkmc8jw5dmnp0gl00q862bbsljplk9"; depends=[Biobase quantsmooth]; }; - bgafun = derive2 { name="bgafun"; version="1.44.0"; sha256="1sp3w0g0sxs6g42mjj76sjpi5ybcvhg6a4sp617713a71dab7276"; depends=[ade4 made4 seqinr]; }; - bgx = derive2 { name="bgx"; version="1.48.1"; sha256="0ygqbqpbrp4hy5dp4g7nn7zrfar855a7bp16dxcv7646vp3yrzk4"; depends=[affy Biobase gcrma Rcpp]; }; - bigmelon = derive2 { name="bigmelon"; version="1.8.0"; sha256="1wc5n5cq05a7qv0b46ywbgg1fbz0s8hyf83g861dxw8jhhmnm717"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; }; - bigmemoryExtras = derive2 { name="bigmemoryExtras"; version="1.30.0"; sha256="0pzqchv9namv73nm2vr6wjny7ghja8bs73s7xp4ixyfg4d1i9h06"; depends=[bigmemory]; }; - bioCancer = derive2 { name="bioCancer"; version="1.10.11"; sha256="0v55y3scj9qmiqjvqm4caj3ccchfv1dzmbc5jxgdb39vw1hjqsc2"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; }; - bioDist = derive2 { name="bioDist"; version="1.54.0"; sha256="1pl6z8yx1pns19y924x79ky4vqx180hifvy7n4mdhv6mjvhjkijl"; depends=[Biobase KernSmooth]; }; - bioassayR = derive2 { name="bioassayR"; version="1.20.1"; sha256="1zf1ykmn3wq6jxb6k1v00qna5wjlh4yy7x35x2k6zqgn7df4607z"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; - biobroom = derive2 { name="biobroom"; version="1.14.0"; sha256="1xfqa666n8h65y277a1g56r1z76x9fn0dnj45cqgx3ddaz0v1nil"; depends=[Biobase broom dplyr tidyr]; }; - biocGraph = derive2 { name="biocGraph"; version="1.44.0"; sha256="0nq8wvssikkcrs3vffpy3pj79iydm44ffsx67q38kg51gc4ykipk"; depends=[BiocGenerics geneplotter graph Rgraphviz]; }; - biocViews = derive2 { name="biocViews"; version="1.50.10"; sha256="06ms82pyc5rxbd9crfvqjxcwpafv0c627i83v80d12925mrc51h8"; depends=[Biobase graph RBGL RCurl RUnit XML]; }; - biomaRt = derive2 { name="biomaRt"; version="2.38.0"; sha256="1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2"; depends=[AnnotationDbi httr progress RCurl stringr XML]; }; - biomformat = derive2 { name="biomformat"; version="1.10.1"; sha256="1a4fhqmvabdpldybhjli5dpnd68qraccvd1f2zf7z2d1s17c9pgq"; depends=[jsonlite Matrix plyr rhdf5]; }; - biomvRCNS = derive2 { name="biomvRCNS"; version="1.22.0"; sha256="0bzi8b4g1ki8gslkb2nkrl4fyrl5lj9qipq8lmr6zj924y3pkmnm"; depends=[GenomicRanges Gviz IRanges mvtnorm]; }; - biosigner = derive2 { name="biosigner"; version="1.10.0"; sha256="04mny1lrgmwd1yy07qhim286xvm34802f12rbpsplb0xzwg09y6i"; depends=[Biobase e1071 randomForest ropls]; }; - biosvd = derive2 { name="biosvd"; version="2.18.0"; sha256="1ngmnk4xakpf451lbx9libxwlsqz7xffaj53awkw5iakzmj7szb9"; depends=[Biobase BiocGenerics NMF]; }; - biotmle = derive2 { name="biotmle"; version="1.6.0"; sha256="0vmff5xpcprx1x45fbbm9bx3wygg6r2zb7z9mnkjjshsinf7wwwb"; depends=[BiocGenerics BiocParallel doFuture dplyr future ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tmle]; }; - biovizBase = derive2 { name="biovizBase"; version="1.30.1"; sha256="0v5gvcx180qn5487i1dph9abadw3ggqwp5yzy41jswzbdc8q6sbm"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer rlang Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; - birta = derive2 { name="birta"; version="1.26.0"; sha256="10k6r3g92ksm90gj8z04vs1psgrr1p0yddrjl5zcwrccczcankpb"; depends=[Biobase limma MASS]; }; - birte = derive2 { name="birte"; version="1.18.0"; sha256="036grna913y55qz72npwq6k27wcvaf7swy3y9nrfh0wg327w4y9a"; depends=[Biobase glmnet limma MASS nem Rcpp RcppArmadillo]; }; - blima = derive2 { name="blima"; version="1.16.0"; sha256="1719skygq6mizvr67klja0z1xqbmfhxgjyi90i9p95sbb6mr1n74"; depends=[beadarray Biobase BiocGenerics Rcpp]; }; - bnbc = derive2 { name="bnbc"; version="1.4.0"; sha256="001m8nal3l1ya5w1f9gh7sgvdli9lv0v8ylkdgmdwjy2wrpkqiij"; depends=[BiocGenerics EBImage GenomeInfoDb GenomicRanges IRanges matrixStats preprocessCore Rcpp S4Vectors SummarizedExperiment sva]; }; - brainImageR = derive2 { name="brainImageR"; version="1.0.0"; sha256="1j5axlx12dpl6y58djqbf6dg146zz94ki43nhi9rjl03aw9bg9fc"; depends=[BiocGenerics ExperimentHub ggplot2 gridExtra randomForest RColorBrewer testthat]; }; - branchpointer = derive2 { name="branchpointer"; version="1.8.0"; sha256="1fgfaf7i9f1rr34p38b87wq5qys7r8wqi99xw4yk154bhsahkdlm"; depends=[biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg38 caret cowplot data_table gbm GenomeInfoDb GenomicRanges ggplot2 IRanges kernlab plyr rtracklayer S4Vectors stringr]; }; - breakpointR = derive2 { name="breakpointR"; version="1.0.0"; sha256="19hpwdpj5mqidy0m5q0ilx3p84ry0ym31g2ld3cnihzi2kxcyqzm"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; }; - bridge = derive2 { name="bridge"; version="1.46.0"; sha256="0fsf8qcl4p63fgzyk9zsr25krz1a34mi79mnxya0n4fxrf3qcq2f"; depends=[rama]; }; - bsseq = derive2 { name="bsseq"; version="1.18.0"; sha256="0r0l4fwaq09n14bvqy01id569zimxwafs3xnp0zn2089512igis7"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 Rhdf5lib S4Vectors scales SummarizedExperiment]; }; - bumphunter = derive2 { name="bumphunter"; version="1.24.5"; sha256="1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; - cTRAP = derive2 { name="cTRAP"; version="1.0.3"; sha256="14rfnqmp2mgnkyhgyvlplv4alnwm909pw586n7nc53r82ph4m0f0"; depends=[cowplot data_table fgsea ggplot2 httr limma pbapply piano plyr R_utils readr rhdf5]; }; - caOmicsV = derive2 { name="caOmicsV"; version="1.12.1"; sha256="1nqa1f5dbx11lfripaz2l7pkymcgi5vbiglhhk0kz4n0p5p1pjz3"; depends=[bc3net igraph]; }; - canceR = derive2 { name="canceR"; version="1.16.02"; sha256="1fzhd2mppzs3jkysyqg6brg62d6afxl2cm6dhnyz1sjp2951bvsv"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; - cancerclass = derive2 { name="cancerclass"; version="1.26.0"; sha256="1fsfxi95iyb2bhy64xdja4231bfs9byzzvdpsf6abd8myqaflcpx"; depends=[binom Biobase]; }; - casper = derive2 { name="casper"; version="2.16.1"; sha256="1wr7l1lri00g3fxafhjkj82y3nlh488x9ayjf4x3bcyv20d0lc2a"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; }; - categoryCompare = derive2 { name="categoryCompare"; version="1.26.0"; sha256="1kb4b833wn5qf3d6vic0jf0p0h6dhgcpjnxnqd6b4bhva0y3jcfd"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; - cbaf = derive2 { name="cbaf"; version="1.4.1"; sha256="04qspghxibf05fjx8sbqq8kxhx0y0lh8v5mv4lzzy13bhms9nfsk"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; }; - ccfindR = derive2 { name="ccfindR"; version="1.2.1"; sha256="0gcbqjlb4jpxw2rswwgld5nazzzsphh8kdaqpjhn96qslkfxqlrw"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; - ccmap = derive2 { name="ccmap"; version="1.8.0"; sha256="1vkkm455nhhg123jwl2kv3gdf3mvw5zab4whym0vh33rm499hrks"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; }; - ccrepe = derive2 { name="ccrepe"; version="1.18.1"; sha256="10c6mypr2q3j420bvldl59h1y58i8l06piwqr1ji80z6r6xk96vx"; depends=[infotheo]; }; - celaref = derive2 { name="celaref"; version="1.0.1"; sha256="0sb1mg2ql09jf7hc5kszh3h9cajma0pdwzf8f58pridwhafw5z0p"; depends=[BiocGenerics dplyr ggplot2 magrittr MAST Matrix readr rlang S4Vectors SummarizedExperiment tibble]; }; - cellGrowth = derive2 { name="cellGrowth"; version="1.26.1"; sha256="0zmn45i6shr2d6q2dg2p2raz38cy6k8363maq4r4648fx2bmvkb2"; depends=[lattice locfit]; }; - cellHTS2 = derive2 { name="cellHTS2"; version="2.46.1"; sha256="1fj1gshgphbbqhywwzvm3xrw8zfp19dc8fi6kbzv20ikf3am9fml"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit prada RColorBrewer splots vsn]; }; - cellTree = derive2 { name="cellTree"; version="1.12.1"; sha256="1qr68f39bqykvjbjp5bw71g41wfp369yc88dqz9wppkzi16vl6z0"; depends=[gplots igraph slam topGO topicmodels xtable]; }; - cellbaseR = derive2 { name="cellbaseR"; version="1.6.1"; sha256="0052wvb6jijs1v8yv1z049n6cy4qcjbrv20gqbsgl14xj0mif26x"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; }; - cellity = derive2 { name="cellity"; version="1.10.1"; sha256="1ifm50ff9q6lwxyi52qzksimnwvd8yddrp7jkidzlykamh5dg05p"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; }; - cellscape = derive2 { name="cellscape"; version="1.6.0"; sha256="062x43n5jq8hwlrlgd1ffgbpnifac79j9dzd35f6phb6vc1g63dl"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; }; - cghMCR = derive2 { name="cghMCR"; version="1.40.0"; sha256="0h2adfwa6afjik7zi6kn8i7gqbn7x2r7rh8kvi8v8c8y08166d3a"; depends=[BiocGenerics CNTools DNAcopy limma]; }; - charm = derive2 { name="charm"; version="2.28.0"; sha256="1shf9f9b0dl5fskify0lqnqnr9rk4hk5rnrx7b028m83zphizxs8"; depends=[Biobase Biostrings BSgenome ff fields genefilter gtools IRanges limma nor1mix oligo oligoClasses preprocessCore RColorBrewer siggenes SQN sva]; }; - chimera = derive2 { name="chimera"; version="1.24.0"; sha256="1zkwf6zbg1151br9kafbqs4k4d5h70lbzjgy4x3q5pj3iqwg6j8p"; depends=[AnnotationDbi Biobase BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges Homo_sapiens Rsamtools TxDb_Hsapiens_UCSC_hg19_knownGene]; }; - chimeraviz = derive2 { name="chimeraviz"; version="1.8.5"; sha256="0hh1a68g0m8i9iqhmy6r9m7j1diaraj3qryk7lzjr2l97d6q4d8j"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph gtools Gviz IRanges org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; }; - chipenrich = derive2 { name="chipenrich"; version="2.6.1"; sha256="0nm55lfac405spccl9f19p5ij8mdaj6lm7qmaf4xqagsaf5x0pa9"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; }; - chipseq = derive2 { name="chipseq"; version="1.32.0"; sha256="1pp1rm5fs3hlar5x4dl3a3b4gara7qwf81dbvka6r1n78hrf9x1b"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; }; - chopsticks = derive2 { name="chopsticks"; version="1.48.0"; sha256="0r52z0hjaxinw11jzg8cyhdpg2g1027vd5aiijwi6bmipdzw4sfk"; depends=[survival]; }; - chroGPS = derive2 { name="chroGPS"; version="2.0.1"; sha256="1bn5s1r927ifhwqifws0wgs7v15fk8922kbm8qdkg5zaqibj5qx7"; depends=[Biobase changepoint cluster ellipse GenomicRanges ICSNP IRanges MASS vegan]; }; - chromDraw = derive2 { name="chromDraw"; version="2.12.0"; sha256="0qqam9vklg2cwsvcp9fm3l3c4lmjzf2lnxrv5dci16f8q55z88cl"; depends=[GenomicRanges Rcpp]; }; - chromPlot = derive2 { name="chromPlot"; version="1.10.0"; sha256="15f7wmak0rp0bfzqsjmz6i8zk5g4axsgk7034qg4jw9hlp0nkd6v"; depends=[biomaRt GenomicRanges]; }; - chromVAR = derive2 { name="chromVAR"; version="1.4.1"; sha256="16q9pmjlaqc7nvaxg9arfsrrnpcyzvz0gb5zq7l3g2jgjp4pfi30"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; }; - chromstaR = derive2 { name="chromstaR"; version="1.8.1"; sha256="0ad8q80r7c2bh4a4qy0n82n0ln6fpwwmabcicpdqlvaiahdnp9ph"; depends=[bamsignals chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; }; - chromswitch = derive2 { name="chromswitch"; version="1.4.1"; sha256="12c9p8val2hfz41kcgph0ms2vfb8dvh754c5z70kyy4wg9n4d28s"; depends=[Biobase BiocParallel cluster dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats NMF rtracklayer S4Vectors tidyr]; }; - cicero = derive2 { name="cicero"; version="1.0.15"; sha256="0awxl47rk6f15x8qb70azjs80fsfd8c78bvr4hgc3dmiyik5frs2"; depends=[assertthat Biobase BiocGenerics data_table dplyr FNN GenomicRanges ggplot2 glasso Gviz igraph IRanges Matrix monocle plyr reshape2 S4Vectors stringr tibble VGAM]; }; - cisPath = derive2 { name="cisPath"; version="1.22.0"; sha256="07ym4ma35vngdbv8fdqf755kiafgrn02bizn77pfkzvrf7xsz5c7"; depends=[]; }; - cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.20.1"; sha256="0fy0bbj2d40532z7a019whf3g7092pj7ypg5p7byimcc2h9ybbh7"; depends=[BiocGenerics BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomicRanges seqinr]; }; - cleaver = derive2 { name="cleaver"; version="1.20.0"; sha256="0b00a5n87hcssnra9j0qfsq260a83g9p35rnhpg8ywv3kk6z85cc"; depends=[Biostrings IRanges S4Vectors]; }; - clippda = derive2 { name="clippda"; version="1.32.0"; sha256="18jcpcwzf89a29i7qlja4nx9dn8n2r14kpjfl9sy2riaf0v9cmqq"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; }; - clipper = derive2 { name="clipper"; version="1.22.0"; sha256="1gihz3dzii0bf048zbna4yj0fcs8pnhyacpmvyapi70iin03nwng"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; }; - clonotypeR = derive2 { name="clonotypeR"; version="1.20.0"; sha256="03k94s5j47mh7hw8m12q7lsyszmf5kpmlc7xsvwbnnazsk15h55v"; depends=[]; }; - clst = derive2 { name="clst"; version="1.30.0"; sha256="1jakdp6ca14n8zc3njwkqibsir6as2nipjsxkanss5rn7s6xvql9"; depends=[lattice ROC]; }; - clstutils = derive2 { name="clstutils"; version="1.30.0"; sha256="0igvcd1dk8njp8fmf8clnx1hjzsbpf6xr7n31qzynzqghdr52660"; depends=[ape clst lattice rjson RSQLite]; }; - clustComp = derive2 { name="clustComp"; version="1.10.0"; sha256="17d86fzadlmv45bxwdnjaw5bcr46zn73y4wqw5xw5rvaawrdc73v"; depends=[sm]; }; - clusterExperiment = derive2 { name="clusterExperiment"; version="2.2.0"; sha256="0r8x21z0clgjbxxdr3iqfmg0nw2pwdidyc41pnbzw9y40lzad4lv"; depends=[ape BiocGenerics cluster DelayedArray dendextend edgeR HDF5Array howmany kernlab limma locfdr matrixStats NMF phylobase RColorBrewer Rcpp RSpectra S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; - clusterProfiler = derive2 { name="clusterProfiler"; version="3.10.1"; sha256="1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"; depends=[AnnotationDbi DOSE enrichplot ggplot2 GO_db GOSemSim magrittr plyr qvalue rvcheck tidyr]; }; - clusterSeq = derive2 { name="clusterSeq"; version="1.6.0"; sha256="0zq0pah3qk4j5grsj3dyc62n222gacjlhr2xw7frwrrbjlxza7b2"; depends=[baySeq BiocGenerics BiocParallel]; }; - clusterStab = derive2 { name="clusterStab"; version="1.54.0"; sha256="0irwzgayssdnz76k13zf27h9s74x8idi26zfsdd2c3av494d3yl9"; depends=[Biobase]; }; - cn_farms = derive2 { name="cn.farms"; version="1.30.0"; sha256="1lmlixab15xq12dxw04yyxd1p65irwhxkgkxsgvw28f922bkmlsg"; depends=[affxparser Biobase DBI DNAcopy ff lattice oligo oligoClasses preprocessCore snow]; }; - cn_mops = derive2 { name="cn.mops"; version="1.28.0"; sha256="14rrvyfyzva1hpdgsn1df6m4q14mc3zdn1lng6klzrni3ifsidjm"; depends=[Biobase BiocGenerics exomeCopy GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; - cnvGSA = derive2 { name="cnvGSA"; version="1.26.0"; sha256="02p4ba2vy75qfp3nlfvm0dmmihi1k1fbcl6ckxlr5hgimm1q034i"; depends=[brglm doParallel foreach GenomicRanges splitstackshape]; }; - coGPS = derive2 { name="coGPS"; version="1.26.0"; sha256="0jsbgx6xdasqii9wcfn4ilf2dfc790lzzby1bhpzlq94nwlr896h"; depends=[]; }; - coMET = derive2 { name="coMET"; version="1.14.0"; sha256="09r81ag9ix4jh3zvwyzym9g7rc7vkyhagcv934r8i4fzzvpiqsz4"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; }; - coRdon = derive2 { name="coRdon"; version="1.0.3"; sha256="1v4zvzff4r54wjgp48l5vazvfy8w0gvvqxxhajm35p6d2bbpfsvd"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; }; - cobindR = derive2 { name="cobindR"; version="1.20.0"; sha256="1bkwjj825srwm3rn3j88p1q35x03f129ca1hk919nnf92psh47nc"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust seqinr yaml]; }; - codelink = derive2 { name="codelink"; version="1.50.0"; sha256="1nfnb9iz8j31ia9979mjvs9gzdbh9zwfy14qxvjrp3dv8d1gf2rx"; depends=[annotate Biobase BiocGenerics limma]; }; - coexnet = derive2 { name="coexnet"; version="1.4.0"; sha256="0751781vsr46xs3dpq2n29li1zipzad9qv6xnfdm34v62yaggy94"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; }; - cogena = derive2 { name="cogena"; version="1.16.0"; sha256="12r86h6fzr6wqvf70jjxf02zm72ks577m6qcv60wiss609c0b0dn"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2]; }; - compEpiTools = derive2 { name="compEpiTools"; version="1.16.0"; sha256="02ygqf2h9bm8vfqjfw0xzd75brcazf1dmhq95l8xqc3gy77cffr6"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; }; - compartmap = derive2 { name="compartmap"; version="1.0.3"; sha256="0p7ww7wgfnnankkjlq9jgqqcw9l9k0k2ynzmgxdqsyndpi9ghmgr"; depends=[GenomicRanges gtools Homo_sapiens minfi mixOmics SummarizedExperiment]; }; - compcodeR = derive2 { name="compcodeR"; version="1.18.1"; sha256="0833zar5zpgns3rlr6nsfagd1ypp62c2779kzajvsrjm61406mrs"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; }; - condcomp = derive2 { name="condcomp"; version="1.0.1"; sha256="1drp9zicf29alh8cq093ns7asl67zhb12mbi0cjd3n1z4i19919j"; depends=[cluster ggplot2 ggrepel outliers]; }; - consensus = derive2 { name="consensus"; version="1.0.3"; sha256="0lylnis33dbnd6vxp3g4pvn1cvzslpy6j2y1j31bw5an1i5lg4l2"; depends=[gplots matrixStats RColorBrewer]; }; - consensusDE = derive2 { name="consensusDE"; version="1.0.6"; sha256="1wakskzc6bcq0a8inacsd062z5sgaqkk8317pa2jdn8kyfqxgq9z"; depends=[airway AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings dendextend DESeq2 EDASeq edgeR GenomicAlignments GenomicFeatures limma pcaMethods RColorBrewer Rsamtools RUVSeq S4Vectors SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm3_ensGene]; }; - consensusOV = derive2 { name="consensusOV"; version="1.4.1"; sha256="0bqqbk2mcj1q5bpyv5gykxpjf3c1gszm5irbdhp1hnkvpy5rxdyw"; depends=[Biobase gdata genefu GSVA limma matrixStats randomForest]; }; - consensusSeekeR = derive2 { name="consensusSeekeR"; version="1.10.0"; sha256="1rww42z71x6d7ckjdm6xa4cvvqazbwghq6na3srq5aarp6pyh34w"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges IRanges rtracklayer S4Vectors stringr]; }; - contiBAIT = derive2 { name="contiBAIT"; version="1.10.1"; sha256="0wf8s1v8kz69s351xy4c9ji6k1k9xg568lg0b525s4q9wdh87xrl"; depends=[BH BiocParallel clue cluster colorspace data_table diagram DNAcopy exomeCopy GenomicAlignments GenomicFiles GenomicRanges ggplot2 gplots gtools IRanges Rcpp reshape2 Rsamtools rtracklayer S4Vectors TSP]; }; - conumee = derive2 { name="conumee"; version="1.16.0"; sha256="095kzjzvwz5l452arkvrmag7mvqsip14xzbnsfk7wzlr5vpk2765"; depends=[DNAcopy GenomeInfoDb GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges minfi rtracklayer]; }; - convert = derive2 { name="convert"; version="1.58.0"; sha256="1z7f4dxlsgknapvwq7dvkhyaq25ns2i53fp085j5yy89aqv12w12"; depends=[Biobase limma marray]; }; - copa = derive2 { name="copa"; version="1.50.0"; sha256="0cl9i2pi0ap9nvhqldsll9vg7k5qlzr0691mp4i7r6qib31xnzpx"; depends=[Biobase]; }; - copynumber = derive2 { name="copynumber"; version="1.22.0"; sha256="0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"; depends=[BiocGenerics GenomicRanges IRanges S4Vectors]; }; - coseq = derive2 { name="coseq"; version="1.6.1"; sha256="03qphm9bq7x4h4n970hd0bpi9sqvjdmg5cmlkzfqwpnbd4njlp0m"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; }; - cosmiq = derive2 { name="cosmiq"; version="1.16.1"; sha256="1lk0778j7famza72h8ppmx4pxnkmm6m6vddz0rw7fbnh3af8j9p2"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; }; - countsimQC = derive2 { name="countsimQC"; version="1.0.1"; sha256="115b806867fnznxdgr786vp7gd536xyz4x94v2s2wpaxwyf65jgs"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; }; - covEB = derive2 { name="covEB"; version="1.8.1"; sha256="197i9lmmq9xj4f9xxf1050blz5ap6nqbkhfpn19594fc88g09dxa"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; }; - covRNA = derive2 { name="covRNA"; version="1.8.0"; sha256="152yhnq13303wkb4p1bqal7qrg2gxwfqsdpgn84m2sz8gm43dxkc"; depends=[ade4 Biobase genefilter]; }; - cpvSNP = derive2 { name="cpvSNP"; version="1.14.0"; sha256="0g4b4i001z5s5g570cpay61c8b8274cy35gp09mb3hjmg5r6rcxp"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; }; - cqn = derive2 { name="cqn"; version="1.28.1"; sha256="062887yp5kalz8zv648a19gh1j5v26hbrv6005416r6z83rwj91q"; depends=[mclust nor1mix preprocessCore quantreg]; }; - crisprseekplus = derive2 { name="crisprseekplus"; version="1.8.0"; sha256="125fnm1mrx38bb2c6inw5c45ckh8ryapjvxx7227jj86a3hcljk7"; depends=[AnnotationDbi BiocManager BSgenome CRISPRseek DT GenomicFeatures GenomicRanges GUIDEseq hash shiny shinyjs]; }; - crlmm = derive2 { name="crlmm"; version="1.40.0"; sha256="1j37ff0pp782isnrzfaw0cac8nxcz09yc4z7xgss78ah3af26nwj"; depends=[affyio beanplot Biobase BiocGenerics ellipse ff foreach illuminaio lattice limma matrixStats mvtnorm oligoClasses preprocessCore RcppEigen SNPchip VGAM]; }; - crossmeta = derive2 { name="crossmeta"; version="1.8.0"; sha256="01d8vx016bw4qm3c6pwws1g3s2v7xppsj2v9gzdzwazpk4sfyikk"; depends=[affxparser affy AnnotationDbi Biobase BiocGenerics BiocManager ccmap data_table doParallel doRNG DT fdrtool foreach GEOquery ggplot2 limma matrixStats metaMA metap miniUI oligo pander plotly RColorBrewer rdrop2 reshape shiny stringr sva]; }; - csaw = derive2 { name="csaw"; version="1.16.1"; sha256="0rbmsikhj60np22j84gxinr354b2i892nqic493jhzziiznl51sl"; depends=[AnnotationDbi BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicFeatures GenomicRanges IRanges limma Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; }; - ctc = derive2 { name="ctc"; version="1.56.0"; sha256="0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"; depends=[amap]; }; - ctsGE = derive2 { name="ctsGE"; version="1.8.1"; sha256="0zwaky1azh7692qz2w64r5f13w1anww2a8wld10238nlnbmyzjrb"; depends=[ccaPP ggplot2 limma reshape2 shiny stringr]; }; - cummeRbund = derive2 { name="cummeRbund"; version="2.24.0"; sha256="1fl8p63zr1jxif95anhqg56cssi44k5y05g7qxpkf2w3siyv1b91"; depends=[Biobase BiocGenerics fastcluster ggplot2 Gviz plyr reshape2 RSQLite rtracklayer S4Vectors]; }; - customProDB = derive2 { name="customProDB"; version="1.22.1"; sha256="0wqjkgrjd3m6dx150039q1srfgp2749bfn8awdbmprl9pp4mkxx8"; depends=[AhoCorasickTrie AnnotationDbi biomaRt Biostrings DBI GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr RCurl Rsamtools RSQLite rtracklayer S4Vectors stringr VariantAnnotation]; }; - cycle = derive2 { name="cycle"; version="1.36.0"; sha256="0kx40mi7dh6k1s3vc32537q8585q8v4applzyw1y2pklap7sxzyl"; depends=[Biobase Mfuzz]; }; - cydar = derive2 { name="cydar"; version="1.6.1"; sha256="1j3d817xlhhxn4p32cms8br1kbpl34zdx502p70m4jd4sb6kr8p1"; depends=[Biobase BiocGenerics BiocNeighbors BiocParallel flowCore Rcpp S4Vectors shiny SingleCellExperiment SummarizedExperiment viridis]; }; - cytolib = derive2 { name="cytolib"; version="1.4.1"; sha256="0fl4p0ddbv0ifd4pyyda9ydfk47dg1rs3qd11wwqfc54ydqzcaha"; depends=[BH RProtoBufLib]; }; - dSimer = derive2 { name="dSimer"; version="1.8.0"; sha256="0pcggyimicsyx9wkgjxny8byyhb31phcr8xygi6sfkm17r2nxkwy"; depends=[AnnotationDbi ggplot2 GO_db igraph org_Hs_eg_db Rcpp reshape2]; }; - daMA = derive2 { name="daMA"; version="1.54.0"; sha256="0mgd90hdq0045bvzkvxfm6vd3i1n8fa0zmwnsyz5kmhavcynbvpj"; depends=[MASS]; }; - dada2 = derive2 { name="dada2"; version="1.10.1"; sha256="0858c4s7sqb54ida79dh3a6d0fxzh3c4pmxmp3vr0cnfndrlk5r1"; depends=[BiocGenerics Biostrings data_table ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; - dagLogo = derive2 { name="dagLogo"; version="1.20.0"; sha256="1h4mhhnmnfqifa1mxk03j1y7w1azai705q95wdji2nvyhi7gkas2"; depends=[biomaRt Biostrings grImport motifStack pheatmap]; }; - dcGSA = derive2 { name="dcGSA"; version="1.10.1"; sha256="1vma7gwl9ai8mj7zxc02g203cljcnyri69jgi7xl963pizya7cnj"; depends=[BiocParallel Matrix]; }; - ddCt = derive2 { name="ddCt"; version="1.38.0"; sha256="1gfxk55f8cgq9bs7rab01qi9093kmjii4833bxcxjhfx1mgsmgzz"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; }; - ddPCRclust = derive2 { name="ddPCRclust"; version="1.2.0"; sha256="1s9k86l0jc3jkwc2y85ccmn3jlfcwp985xhjfnv43rlfsi181063"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; - debrowser = derive2 { name="debrowser"; version="1.10.9"; sha256="1xdqw7scpzc4mw73f5la7km0yyvzhl5w9kxigpnlypba0npslpby"; depends=[annotate AnnotationDbi clusterProfiler colourpicker d3heatmap DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva]; }; - decontam = derive2 { name="decontam"; version="1.2.1"; sha256="0zi5nc39xvdrqdikqfvwhi5jly2gqv3z9r4wwbw78ijgwblvd8n1"; depends=[ggplot2 reshape2]; }; - deepSNV = derive2 { name="deepSNV"; version="1.28.0"; sha256="0maswzsfv9rw01v9alq9jbifc8lg6g2h65338v9chb05dkj03baj"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; }; - deltaGseg = derive2 { name="deltaGseg"; version="1.22.0"; sha256="02mjlrs3rvlbqdsw9nw03y5ifzkfy1n5r7h4811ghvizy8cdxpqj"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; }; - derfinder = derive2 { name="derfinder"; version="1.16.1"; sha256="1wdig8zfpq1635b83npmram5zwxslgfgv3npswkjjjnbfzngwz2m"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; - derfinderHelper = derive2 { name="derfinderHelper"; version="1.16.1"; sha256="1a37q7gkg16wyjznbjgn974kmw0rh2dmknvbf9rpzp9hcibzkcqf"; depends=[IRanges Matrix S4Vectors]; }; - derfinderPlot = derive2 { name="derfinderPlot"; version="1.16.1"; sha256="0pa4ycm3f1bim8byy8ygb8z2r7441rwhmbj7y538scihrsk1q03k"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer RefManageR reshape2 S4Vectors scales]; }; - destiny = derive2 { name="destiny"; version="2.12.0"; sha256="1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"; depends=[Biobase BiocGenerics ggplot2 ggthemes igraph Matrix proxy Rcpp RcppEigen scales scatterplot3d smoother SummarizedExperiment VIM]; }; - dexus = derive2 { name="dexus"; version="1.22.1"; sha256="109sk2nxaqx0jalw06r3ydy6wdbac76j66sh9431b480p6bcgf1r"; depends=[BiocGenerics]; }; - diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.64.0"; sha256="00f088phbix7wrcjrpf3n2a2ps102sbc85f4fg5sqwdw6bvchk9c"; depends=[minpack_lm]; }; - diffHic = derive2 { name="diffHic"; version="1.14.0"; sha256="1yjsvwwai9jflg743nyksj7krm0f2pdy2y2rwnmd3cpwh73yy6al"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; }; - diffcoexp = derive2 { name="diffcoexp"; version="1.2.0"; sha256="1kkm0mw7q81yls750ky9rvx0n9iljgq8j5p9h08yxpr46jc3j8k0"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; }; - diffcyt = derive2 { name="diffcyt"; version="1.2.23"; sha256="08fsvn0phj4f3ih65vizi6bxj6yfwpanran5p79iv28gxbnxzll0"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; }; - diffloop = derive2 { name="diffloop"; version="1.10.0"; sha256="0fi1vvzfifhdgcnal1axn69dqbgpjqsicjgqw6gj41db50zi1fi6"; depends=[Biobase biomaRt data_table dplyr edgeR foreach GenomeInfoDb GenomicRanges ggplot2 IRanges limma locfit matrixStats pbapply plyr readr reshape2 rtracklayer S4Vectors statmod Sushi]; }; - diffuStats = derive2 { name="diffuStats"; version="1.2.0"; sha256="1hg8scxhndgp0r4m5r7rjliirb4371g9d3lqx2h9mgshadwz5h0r"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; }; - diggit = derive2 { name="diggit"; version="1.14.0"; sha256="1kpi1ahwc90mpfwmy6rsf4argf7fss99lr2v0s99aj39m3lwd2dw"; depends=[Biobase ks viper]; }; - discordant = derive2 { name="discordant"; version="1.6.1"; sha256="12zh1qm7l7zq310y4n5fimia1jkxm3ia81br0illyna0kx10b9wq"; depends=[Biobase biwt gtools MASS]; }; - dks = derive2 { name="dks"; version="1.28.0"; sha256="0md8x07f117clhxmmrqaki5g5y8r13c4yrw8vk6yvcsf9prybdah"; depends=[cubature]; }; - dmrseq = derive2 { name="dmrseq"; version="1.2.5"; sha256="1dlzkflfklipirwiam2bi65j6fy9kcpgigyayfiwss3l1nr9dz70"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; - doppelgangR = derive2 { name="doppelgangR"; version="1.10.1"; sha256="14jlrvx6xb6h8x9qg0fm0hb11dk906ja8vfl1wn6wgdrh8fw6brl"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; }; - drawProteins = derive2 { name="drawProteins"; version="1.2.0"; sha256="13zqpghzpqg92i4mlfmvwx1l1mb7swqmyhisqjp546jzs7vixv25"; depends=[dplyr ggplot2 httr readr stringr]; }; - dualKS = derive2 { name="dualKS"; version="1.42.0"; sha256="0mn0mjzncd53wq0jwq2gfcj3mcsfl81hgsaxnf1dqjwqnw4jy1y3"; depends=[affy Biobase]; }; - dupRadar = derive2 { name="dupRadar"; version="1.12.1"; sha256="1dmkzhdwzw2r0srwi96g0csxcsg2m8xh1446p75byjarvmyzmqh8"; depends=[Rsubread]; }; - dyebias = derive2 { name="dyebias"; version="1.42.0"; sha256="1ml85klh9mwxmz8h2yjagx4sl0dnzg4ijk4pa154njznxr8kqccz"; depends=[Biobase marray]; }; - easyRNASeq = derive2 { name="easyRNASeq"; version="2.18.4"; sha256="16ffm3gdag8fdm8pbq7pnxmrzndbig9ryw981hcplk847ij1rxjc"; depends=[Biobase BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD Rsamtools S4Vectors ShortRead SummarizedExperiment]; }; - ecolitk = derive2 { name="ecolitk"; version="1.54.0"; sha256="0gbw2kdfnyjlq0paqy8hlz8qmaczfa5qx9wzj3ax3vms5v6n58qp"; depends=[Biobase]; }; - edge = derive2 { name="edge"; version="2.14.0"; sha256="0gcwnw9c6qc9b207vlchnw59d025jrdm4b7w5iiw721djwwawdzf"; depends=[Biobase jackstraw MASS qvalue snm sva]; }; - edgeR = derive2 { name="edgeR"; version="3.24.3"; sha256="15yimsbsxmxhlsfmgw5j7fd8qn08zz4xqxrir1c6n2dc103y22xg"; depends=[limma locfit Rcpp]; }; - eegc = derive2 { name="eegc"; version="1.8.1"; sha256="14jjd27hblz1ls1463vd4ymdq58h9as82lj160smy0n8jqpc5nhh"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; }; - eiR = derive2 { name="eiR"; version="1.22.0"; sha256="07lnpgaplw6d63c3wjas5n8rxhgmk75qkq3nvp7w26lmgi4ysz6z"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; }; - eisa = derive2 { name="eisa"; version="1.34.0"; sha256="1717bpmrr1kmd1a8rqlarhqcrk786vjw55shn5sd8c89f25vspdx"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; }; - enrichplot = derive2 { name="enrichplot"; version="1.2.0"; sha256="0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"; depends=[AnnotationDbi cowplot DOSE europepmc ggplot2 ggplotify ggraph ggridges GOSemSim gridExtra igraph purrr RColorBrewer reshape2 UpSetR]; }; - ensemblVEP = derive2 { name="ensemblVEP"; version="1.24.2"; sha256="02akxzgf4q6n41pghx2fwk3l9b74db0vdlycnvv868d0rfb11d0x"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; - ensembldb = derive2 { name="ensembldb"; version="2.6.8"; sha256="0gijx2l2y00h6gfj3gfr7rd4vva6qf2vkfdfy5gdmvqlxy84ka38"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; - epiNEM = derive2 { name="epiNEM"; version="1.6.0"; sha256="1pzcajgqsm6mvw8i7aav0918856ghndrdp93831s6zmdkgxzpw2v"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; }; - epigenomix = derive2 { name="epigenomix"; version="1.22.0"; sha256="0cyf35fygr3rgkcfqhb9p9xgl1lydqprzhn3m189yqm3xqck41il"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; }; - epivizr = derive2 { name="epivizr"; version="2.12.0"; sha256="0ms29c5vl0nn8p4v1l5falmwc8xb6wa8fjbfwrgpz8dphidp7mnm"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; }; - epivizrChart = derive2 { name="epivizrChart"; version="1.4.0"; sha256="03dnkx8zqrhgijipv72ylcrwparqjihzld2ln6dir989kwv75f7l"; depends=[BiocGenerics epivizrData epivizrServer htmltools rjson]; }; - epivizrData = derive2 { name="epivizrData"; version="1.10.0"; sha256="0m7bn9v9j8jsja36x5vj2bs9wg3dw5845r47mw4200j1j4irj9jb"; depends=[Biobase ensembldb epivizrServer GenomeInfoDb GenomicFeatures GenomicRanges IRanges OrganismDbi S4Vectors SummarizedExperiment]; }; - epivizrServer = derive2 { name="epivizrServer"; version="1.10.0"; sha256="17h7cghi9md7yzny07jc0749cpwx5jda78vk9g2db0bf6q91qjq6"; depends=[httpuv mime R6 rjson]; }; - epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.10.0"; sha256="0jvx2kc0wqq7rzi1a3lv94i33cgcqhdpny4563kgjcz9g3qaggsd"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; }; - erccdashboard = derive2 { name="erccdashboard"; version="1.16.1"; sha256="0xf5nfzjp0jbhyvcia0bxj8rwcmd033gxgvrwrlcq2535v27sdz9"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; }; - erma = derive2 { name="erma"; version="0.14.0"; sha256="0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel GenomeInfoDb GenomicFiles GenomicRanges ggplot2 Homo_sapiens IRanges rtracklayer S4Vectors shiny SummarizedExperiment]; }; - esATAC = derive2 { name="esATAC"; version="1.4.5"; sha256="0qi6f6pdyjzvsvxl6k5517vkb9c59wwf09439a4g5jx2hp383swq"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; }; - esetVis = derive2 { name="esetVis"; version="1.8.0"; sha256="0n2b7qkgy0gh9jfxi5mgsr8g41141435maq1yniw9mqa3hddwjjp"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; }; - eudysbiome = derive2 { name="eudysbiome"; version="1.12.0"; sha256="09lhzfhlmrw6f50c6d21lmyfh3k4hwrg6waiv1qjg6iavhnbc2a0"; depends=[Biostrings plyr R_utils Rsamtools]; }; - exomeCopy = derive2 { name="exomeCopy"; version="1.28.0"; sha256="1y475ka8lkf3mh4xj0qvgk0nd0gf497dym9bvl5wpss1fqsks6im"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; }; - exomePeak = derive2 { name="exomePeak"; version="2.16.0"; sha256="0i063k0b9d6vvixp52qkg63nlpqzbq2dhf0ylgwchjjk4zsdz5vn"; depends=[GenomicAlignments GenomicFeatures Rsamtools rtracklayer]; }; - explorase = derive2 { name="explorase"; version="1.46.0"; sha256="0h12i2fh7jm0xq0mxy37rcp3pbg18l88l380jsb9jn02rrgkirkd"; depends=[limma rggobi RGtk2]; }; - fCCAC = derive2 { name="fCCAC"; version="1.8.0"; sha256="04mzxvvm1yssdjdibppbl5yv6zpssk3chm222nhs2h7mn4a30rwq"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; - fCI = derive2 { name="fCI"; version="1.12.0"; sha256="0wxc6nhl5gcz70i9nbj7caxgif3bpajng8h8pckarflms1va2ic0"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; - fabia = derive2 { name="fabia"; version="2.28.0"; sha256="1ps10cqldbz99rszxqznqc3vlci4fmhyhwcim8bfch197b1pnfl5"; depends=[Biobase]; }; - factDesign = derive2 { name="factDesign"; version="1.58.0"; sha256="113sjbx1r7yzps0mjpka5mf0mx324z4vg0adl7k965p3r0cv3jwm"; depends=[Biobase]; }; - farms = derive2 { name="farms"; version="1.34.0"; sha256="02vb8cy2j53l05naifrafw4pa48ay3hbsxrlm5s3nbmy4cma6rwr"; depends=[affy Biobase MASS]; }; - fastLiquidAssociation = derive2 { name="fastLiquidAssociation"; version="1.18.0"; sha256="109db3kv8rf7dwlsn2cyv5s44b86nmzj746awf28rc03f6ih8f13"; depends=[doParallel Hmisc impute LiquidAssociation preprocessCore WGCNA]; }; - fastseg = derive2 { name="fastseg"; version="1.28.0"; sha256="1l8mdjpfpgwqdss2ywjkb8b4h55wf8v6kmyxdlvy04ds2hj16sb1"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors]; }; - fdrame = derive2 { name="fdrame"; version="1.54.0"; sha256="1srv11bwyjxlvgv5hky4afwn2bhc8kdvra61jc1dn81qaj5vx41a"; depends=[]; }; - ffpe = derive2 { name="ffpe"; version="1.26.0"; sha256="1bcpdj978wiwfwfbpvnj622wqq4axh82djn17l5vrm20p2hgm74n"; depends=[affy Biobase BiocGenerics lumi methylumi sfsmisc TTR]; }; - fgsea = derive2 { name="fgsea"; version="1.8.0"; sha256="0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"; depends=[BiocParallel data_table fastmatch ggplot2 gridExtra Matrix Rcpp]; }; - flagme = derive2 { name="flagme"; version="1.38.1"; sha256="1llzkq5944kgh32xns67f8bcfvpgia809b1ly1nfhpa2mpfsvyr1"; depends=[CAMERA gcspikelite gplots MASS SparseM xcms]; }; - flipflop = derive2 { name="flipflop"; version="1.20.0"; sha256="100ia0j4ir61ihriyz36jnxpa9s4ivs35fifs4yzfiysf7lma3al"; depends=[GenomicRanges IRanges Matrix]; }; - flowAI = derive2 { name="flowAI"; version="1.12.7"; sha256="1s4mll9zdn84dlf08p91lacs70rijq2rv717f2rk6m71a48l6ac4"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; }; - flowBeads = derive2 { name="flowBeads"; version="1.20.1"; sha256="06w9lfsam3mv9gv6qigsjw9vl169kcyaa7vrh2ii138gry20b9qz"; depends=[Biobase flowCore knitr rrcov xtable]; }; - flowBin = derive2 { name="flowBin"; version="1.18.1"; sha256="1fdj5ziyc10fp27jarx18z97vxnf7d5zy2nwbia6x441svrvc534"; depends=[BiocGenerics class flowCore flowFP limma snow]; }; - flowCHIC = derive2 { name="flowCHIC"; version="1.16.1"; sha256="1472c1jdg9zk94pw84nbr8042rh7k7mrdbyjncqcigrx12dhgdh6"; depends=[EBImage flowCore ggplot2 hexbin vegan]; }; - flowCL = derive2 { name="flowCL"; version="1.20.1"; sha256="013b81ab3pmfb3n4430ihwc2qbgqf3iyyykzmqdhqs8llcrpqvph"; depends=[graph Rgraphviz SPARQL]; }; - flowClean = derive2 { name="flowClean"; version="1.20.0"; sha256="0m8n75gkf1dwhs4hyk1jfqvsmb2lymvi0znikb1gi8bkh9224wvk"; depends=[bit changepoint flowCore sfsmisc]; }; - flowClust = derive2 { name="flowClust"; version="3.20.1"; sha256="1wk2hwc9fbhjqw0cic3mgh5xg82nwg0m6548b5cvn5f8ywxs2f4m"; depends=[Biobase BiocGenerics clue corpcor ellipse flowCore flowViz graph mnormt]; }; - flowCore = derive2 { name="flowCore"; version="1.48.1"; sha256="04cmydy10i1zrd293cjam7v8i1habm27m5ggpp52jcsy7db9gg7p"; depends=[BH Biobase BiocGenerics corpcor graph MASS matrixStats Rcpp rrcov]; }; - flowCyBar = derive2 { name="flowCyBar"; version="1.18.1"; sha256="0lnfn2xxd3zbr1jn1vdd6b6yaljddn525fsb7g0i7nsl3py89nfy"; depends=[gplots vegan]; }; - flowDensity = derive2 { name="flowDensity"; version="1.16.1"; sha256="0kmy3k54aghv1vkdmply5pwyr8dxfipa1qi1b7xrqa7zbwa8dxq4"; depends=[car flowCore flowWorkspace gplots RFOC rgeos sp]; }; - flowFP = derive2 { name="flowFP"; version="1.40.1"; sha256="1dq634pw4d89gmqw71nzb2paqlzkm2q53xv9rbl4rpglxb3325gb"; depends=[Biobase BiocGenerics flowCore flowViz]; }; - flowFit = derive2 { name="flowFit"; version="1.20.1"; sha256="0f03p0jki13lip694ahd0ym3ixlmj60vkspkzcwq88mpkvmj03jn"; depends=[flowCore flowViz gplots kza minpack_lm]; }; - flowMap = derive2 { name="flowMap"; version="1.20.1"; sha256="0bsy52jhgj81xd20ycdz35n70k71c40hx5lm25gh5v6sxh5598qw"; depends=[abind ade4 doParallel Matrix reshape2 scales]; }; - flowMatch = derive2 { name="flowMatch"; version="1.18.1"; sha256="03qkisbfzpkz6a4l91gg8biyk5apc2cjqrvilrf9yawp2gypff62"; depends=[Biobase flowCore Rcpp]; }; - flowMeans = derive2 { name="flowMeans"; version="1.42.1"; sha256="1jxhga0wlgn69h4mplzb140grxaxxb0psjgnr9jkcm9c6d6mh9qp"; depends=[Biobase feature flowCore rrcov]; }; - flowMerge = derive2 { name="flowMerge"; version="2.30.1"; sha256="1dn6wxaix56r3fw273prbajc84h1k1b03q6wh0pfhy0gr6qk8wgw"; depends=[feature flowClust flowCore foreach graph Rgraphviz rrcov snow]; }; - flowPeaks = derive2 { name="flowPeaks"; version="1.28.1"; sha256="08g8bnb6h9gc34qx511gd5r9wrfxd6wr1wfzgazswc3idg5pqli6"; depends=[]; }; - flowPloidy = derive2 { name="flowPloidy"; version="1.8.0"; sha256="0s2d541id8mf3igidn5n7v6d3g21yaskzc7kx9zvywx9391sd9qx"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; }; - flowPlots = derive2 { name="flowPlots"; version="1.30.1"; sha256="1ygbd62kyqpmlln55m65n0jb8k7kdqxpihwlrp5yickxv7g99zx6"; depends=[]; }; - flowQB = derive2 { name="flowQB"; version="2.10.1"; sha256="0cpp6pn1w2ccixxclx6cmv7hzsqc0bcsbwyy1vz2lvwrrmvsk8z3"; depends=[extremevalues flowCore]; }; - flowStats = derive2 { name="flowStats"; version="3.40.1"; sha256="0krj1x5jpzl6ravqmb7ccgmdf246627sd32zp8sblb1fz9nr0pzp"; depends=[Biobase BiocGenerics cluster fda flowCore flowViz flowWorkspace KernSmooth ks lattice MASS ncdfFlow RColorBrewer]; }; - flowTime = derive2 { name="flowTime"; version="1.6.1"; sha256="1an5cx6dbl6y7llss1w27v5csz7pvfng7490ig3fynnkfldl8n52"; depends=[flowCore plyr]; }; - flowTrans = derive2 { name="flowTrans"; version="1.34.1"; sha256="0wav5y4gzbciyvv9php7lkhqr5h1gwk42qx0665df3zcbwxkahcb"; depends=[flowClust flowCore flowViz]; }; - flowType = derive2 { name="flowType"; version="2.20.1"; sha256="0dpbkcf7rh1sf8hi5mmxjq6nd72w8xhjcxf2lzfn0iyxvdfb76w3"; depends=[BH Biobase flowClust flowCore flowMeans flowMerge Rcpp rrcov sfsmisc]; }; - flowUtils = derive2 { name="flowUtils"; version="1.46.1"; sha256="0vk8xq623p6pfp92fllza2vyxm4b92w98dc6v3d9ik88nyp1ppzz"; depends=[Biobase corpcor flowCore graph RUnit XML]; }; - flowVS = derive2 { name="flowVS"; version="1.14.1"; sha256="06kprjxrjywvc1w5ic1753npz5p4k8fhqx6361wqzzzhzihj6gy6"; depends=[flowCore flowStats flowViz]; }; - flowViz = derive2 { name="flowViz"; version="1.46.1"; sha256="0php2rng4da7jk98rvmkfwm994qnqkrlqmqpqy4kl19w3gsc00i1"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; }; - flowWorkspace = derive2 { name="flowWorkspace"; version="3.30.2"; sha256="19ifpwpk9rmmfm647zm419k50hna8ib0ad75l04xbggdm6s3vm41"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra matrixStats ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; }; - flowcatchR = derive2 { name="flowcatchR"; version="1.16.0"; sha256="0cwfm8d3s7nvkfm0zfx84mcamyszc8cwwy7b9rn9m27rj3q80f1z"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; - fmcsR = derive2 { name="fmcsR"; version="1.24.0"; sha256="0dl39066y0s391hczpi3482dwwpsp1767f6n881n00sv7pb4znxy"; depends=[BiocGenerics ChemmineR RUnit]; }; - focalCall = derive2 { name="focalCall"; version="1.16.0"; sha256="06x6d5j17wabdy03r4h9clmdp69wbxgzpsvalrmg8l4yyj9z7lrc"; depends=[CGHcall]; }; - frma = derive2 { name="frma"; version="1.34.0"; sha256="1g48s0kji9ln4z80h704j1rc5vji9g8kx8mgngi95k7vj744firg"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; }; - frmaTools = derive2 { name="frmaTools"; version="1.34.0"; sha256="1n1i5xsn38ml7h34pkv4xlx8yvrf4vpcjrz92sfzmrff531gf3a2"; depends=[affy Biobase DBI preprocessCore]; }; - funtooNorm = derive2 { name="funtooNorm"; version="1.6.0"; sha256="0s4vafjskzyc6hf616cbi7g9prf6lh7fmi7zywr97pr11390n7qg"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; }; - gCMAP = derive2 { name="gCMAP"; version="1.26.0"; sha256="1ql9nxlj4wgc22g699lxsn57iam7k3w33v3cinhywsy9zfswawh9"; depends=[annotate AnnotationDbi bigmemory bigmemoryExtras Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; }; - gCMAPWeb = derive2 { name="gCMAPWeb"; version="1.22.0"; sha256="0jvn3h3hn2b8av0c901gbidhrkgkhhm4027qymn5dhg4xsg2dayg"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; }; - gCrisprTools = derive2 { name="gCrisprTools"; version="1.10.1"; sha256="148ggbbhvg0ja55zs1vlcjpjgcc50mgfq58ixfi7pifiaszzwh6s"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; }; - gQTLBase = derive2 { name="gQTLBase"; version="1.14.0"; sha256="1lbk1m1mkvbk30flk5pf3pcrnm2s0sj5r48kbjgad39dsvd8zgqx"; depends=[BatchJobs BBmisc BiocGenerics bit doParallel ff ffbase foreach GenomicFiles GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; }; - gQTLstats = derive2 { name="gQTLstats"; version="1.14.1"; sha256="1rkbnb3h02fdksc4nacqvmq4jgbj9fz4hm7j51yr2ggcgcykwraa"; depends=[AnnotationDbi BatchJobs BBmisc beeswarm Biobase BiocGenerics doParallel dplyr erma ffbase foreach GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges ggbeeswarm ggplot2 gQTLBase HardyWeinberg Homo_sapiens IRanges limma mgcv plotly reshape2 S4Vectors shiny snpStats SummarizedExperiment VariantAnnotation]; }; - gaga = derive2 { name="gaga"; version="2.28.1"; sha256="017ga7m85qzxvfvg13gilsikc06vr8ggfp07aw36gdn9q8by76d5"; depends=[Biobase coda EBarrays mgcv]; }; - gage = derive2 { name="gage"; version="2.32.1"; sha256="02g796sb1800ff0f1mq9f2m5wwzpf8pnfzajs49i68dhq2hm01a8"; depends=[AnnotationDbi graph KEGGREST]; }; - gaggle = derive2 { name="gaggle"; version="1.50.0"; sha256="1yj10aahr1pmn7kspiplczalr1awmybr320y49cadh17l3p3i224"; depends=[graph rJava RUnit]; }; - gaia = derive2 { name="gaia"; version="2.26.0"; sha256="1a3lmazx5dlb484llfvwk6b4g89r3dcbmkjz7wah44kpyp0k5lrv"; depends=[]; }; - garfield = derive2 { name="garfield"; version="1.10.0"; sha256="1hcb4dvhir20ldfr7zrd0b3xcdpkafb0sc3gwns4651a9hs2cx8j"; depends=[]; }; - gcapc = derive2 { name="gcapc"; version="1.6.0"; sha256="00jv9c231s4zr02nl11qcs8qlbwklyc0iis1c4n2ifkp8kcd1c34"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; }; - gcatest = derive2 { name="gcatest"; version="1.12.0"; sha256="14902mc3vnnj64xxhj5dzd787r59wj0dryn074n4yyw0lyzfydwk"; depends=[lfa]; }; - gcrma = derive2 { name="gcrma"; version="2.54.0"; sha256="1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; }; - gdsfmt = derive2 { name="gdsfmt"; version="1.18.1"; sha256="1axbs23armc8r4nmfnhv6ripxzh551lgwd0580nknif4jj1a98ga"; depends=[]; }; - geNetClassifier = derive2 { name="geNetClassifier"; version="1.22.0"; sha256="079v4jrscq93kapv4676d4zsy3rk7j547pn9hsj7fi0sypv9sg4h"; depends=[Biobase e1071 EBarrays minet]; }; - geecc = derive2 { name="geecc"; version="1.16.1"; sha256="0axbina6xvv9l8ymswlxa989kzif2cy5njfis8g6pfnx0dfmnrmp"; depends=[gplots hypergea MASS Rcpp]; }; - genArise = derive2 { name="genArise"; version="1.58.0"; sha256="0drncw83b214w8fk11z3dilshd9p9z4irb23gbvkq67xm62nbkxn"; depends=[locfit tkrplot xtable]; }; - genbankr = derive2 { name="genbankr"; version="1.10.0"; sha256="18pw66ilh7mnlar94885k182hay05vana7pjki38bb2jbifk4m2f"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; }; - geneAttribution = derive2 { name="geneAttribution"; version="1.8.0"; sha256="1wngaq654gzp2llk8zk8z3gmnpb3lwx4l6sfi9dn8n551q6lbbcg"; depends=[BiocGenerics GenomeInfoDb GenomicFeatures GenomicRanges IRanges org_Hs_eg_db rtracklayer]; }; - geneClassifiers = derive2 { name="geneClassifiers"; version="1.6.0"; sha256="0nxp2jmrq3fyhvgys4gxycqc7v2nixsa3mk57fq3339xilcxzycp"; depends=[Biobase BiocGenerics]; }; - geneRecommender = derive2 { name="geneRecommender"; version="1.54.0"; sha256="1b6y5ilz1ffsqsb5y667sa9fi4h6hpwk4wgdiy13lq2vry9x7j0w"; depends=[Biobase]; }; - geneRxCluster = derive2 { name="geneRxCluster"; version="1.18.0"; sha256="0kg42vy1asv5gak2d9h3fm679yfai7d7n56nqig3dny5a0g04fmc"; depends=[GenomicRanges IRanges]; }; - geneXtendeR = derive2 { name="geneXtendeR"; version="1.8.0"; sha256="1nkaxzw8vdxafb9nb39lwdb6qj8z54p19l8rw1rdjy8dxlia262n"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; }; - genefilter = derive2 { name="genefilter"; version="1.64.0"; sha256="0p64s1n1627yafnp25wjr4b22p34lqw574fx2qg4s1m0lffh1z6i"; depends=[annotate AnnotationDbi Biobase S4Vectors survival]; }; - genefu = derive2 { name="genefu"; version="2.14.0"; sha256="1dapkgmjwxr6c62l72h217xrjnycnc3sc7qclmbrbwjl42c6ma1f"; depends=[AIMS amap biomaRt iC10 limma mclust survcomp]; }; - geneplast = derive2 { name="geneplast"; version="1.8.0"; sha256="06xvdsfjqg8jx8b1g8i829i8x8p2bxv57hzflh08nd6n91fys6qn"; depends=[ape igraph snow]; }; - geneplotter = derive2 { name="geneplotter"; version="1.60.0"; sha256="10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; }; - genoCN = derive2 { name="genoCN"; version="1.34.0"; sha256="164d9cwp6mngmmvk1lc7xs03w9sqqx7b3w4mrx94xg5f4k2jzv3m"; depends=[]; }; - genomation = derive2 { name="genomation"; version="1.14.0"; sha256="0g0v4alfpqlinqinjnyzl3mrjnpbdx9ri34mcaiqbvbvg8ic8wvg"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer RUnit S4Vectors seqPattern]; }; - genomeIntervals = derive2 { name="genomeIntervals"; version="1.38.0"; sha256="09ck7d1lklxh5rr8k4rfswlyi41a94siqpqfp6byf34qjhv9mxvv"; depends=[BiocGenerics GenomeInfoDb GenomicRanges intervals IRanges S4Vectors]; }; - genomes = derive2 { name="genomes"; version="3.12.0"; sha256="18pwqjr01qwjn93vyf2pfp5n88djyb0vln78m8kl598pcxr7ifkh"; depends=[curl readr]; }; - genoset = derive2 { name="genoset"; version="1.38.0"; sha256="1z0iwp5pp3655kd63p3jf5fficd61p1i0g06p2n6pw4q38dp2h28"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; - genotypeeval = derive2 { name="genotypeeval"; version="1.14.0"; sha256="0xi0n87g5qh1yswr3whv8wvmxswd66j6g8662qsfgy3cs69hxl3m"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; }; - genphen = derive2 { name="genphen"; version="1.10.3"; sha256="0hjfgy3q4x1ib91cxgszay7fvjaiqi62915pg4z3hd9xd9lpjiqn"; depends=[BH Biostrings doParallel e1071 foreach ranger Rcpp RcppEigen rstan rstantools StanHeaders]; }; - gep2pep = derive2 { name="gep2pep"; version="1.2.0"; sha256="1sxkps92hf85svngd5511j3sbwn8904nn9ijn168v7xzzmld3z5y"; depends=[Biobase digest foreach GSEABase iterators repo rhdf5 XML]; }; - gespeR = derive2 { name="gespeR"; version="1.14.1"; sha256="1d8jvwnmnd27860n9qk5500mi73kdnvzwkfsqjp0xzz6ji5l9khs"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; }; - ggbio = derive2 { name="ggbio"; version="1.30.0"; sha256="0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 rlang Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; }; - ggcyto = derive2 { name="ggcyto"; version="1.10.2"; sha256="0nhwrsc4drswpyz6w3v3h5q0cwzi92a0kzx47n3x6drdjdrv4w21"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer rlang scales]; }; - ggtree = derive2 { name="ggtree"; version="1.14.6"; sha256="0jp4djkjvhvidp8ic44wq527rjzsh5awqfll2g9bdlypmjs21494"; depends=[ape dplyr ggplot2 magrittr purrr rlang rvcheck scales tibble tidyr tidytree treeio]; }; - girafe = derive2 { name="girafe"; version="1.34.0"; sha256="13hk8rfldbwadqhy5mqcdzggili3ib6whwqcf85pl72x627iif5j"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; - glmSparseNet = derive2 { name="glmSparseNet"; version="1.0.0"; sha256="0aqcnqmnl977yc7lp9gb8a4hqaxdh2pjw2lhiw3vly933xzd78sc"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet loose_rock Matrix MultiAssayExperiment readr reshape2 rlang sparsebn sparsebnUtils STRINGdb stringr SummarizedExperiment survminer]; }; - globalSeq = derive2 { name="globalSeq"; version="1.10.1"; sha256="1vvhqn04b0kl0xdyp7ga4dlbvh15gw0f5nr8ssw7rr1flzcp1jik"; depends=[]; }; - globaltest = derive2 { name="globaltest"; version="5.36.0"; sha256="16v8rn25n87kk892c3yvmqdv03csqdrzp7krcr8w2y0wznys2cqn"; depends=[annotate AnnotationDbi Biobase survival]; }; - gmapR = derive2 { name="gmapR"; version="1.24.2"; sha256="0j4k5r2lx0kng2826vi9535pc7lflgqvwsqcq7bkbrzmc287k465"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; - goProfiles = derive2 { name="goProfiles"; version="1.44.0"; sha256="0rpks421g0rbdcfnkfqpd5l22cysdcfljnmngq9pbgh04wpwi8f1"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; }; - goSTAG = derive2 { name="goSTAG"; version="1.6.1"; sha256="0ib9a1v9zblysmk7a6wrg6cj1q6is2s9mranb28nn2r067kfx77l"; depends=[AnnotationDbi biomaRt GO_db memoise]; }; - goTools = derive2 { name="goTools"; version="1.56.0"; sha256="0w2mb8g5fnn7vm35cqw437f2sdiba4c72ay1n7frh0z1xc7hqc3r"; depends=[AnnotationDbi GO_db]; }; - goseq = derive2 { name="goseq"; version="1.34.1"; sha256="1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; }; - gpart = derive2 { name="gpart"; version="1.0.3"; sha256="0aqz4b8qbll80xqrf5x9y4y0iw3f94ncvnhw3ifalj2rh39p15cw"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; }; - gpls = derive2 { name="gpls"; version="1.54.0"; sha256="14sffq2h6hqlzaq1nzw34rkg7nnshfp6k5r3wyvavq6k25384jr0"; depends=[]; }; - gprege = derive2 { name="gprege"; version="1.26.0"; sha256="0b2zrxggljfgr8w2ns7h80ymqrvfi8kaliy32k2najm089kpv8dy"; depends=[gptk]; }; - graph = derive2 { name="graph"; version="1.60.0"; sha256="1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"; depends=[BiocGenerics]; }; - graphite = derive2 { name="graphite"; version="1.28.2"; sha256="0jdi5s7ffl7snwxrbk1nj8vb4db5wv328ipypyl8ddrzk6rljcy5"; depends=[AnnotationDbi checkmate graph httr rappdirs]; }; - groHMM = derive2 { name="groHMM"; version="1.16.0"; sha256="1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; }; - gsean = derive2 { name="gsean"; version="1.2.1"; sha256="0amx19163pfff16hncphh4nccdp7br2f1v5ddzynzx8drslywz1p"; depends=[fgsea PPInfer]; }; - gtrellis = derive2 { name="gtrellis"; version="1.14.0"; sha256="17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"; depends=[circlize GenomicRanges GetoptLong IRanges]; }; - gwascat = derive2 { name="gwascat"; version="2.14.0"; sha256="1fnyjydhicq4ayrv0lqjv48h9bd72h40s6l82g1h2ng0icwz38g0"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 gQTLstats graph Gviz Homo_sapiens IRanges Rsamtools rtracklayer S4Vectors snpStats SummarizedExperiment VariantAnnotation]; }; - gwasurvivr = derive2 { name="gwasurvivr"; version="1.0.0"; sha256="0f1p2l6ypbrnaqlmqsjz5rfa6afd4kqhkrniqi7hfwjza7myrcvp"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; }; - h5vc = derive2 { name="h5vc"; version="2.16.0"; sha256="1jhl2cv8rd9sfw5adm81ncpz3ysyb9wdvjzqg7k48rh5ycgi9whz"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rsamtools S4Vectors]; }; - hapFabia = derive2 { name="hapFabia"; version="1.24.0"; sha256="1y14gmm4vj5qvnkbssqr4scqrl86v949kd6y0ic48p5rlqcgsjj3"; depends=[Biobase fabia]; }; - heatmaps = derive2 { name="heatmaps"; version="1.6.0"; sha256="1srppr0y50y2j9ajscc93778jk2s7pnaqnf4h7yf12cx8185izsj"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; }; - hiAnnotator = derive2 { name="hiAnnotator"; version="1.16.0"; sha256="0hbrrvdl41nidsihyalnqridg87gidpnzdb6scf07jyfqmdym862"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; }; - hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.18.0"; sha256="0azmgzczkbjhg8fpl7js4g3s44lna3jzsdccchfv715smykxs24n"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl rSFFreader sonicLength]; }; - hicrep = derive2 { name="hicrep"; version="1.6.0"; sha256="0j92hg6qk9rd84lkl63zirwyydvnsrsgwibyv8ndrap4nw9hiswv"; depends=[]; }; - hierGWAS = derive2 { name="hierGWAS"; version="1.12.0"; sha256="0fsp5zyaz7kdgyyfnzvzcvsscxh69skvkn245sw41svq3gyswpcl"; depends=[fastcluster fmsb glmnet]; }; - hierinf = derive2 { name="hierinf"; version="1.0.0"; sha256="0p0kxqap5qdrfgh6jcn94c7hdk9k3xp178wz5ip1c3x3pqj30ndh"; depends=[fmsb glmnet]; }; - hipathia = derive2 { name="hipathia"; version="1.4.1"; sha256="1hnq2rl2g1an7q2hxc3s7sn1hynhapmb5qjj4ishcpv0irygb8ha"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; }; - hmdbQuery = derive2 { name="hmdbQuery"; version="1.2.0"; sha256="0wliaddym62p9gf57y349q854jsng5chh5jd0gh3j3pdg5nlb7c0"; depends=[S4Vectors XML]; }; - hopach = derive2 { name="hopach"; version="2.42.0"; sha256="0mrc9yw1gwk6nx0bdcckphd5n13si3yvf3brn5yyg6xnl1b019c3"; depends=[Biobase BiocGenerics cluster]; }; - hpar = derive2 { name="hpar"; version="1.24.0"; sha256="1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"; depends=[]; }; - htSeqTools = derive2 { name="htSeqTools"; version="1.30.0"; sha256="11lywvkgl07fd2f82j00lw8zbvdg4g2aaa2w670vhh24v5w38xng"; depends=[Biobase BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges MASS S4Vectors]; }; - hyperdraw = derive2 { name="hyperdraw"; version="1.34.0"; sha256="0widxxs8rk9xmpzwj4pmxg5px2ym2g2psqiwnqnhvd0pqhfpssvr"; depends=[graph hypergraph Rgraphviz]; }; - hypergraph = derive2 { name="hypergraph"; version="1.54.0"; sha256="1qhn3y3wvh2azbcabi95zbpdlv0y1fhrw3l8w7qgi78asiq5b3jp"; depends=[graph]; }; - iASeq = derive2 { name="iASeq"; version="1.26.1"; sha256="1qnpdsqpgi9bp39vyhdhjajdq552gd0q5pb23p274w3zr9sw6v6h"; depends=[]; }; - iBBiG = derive2 { name="iBBiG"; version="1.26.0"; sha256="02pw4v01ck6kfpylbymy46wsavcpf1q9xmrz1fywb1z5rday2kdb"; depends=[ade4 biclust xtable]; }; - iBMQ = derive2 { name="iBMQ"; version="1.22.0"; sha256="08lw0a4c9gp3vx6ggrxmsr2lgikfzw5gdw3ri08f89cqqmb6cazi"; depends=[Biobase ggplot2]; }; - iCARE = derive2 { name="iCARE"; version="1.10.3"; sha256="1m58fprg00ns55cgbd63dn9276hx3351r69cwskrrsl68kza3i2r"; depends=[gtools Hmisc plotrix]; }; - iCNV = derive2 { name="iCNV"; version="1.2.1"; sha256="10kqd00sfq1v6lyydif7a8nwc4xg9z3db70p1c3s4y2iyia2kzdk"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; - iCOBRA = derive2 { name="iCOBRA"; version="1.10.0"; sha256="0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"; depends=[dplyr DT ggplot2 limma reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; - iCheck = derive2 { name="iCheck"; version="1.12.0"; sha256="0wsgplym9kf1v7lvnnkxxgs9d9ahhb456vs9kgxydik94hyxpiz4"; depends=[affy Biobase GeneSelectMMD gplots limma lmtest lumi MASS preprocessCore randomForest rgl scatterplot3d]; }; - iChip = derive2 { name="iChip"; version="1.36.0"; sha256="1ak11v8xywgqximfy99g3d2lyci7pj0r4p1yy6g77j8bwf1frz5d"; depends=[limma]; }; - iClusterPlus = derive2 { name="iClusterPlus"; version="1.18.0"; sha256="08w6f1ad1mc05ws7jdq1j6sn3rflbdp1q5nii09a6qjx83micr4n"; depends=[]; }; - iGC = derive2 { name="iGC"; version="1.12.0"; sha256="1m3mhxkvxsswmk6sqd78brx94pwyzc3z71kv2dzxj1409g6s1h25"; depends=[data_table plyr]; }; - iPAC = derive2 { name="iPAC"; version="1.26.0"; sha256="01s5sgkid33jhzkjk7mdkdn48asp4ibj8b9r5cx5f3ngmkbfpdql"; depends=[Biostrings gdata multtest scatterplot3d]; }; - iSEE = derive2 { name="iSEE"; version="1.2.4"; sha256="0n6xc7h655vr0n5m8kkrzqda7nyjm4ixbgymf14imwrw37h3arzx"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; }; - iSeq = derive2 { name="iSeq"; version="1.34.0"; sha256="0hlslyypijb4w9m01xkn6r8svs0kkp4nbv4xdz844pvyyxcn4afc"; depends=[]; }; - iasva = derive2 { name="iasva"; version="1.0.1"; sha256="1cmbsa75fhs5zxjlfijwknk5s5i6w9q7r7xn34m3hz0y9asg62fc"; depends=[BiocParallel cluster irlba SummarizedExperiment]; }; - ibh = derive2 { name="ibh"; version="1.30.0"; sha256="0wghj4qbnfg7zy1pbz580x9m1wszlhiyc34s9sd4q5spviz8dxh5"; depends=[simpIntLists]; }; - icetea = derive2 { name="icetea"; version="1.0.1"; sha256="11l0m6r6rrw8g4r7zabf6sy894sa9bqcsr6x7kbnk3hdmr3lcwfh"; depends=[BiocGenerics BiocParallel Biostrings csaw edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; - ideal = derive2 { name="ideal"; version="1.6.1"; sha256="0d3rym7lfnaqpr7dlcxq2mf0p2wh45y9glx5m3isf5z352y81bd9"; depends=[AnnotationDbi BiocParallel d3heatmap DESeq2 dplyr DT GenomicRanges ggplot2 GO_db goseq GOstats gplots IHW IRanges knitr limma pcaExplorer pheatmap rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; - idiogram = derive2 { name="idiogram"; version="1.58.0"; sha256="0m4p1ar2z7wj8zk24kiazwr8i55b0b6i7j03skqzcgy5jdv3jzyp"; depends=[annotate Biobase plotrix]; }; - igvR = derive2 { name="igvR"; version="1.2.0"; sha256="1g5q877hpwckf3m2qvgysvwa9ggxg99mbmk0vkqsyamqxh74pwx6"; depends=[BiocGenerics BrowserViz GenomicRanges httpuv rtracklayer VariantAnnotation]; }; - illuminaio = derive2 { name="illuminaio"; version="0.24.0"; sha256="1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"; depends=[base64]; }; - imageHTS = derive2 { name="imageHTS"; version="1.32.1"; sha256="10syni3cfl1n4p7gkskkcd0vrfkzg95kjrr16hbvypndrfp3wmhg"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; }; - immunoClust = derive2 { name="immunoClust"; version="1.14.1"; sha256="0ncb6szwd5ghh5x3bi9d3dqmfgyjawhflsc1rxbmyf3qs67796my"; depends=[flowCore lattice]; }; - impute = derive2 { name="impute"; version="1.56.0"; sha256="08z0pj1dz5iq967nwj67qyka7ir7m5an2ggv7bsrlz3apzfsla33"; depends=[]; }; - intansv = derive2 { name="intansv"; version="1.22.0"; sha256="1gj6sxh84v5g7nriskyg7jx0z3kqmicymv53651cgr66wc86z2lm"; depends=[BiocGenerics GenomicRanges ggbio IRanges plyr]; }; - interactiveDisplay = derive2 { name="interactiveDisplay"; version="1.20.0"; sha256="1zlxmj8wwn916xf7qkvpapsqg9i53bywn2z3xny3yj6jp9xmibff"; depends=[AnnotationDbi BiocGenerics Category ggplot2 gridSVG interactiveDisplayBase plyr RColorBrewer reshape2 shiny XML]; }; - interactiveDisplayBase = derive2 { name="interactiveDisplayBase"; version="1.20.0"; sha256="04xz3dkwan2s5ic1mwkdfnggm0l41mgqfagx160bcsrpkw6z7ark"; depends=[BiocGenerics shiny]; }; - inveRsion = derive2 { name="inveRsion"; version="1.30.0"; sha256="0qaxl6arlx2zki5gkic52b575ickh7mzwls70xyqj8342hyxhi30"; depends=[haplo_stats]; }; - ipdDb = derive2 { name="ipdDb"; version="1.0.0"; sha256="049hzzj2x7wwd4ybjbq6vrc4kg21fcx7yxj501lyyp1qddvvrmvs"; depends=[AnnotationDbi AnnotationHub assertthat Biostrings DBI GenomicRanges IRanges RSQLite]; }; - isobar = derive2 { name="isobar"; version="1.28.1"; sha256="0zh6qj9jjwp1wgwg9n47g01xxwdi8janiv3iy89a3jc62mm1ddpc"; depends=[Biobase biomaRt distr ggplot2 plyr]; }; - isomiRs = derive2 { name="isomiRs"; version="1.10.1"; sha256="18fhm2w1j92sj7pw6hhi58slv4sni09mf10s9ihm2xphv10qysym"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors SummarizedExperiment tibble tidyr]; }; - iterClust = derive2 { name="iterClust"; version="1.4.0"; sha256="12nm79j67ls330lnld1wf4xdjxnfi15yjd8x5ibppv9ccsq6vlrn"; depends=[Biobase cluster]; }; - iterativeBMA = derive2 { name="iterativeBMA"; version="1.40.0"; sha256="0x3fk3faslrcc24wrchdy57ip2nq49dr0l5yf99ihr1gnkfzjrsr"; depends=[Biobase BMA leaps]; }; - iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.40.0"; sha256="1k6pivwa69n1ppwvfdr90nlm7lw2kji2p1s6s35dc9463a6qyh7r"; depends=[BMA leaps survival]; }; - iteremoval = derive2 { name="iteremoval"; version="1.2.0"; sha256="0xmx4k6h8ii2mfqik5kkx7gwmhn4br8a7pnqv4bk9dbvphaqknk8"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; }; - ivygapSE = derive2 { name="ivygapSE"; version="1.4.0"; sha256="0r9j2r0n5hw75ylbc8scq070p4kazc4m9vrjcbxvfkyv22qppjr2"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; }; - joda = derive2 { name="joda"; version="1.30.0"; sha256="1v21j6maydhfxixfa27napp1k59f1jngz7p9hidijmm4nqbg4w60"; depends=[bgmm RBGL]; }; - karyoploteR = derive2 { name="karyoploteR"; version="1.8.8"; sha256="0hfv89383m5l4r3aswgscjl2r35b7k7wlgslj8il41grbzz3a55p"; depends=[bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; }; - kebabs = derive2 { name="kebabs"; version="1.16.0"; sha256="1ibxymqpiq85a5zs5wrngkyjqvwb4n5k2jxiics4mqv28pg34023"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; - keggorthology = derive2 { name="keggorthology"; version="2.34.0"; sha256="107wi6mlrz15pgwg7jrlb3q771v0yhxqph5i5c0h6v3yzr47xx15"; depends=[AnnotationDbi DBI graph hgu95av2_db]; }; - kimod = derive2 { name="kimod"; version="1.10.0"; sha256="081vanahyk3figp6jc9cjvq9lrn1mchc08wbw79f6k5sind4ic7z"; depends=[Biobase cluster]; }; - kissDE = derive2 { name="kissDE"; version="1.2.0"; sha256="0vqg7gjcj6z0v5ngj3z6zrmh5kdyk7hghj38yv7vp36miiqzrlw6"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; }; - lapmix = derive2 { name="lapmix"; version="1.48.0"; sha256="12s3k81bysmmqc6r524jsx9yv0vyd5ppw1xs7myk2y7067355wxc"; depends=[Biobase]; }; - ldblock = derive2 { name="ldblock"; version="1.12.1"; sha256="01lf74pby7si2g3kgc10qzr6lkcbigqcgqs2j3anc38vzxv0zhwv"; depends=[BiocGenerics erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; }; - les = derive2 { name="les"; version="1.32.0"; sha256="0iv4srhkirw2ix0a2bv44byydwxgihy027wahcskamm6dzk0k9lz"; depends=[boot fdrtool gplots RColorBrewer]; }; - levi = derive2 { name="levi"; version="1.0.0"; sha256="177zjvijca57f0hr4wb3zr83is3bgag5yfc07p9azic64ilwfqdb"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 shiny shinydashboard shinyjs testthat xml2]; }; - lfa = derive2 { name="lfa"; version="1.12.0"; sha256="1lvkycg4d7grqj7x5s3bcq2h4936kvd75r029zsa9mxdakc94kld"; depends=[corpcor]; }; - limma = derive2 { name="limma"; version="3.38.3"; sha256="08va8jggmv61wym955mnb1n31mgikrmjys7dl1kp5hp3yia8jg7l"; depends=[]; }; - limmaGUI = derive2 { name="limmaGUI"; version="1.58.0"; sha256="0fjq8qr5f6cv0bx4sfinnjiy0jc3dymlzhfkrxbd0c24fw35m3f4"; depends=[limma R2HTML tkrplot xtable]; }; - lmdme = derive2 { name="lmdme"; version="1.24.0"; sha256="069s419q5ca4py0c5r392kl08pmb6fnm76vsznqkbbl4g1yclyp3"; depends=[limma pls stemHypoxia]; }; - loci2path = derive2 { name="loci2path"; version="1.2.0"; sha256="1aps0yq7wg5gi9nacg5znfa5bf9i8ijf0qv5xn03s4rbzbwxwlfz"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; - logicFS = derive2 { name="logicFS"; version="2.2.0"; sha256="1kvwcm2b66hqlpf693s0cy8sr7sgxqvcdg1czwj7f77hf9ys3x40"; depends=[LogicReg mcbiopi survival]; }; - logitT = derive2 { name="logitT"; version="1.40.0"; sha256="1xmyixzihnv6svxhk76f695fs641p3zwj3k6xk5ds2989p6zkymy"; depends=[affy]; }; - lol = derive2 { name="lol"; version="1.30.0"; sha256="0z78jddb3cv5w26rm3bh27b3qqc2fbf3lv57xj8aq8fvya2w4ma2"; depends=[Matrix penalized]; }; - lpNet = derive2 { name="lpNet"; version="2.14.0"; sha256="1b3xsaq8ibsiz5895q6qqa632wlg08ca5sxm82ppm70fddpy26fd"; depends=[lpSolve nem]; }; - lpsymphony = derive2 { name="lpsymphony"; version="1.10.0"; sha256="0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"; depends=[]; }; - lumi = derive2 { name="lumi"; version="2.34.0"; sha256="1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"; depends=[affy annotate AnnotationDbi Biobase DBI GenomicFeatures GenomicRanges KernSmooth lattice MASS methylumi mgcv nleqslv preprocessCore RSQLite]; }; - mAPKL = derive2 { name="mAPKL"; version="1.12.0"; sha256="1bp8xpcrz7d76lazp72p25rzp3gcmr2z4cyhcgbg678gpsp61lj9"; depends=[AnnotationDbi apcluster Biobase clusterSim e1071 igraph limma multtest parmigene reactome_db]; }; - mBPCR = derive2 { name="mBPCR"; version="1.36.0"; sha256="0vsb87518x770li85jdkns1qsabmixsn8mvh96hamr0adcwvgzrz"; depends=[Biobase oligoClasses SNPchip]; }; - mCSEA = derive2 { name="mCSEA"; version="1.2.2"; sha256="0lan3ycvlg2z21wih4dnmiiq2al0jspqbv974pfak57s8h6vznrj"; depends=[fgsea GenomicFeatures GenomicRanges ggplot2 Gviz Homo_sapiens IRanges limma mCSEAdata S4Vectors SummarizedExperiment]; }; - maCorrPlot = derive2 { name="maCorrPlot"; version="1.52.0"; sha256="11gg32sj2iyd3l7hxlqlhgd8adcgsfdz7n5lypsz1d7d3y760f7y"; depends=[lattice]; }; - maPredictDSC = derive2 { name="maPredictDSC"; version="1.20.0"; sha256="00m792cgx3v6gp81axpqf48bdxkl8l2gnl6fvsx3xbsk4akm33p2"; depends=[affy AnnotationDbi caret class e1071 gcrma hgu133plus2_db limma LungCancerACvsSCCGEO MASS ROC ROCR]; }; - maSigPro = derive2 { name="maSigPro"; version="1.54.0"; sha256="15bndkrwafj1vg2ik0s5003dzs65ibyhgz79ya5gry0b5h365qri"; depends=[Biobase MASS mclust venn]; }; - maanova = derive2 { name="maanova"; version="1.52.0"; sha256="1p1g5p2qflcgk24h1ww0nj4nnfas5pyg1caw2bgxrqyb161rl90x"; depends=[Biobase]; }; - macat = derive2 { name="macat"; version="1.56.0"; sha256="11jvvs3w1kiv2lvjwgzcxr5xy3m7c6b56bvhs8kiwf5lkqrqw6kn"; depends=[annotate Biobase]; }; - made4 = derive2 { name="made4"; version="1.56.0"; sha256="05bk877d81jjifj6rgrx0j2fhlsnmy8s093fnpqp7khrjwqh3zhn"; depends=[ade4 gplots RColorBrewer scatterplot3d]; }; - maftools = derive2 { name="maftools"; version="1.8.10"; sha256="0r6m258qmhq6qfylp6hc8bfqaix69w9s3d4xzaaz2n0448q4qf27"; depends=[Biostrings BSgenome cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson survival wordcloud]; }; - maigesPack = derive2 { name="maigesPack"; version="1.46.0"; sha256="07rd63lifw4vmf2cxb7lwmnwpynv39ac0h2dd97dvjwqzj6kq1cs"; depends=[convert graph limma marray]; }; - makecdfenv = derive2 { name="makecdfenv"; version="1.58.0"; sha256="0djhh5kj4ymxjk1qhpx8kcy8cjzx3syx6na7v52aqhys0zssdbip"; depends=[affy affyio Biobase zlibbioc]; }; - manta = derive2 { name="manta"; version="1.28.1"; sha256="0lzwh3yi41hrqm25ili464n1cl22q7v00kgl20b412zfyx4rn7y5"; depends=[caroline edgeR Hmisc]; }; - mapscape = derive2 { name="mapscape"; version="1.6.0"; sha256="148b7g4qiczc215x9nrggjqzjbsd4wxwydjxsfbsmy51db7n4gp2"; depends=[base64enc htmlwidgets jsonlite stringr]; }; - marray = derive2 { name="marray"; version="1.60.0"; sha256="1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"; depends=[limma]; }; - martini = derive2 { name="martini"; version="1.2.0"; sha256="072k0wphk4nl096wvbfrn0v1sgryg74ay6r9jqci7pzmninc0kci"; depends=[igraph Matrix Rcpp RcppEigen Rgin S4Vectors snpStats]; }; - maser = derive2 { name="maser"; version="1.0.0"; sha256="08zfqzbryir2sf5a5bmdy63a9ix983kkn281flfbwm81694wx7pg"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; - maskBAD = derive2 { name="maskBAD"; version="1.26.0"; sha256="0nkc7s219b9vhc3fl01ji94pxls0r8li042k8lrq8jx1g940smh4"; depends=[affy gcrma]; }; - massiR = derive2 { name="massiR"; version="1.18.0"; sha256="1fsic9w4bkkmi177f1f8lk4835cs2y4r5dy5vf71nc89y4jg7h67"; depends=[Biobase cluster diptest gplots]; }; - matchBox = derive2 { name="matchBox"; version="1.24.0"; sha256="0whhbp49imvrl0a4xdmmbz8fz8vv9i19168smm7xq2p7wa1am364"; depends=[]; }; - matter = derive2 { name="matter"; version="1.8.3"; sha256="03hsgl0k48j458aa20s4xxrpslypllg74qf6yr9irx9h939hszwm"; depends=[biglm BiocGenerics digest irlba]; }; - mcaGUI = derive2 { name="mcaGUI"; version="1.30.0"; sha256="0id5zlpk8zdim8gmmh61dabirg52kmbi63dx316838idk4i06a5h"; depends=[bpca foreign gWidgets gWidgetsRGtk2 lattice MASS OTUbase proto vegan]; }; - mdgsa = derive2 { name="mdgsa"; version="1.14.0"; sha256="01yh036hy3jn1q76bz2whfdf2qjs5xra7570rf25fff824cbszdk"; depends=[AnnotationDbi cluster DBI GO_db KEGG_db Matrix]; }; - mdp = derive2 { name="mdp"; version="1.2.1"; sha256="1rmkzjd2f7f1dnla8rlywhwih5lpi742br1gsrrl5i61lgy61fbl"; depends=[ggplot2 gridExtra]; }; - mdqc = derive2 { name="mdqc"; version="1.44.0"; sha256="0w4455xqkwwz8bhac36sxkqziq9pacp8n81zc3b1wwcwf95m2r6q"; depends=[cluster MASS]; }; - meshes = derive2 { name="meshes"; version="1.8.0"; sha256="0lc0mmvmrfzirqc0ydhzwdpq7d6rb8ffi8ka52qs6wc6nfqb6qg8"; depends=[AnnotationDbi DOSE enrichplot GOSemSim MeSH_db rvcheck]; }; - meshr = derive2 { name="meshr"; version="1.18.0"; sha256="12rwfqjpa9bzgrm3yqfz7h8v22icps8dr709lmp7k1jx9jbzp3gs"; depends=[BiocGenerics Category cummeRbund fdrtool MeSH_Aca_eg_db MeSH_AOR_db MeSH_Bsu_168_eg_db MeSH_db MeSH_Hsa_eg_db MeSH_PCR_db MeSH_Syn_eg_db MeSHDbi org_Hs_eg_db RSQLite S4Vectors]; }; - messina = derive2 { name="messina"; version="1.18.0"; sha256="1dhl6l5ids2ffsfbc9jk36ihrpsd161w9c1j93jvdvpa6130jl6f"; depends=[foreach ggplot2 plyr Rcpp survival]; }; - metaArray = derive2 { name="metaArray"; version="1.60.0"; sha256="049xwhycw2czzshvy5rc4plngaylwrj3ilk7dzynksn7av6sz4zd"; depends=[Biobase MergeMaid]; }; - metaCCA = derive2 { name="metaCCA"; version="1.10.0"; sha256="1h3xnrnlpbrjvrjpifm6i4kzyfgc2a0gnzpxya9lj105m9svpvca"; depends=[]; }; - metaMS = derive2 { name="metaMS"; version="1.18.1"; sha256="0ygci9hny7p90wf6inzw8qgbm8vl82d2n2wvcac5vdh8rsc4rdcp"; depends=[BiocGenerics CAMERA Matrix robustbase xcms]; }; - metaSeq = derive2 { name="metaSeq"; version="1.22.1"; sha256="00jwcgcx250v9glqxc1d0cvydn2jqzxxq62jmwskv87av68ppqbs"; depends=[NOISeq Rcpp snow]; }; - metabomxtr = derive2 { name="metabomxtr"; version="1.16.1"; sha256="1nz1higya3i7lbmqgxv5fa4nxwpm7b2fvsa69x52b36i0z70y7lc"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; }; - metagene = derive2 { name="metagene"; version="2.14.0"; sha256="09krnp862jz8mgjyp6v5ynvsrl4asfvzsvi21rj8af5b0ywkwvwg"; depends=[BiocParallel data_table DBChIP EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; }; - metagenomeFeatures = derive2 { name="metagenomeFeatures"; version="2.2.3"; sha256="0dirj9xsn13jz572j0z37997s3nhgb3l1gqm67giarbp1h0nw20l"; depends=[ape Biobase Biostrings dbplyr DECIPHER dplyr lattice lazyeval magrittr RSQLite S4Vectors stringr]; }; - metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.24.1"; sha256="0zsb9vilmkvmx7vhw4074qgkxi5xd0kihzx2q5bi7l2zjd152y78"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer]; }; - metahdep = derive2 { name="metahdep"; version="1.40.0"; sha256="02xw6pb6688hhgq3213s55sb73qmd6xjfaqk7bz4ci7m4ilf6c2k"; depends=[]; }; - metaseqR = derive2 { name="metaseqR"; version="1.22.1"; sha256="0nrvm55jx25mwrdg9p52mlbvvcqcvkbg2z1i9g5fhb0c7llcrldx"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; }; - metavizr = derive2 { name="metavizr"; version="1.6.2"; sha256="18hcd11i4n6l8kf1i0a8zlx2bzr3964lijgbwvkg8bghy288n4jm"; depends=[Biobase data_table digest epivizr epivizrData epivizrServer epivizrStandalone GenomeInfoDb httr metagenomeSeq phyloseq vegan]; }; - methInheritSim = derive2 { name="methInheritSim"; version="1.4.1"; sha256="0cshckvhrvlq9wgcjk3z2bi1qfq1my947rwvdma5la8ydf3x1i5w"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges methylKit msm S4Vectors]; }; - methVisual = derive2 { name="methVisual"; version="1.34.0"; sha256="09ss0s5z950m6v2y037v8qwsp238w73302ls1xh9ps8gkz05a800"; depends=[Biostrings ca gridBase gsubfn IRanges plotrix sqldf]; }; - methimpute = derive2 { name="methimpute"; version="1.4.1"; sha256="1xcparys2ifv2y5rp8ih558l8apnw5b3mjnkkc29szf38mzk9a1r"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; }; - methyAnalysis = derive2 { name="methyAnalysis"; version="1.24.0"; sha256="0afgaf3xl2dnpl86agbx44fiq4i5i96535p3hd9y845xdq5ymvnp"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges genoset Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; }; - methylGSA = derive2 { name="methylGSA"; version="1.0.4"; sha256="0zkq3cnir2n01syc8122wy8yznlal60lhi9a97f1yayc95mddl66"; depends=[AnnotationDbi clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg stringr]; }; - methylInheritance = derive2 { name="methylInheritance"; version="1.6.1"; sha256="0n11jkka37aqmirn73hl8kabilb220i1pv10i62jzq623sqpdsz9"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; }; - methylKit = derive2 { name="methylKit"; version="1.8.1"; sha256="1zcfwy7i10aqgnf7r0c41hakb5aai3s3n9y8pc6a98vimz51ly2z"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; }; - methylMnM = derive2 { name="methylMnM"; version="1.20.0"; sha256="0sd3vj58yfscngpcl9hys2nys3siq1h2ask5r8j6jx6yz3qs91xd"; depends=[edgeR statmod]; }; - methylPipe = derive2 { name="methylPipe"; version="1.16.0"; sha256="1qrvf0kf1948v2bhkxv979p6cr8mknmqkb04hz30bm8fqpmn1wfw"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; }; - methylumi = derive2 { name="methylumi"; version="2.28.0"; sha256="14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; }; - methyvim = derive2 { name="methyvim"; version="1.4.0"; sha256="1scybf1hdzyvjmcbfbqpbwph38alp594lj3ggxcdgfxvjapq3rsb"; depends=[BiocGenerics BiocParallel bumphunter cluster doFuture dplyr future GenomeInfoDb ggplot2 ggsci gridExtra gtools IRanges limma minfi S4Vectors SummarizedExperiment superheat tmle]; }; - mfa = derive2 { name="mfa"; version="1.4.1"; sha256="0khilki6kp63lij5nfcl36j161aqndr385p15fnmvg38qql88px7"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; }; - mgsa = derive2 { name="mgsa"; version="1.30.0"; sha256="0b30hlqyx8aw8a9naln2m5k8lgkr9f9fgv1mwnww5xiwqdnbqfcw"; depends=[gplots]; }; - miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.6.0"; sha256="0gb7vg35wff0kckb6dqkggvshdy43q04f07niiqamnl71h59wjh7"; depends=[]; }; - miRLAB = derive2 { name="miRLAB"; version="1.12.0"; sha256="0vpvd93zrz4ihcinpwppc954585vjafmcpj1rpamqkyi2giyxldm"; depends=[Category ctc dplyr energy entropy glmnet GOstats gplots heatmap_plus Hmisc httr impute InvariantCausalPrediction limma org_Hs_eg_db pcalg RCurl Roleswitch stringr SummarizedExperiment TCGAbiolinks]; }; - miRNAmeConverter = derive2 { name="miRNAmeConverter"; version="1.10.0"; sha256="0wkkgqki7sv92adwzxay6xjyfx921ll8yh6aw2yp0mdgk9021zr8"; depends=[AnnotationDbi DBI miRBaseVersions_db reshape2]; }; - miRNApath = derive2 { name="miRNApath"; version="1.42.0"; sha256="1hrnnvp3y2q8ldmlq2pdyd3dpkqpyrhhgzqms3mc7djnv6ybv3cd"; depends=[]; }; - miRNAtap = derive2 { name="miRNAtap"; version="1.16.0"; sha256="1iy4gks0c0alg5bl1l40fdja6wffm0hjv40xvny9s1g036zmqca6"; depends=[AnnotationDbi DBI plyr RSQLite sqldf stringr]; }; - miRSM = derive2 { name="miRSM"; version="1.0.0"; sha256="09z2ca1qpf2m3s5cc59y4xzcixlbl847c17lx1kmrakabqpsxy8i"; depends=[BiBitR BicARE biclust Biobase dynamicTreeCut fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MCL miRsponge NMF PMA Rcpp rqubic runibic s4vd SummarizedExperiment WGCNA]; }; - miRcomp = derive2 { name="miRcomp"; version="1.12.0"; sha256="17b6bq70d6ly09vma5mdlk54620jdxw6k4bwdyxgghyk7kwmd753"; depends=[Biobase KernSmooth miRcompData]; }; - miRmine = derive2 { name="miRmine"; version="1.4.0"; sha256="0zfdm5d6ifkq55v38xcjwzq19ifh6jgbg1pjp298mn15yjsjzfj1"; depends=[SummarizedExperiment]; }; - miRsponge = derive2 { name="miRsponge"; version="1.8.2"; sha256="0cpbhbjsb7sr3rjmc4cjn18j2rycma941qrwcjz8gyd4kgafd78f"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL org_Hs_eg_db Rcpp ReactomePA survival varhandle]; }; - microRNA = derive2 { name="microRNA"; version="1.40.0"; sha256="1asrjljh4bxgzvbgnp72sqyqv13kvzbfdn3jy01v3l98dppjnwsf"; depends=[Biostrings]; }; - microbiome = derive2 { name="microbiome"; version="1.4.2"; sha256="0amla1m69axhlslbg1pbvl61qyxb6qjpdfd5g2j8b116h8xrmyab"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; }; - mimager = derive2 { name="mimager"; version="1.6.0"; sha256="097fv7wfj0wj0chijcl5v52lf35pc48va1ddsq6qii5xzi626cpd"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; }; - minet = derive2 { name="minet"; version="3.40.0"; sha256="0hb1k3p750qykmqjz59yjak5h8vmnln8zcp2dffjnqvwgn78i23w"; depends=[infotheo]; }; - minfi = derive2 { name="minfi"; version="1.28.4"; sha256="1sjwwqb0syngvj75saaky9y06hbxsawhhcmfvavzkhicxipafv7r"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; }; - mirIntegrator = derive2 { name="mirIntegrator"; version="1.12.0"; sha256="1vgl2kz4jahrw885gib7yaxwliij1ric9mmsad8v4zravw7d9knj"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; }; - missMethyl = derive2 { name="missMethyl"; version="1.16.0"; sha256="0axssdkyvdfpq7r47sckbbp7w8wa06j1ncskcn2w9f95nl1dbya5"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; }; - missRows = derive2 { name="missRows"; version="1.2.0"; sha256="0fgw36358z0lc0ppkpy49vw1p2k2w3ji01apff8gpkfb310zipwc"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; }; - mitoODE = derive2 { name="mitoODE"; version="1.20.1"; sha256="17cppvvvbpa4k62wrih3q61mrkc3145d5macq0sp6vh2vag61xdm"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; }; - mixOmics = derive2 { name="mixOmics"; version="6.6.2"; sha256="00mq3ikxnx8msgvciqjzis5n83klbzkp5nlk47hl41zksxnyknwm"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; }; - mogsa = derive2 { name="mogsa"; version="1.16.0"; sha256="14rl7md4bdpb24cxj5pmr196dy0amih8l4611kgwbrvdm9k13d3s"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; }; - monocle = derive2 { name="monocle"; version="2.10.1"; sha256="0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; }; - mosaics = derive2 { name="mosaics"; version="2.20.0"; sha256="1536y2fizmi7jafq7bhbv8bzpf5b97dfskpg9a7v4c9xv6isagnx"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; }; - motifRG = derive2 { name="motifRG"; version="1.26.0"; sha256="1wxww6i0jgyapqclcwy0zzf9kqjvrvylr89z7yhg1izi7jnw2fka"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 IRanges seqLogo XVector]; }; - motifStack = derive2 { name="motifStack"; version="1.26.0"; sha256="1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; }; - motifbreakR = derive2 { name="motifbreakR"; version="1.12.0"; sha256="191w8nzjm1lkgbzlhixnfvpgadq2mlhmwk7ai8xaadmxckrf494a"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr TFMPvalue VariantAnnotation]; }; - motifcounter = derive2 { name="motifcounter"; version="1.6.0"; sha256="04i8s6r26kir9fcqbvy1wfxrav5imwj4r0sqvsf4vq2jxkwb4brr"; depends=[Biostrings]; }; - motifmatchr = derive2 { name="motifmatchr"; version="1.4.0"; sha256="1s65gr15iil1y8sa7wggrj5sb0mgw6vgs2qrmk1xka9zqjx957kv"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; }; - mpra = derive2 { name="mpra"; version="1.4.1"; sha256="0wwn5cix0npk8lhsmk9dzagnfrqcn9x22wzgf5kq3xk4gwaraqdw"; depends=[BiocGenerics limma S4Vectors scales statmod SummarizedExperiment]; }; - msPurity = derive2 { name="msPurity"; version="1.8.1"; sha256="00v9bgwjkgkwkpf5yq13snncayn76iyp0k6r7lbq1lhf5p4cxw6m"; depends=[DBI doSNOW fastcluster foreach ggplot2 mzR plyr Rcpp reshape2 RSQLite stringr]; }; - msa = derive2 { name="msa"; version="1.14.0"; sha256="1g0ny0hjnzwqh9kbp6n770vfdvxsl95vhiydjqasma2hz205plf9"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; }; - msgbsR = derive2 { name="msgbsR"; version="1.6.1"; sha256="0q7hz3ca4x0nagk9f65vni3qn5z08irmxc5344rgn9mscafchfbv"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; }; - msmsEDA = derive2 { name="msmsEDA"; version="1.20.1"; sha256="1jrlxgzh3kdr9nhr9qd7hi5ahg9r2589drhq4klkcrwvfy013j7b"; depends=[gplots MASS MSnbase RColorBrewer]; }; - msmsTests = derive2 { name="msmsTests"; version="1.20.1"; sha256="08w3hmmmhxx5dvki5sfgxrhdqfy1xdxcbnpy4nvszhgmyc18zjzp"; depends=[edgeR msmsEDA MSnbase qvalue]; }; - multiClust = derive2 { name="multiClust"; version="1.12.0"; sha256="0ddk1sl9zsc4dgrxasnqa2h341blirpwzygl89wh2k4ga0wsmw6q"; depends=[amap cluster ctc dendextend mclust survival]; }; - multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.0.0"; sha256="0aixi21zmj2lc54cmkqc9k596nll01nyxhpkkzx40lv7jihw6p1c"; depends=[BiocParallel BLMA data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare metap pbapply pheatmap qqman]; }; - multiMiR = derive2 { name="multiMiR"; version="1.4.0"; sha256="1mip48rcqk47sj5sdqi2rxcwsd6l6v3nssnnkx41mpx8amn3cigb"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; - multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.6.0"; sha256="0h7spx39c079mzpbnbg4fv7bfnrdqz95101zxd4cdsffjk5zrly8"; depends=[doParallel foreach SummarizedExperiment]; }; - multiscan = derive2 { name="multiscan"; version="1.42.0"; sha256="1h5b55j0m4znp9gpzqdv974vvxhlbskxy9m474g8y72q0zbri4gk"; depends=[Biobase]; }; - multtest = derive2 { name="multtest"; version="2.38.0"; sha256="0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"; depends=[Biobase BiocGenerics MASS survival]; }; - muscle = derive2 { name="muscle"; version="3.24.0"; sha256="1v0n6ncq467kpfli498gddz0r6ilkhjfw0q9srl1gcknz5y2frsw"; depends=[Biostrings]; }; - mygene = derive2 { name="mygene"; version="1.18.0"; sha256="03knrfbqm9hr30l3s58jkqyl6sl83p1vf4zyahr1ld0qrw81pvx7"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; }; - myvariant = derive2 { name="myvariant"; version="1.12.0"; sha256="1vsp8m6rwyk09i0rg5j8w29vgn5hzz7fh8gc2fbjbg3icls26gn8"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; }; - mzID = derive2 { name="mzID"; version="1.20.1"; sha256="15yd4bdxprw3kg7zj2k652y3yr3si781iw28jqvnkm0gsc23rd0c"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; }; - mzR = derive2 { name="mzR"; version="2.16.2"; sha256="19fn58zl59kd0hsjjc6y975y9187nfls0028a4k3v0s9wfg5b3vn"; depends=[Biobase BiocGenerics ncdf4 ProtGenerics Rcpp Rhdf5lib zlibbioc]; }; - ncdfFlow = derive2 { name="ncdfFlow"; version="2.28.1"; sha256="1nabfa8nz6plw8w2xfla0xffqmxyk699dbv9615cazhf6vl6289f"; depends=[BH Biobase BiocGenerics flowCore flowViz Rcpp RcppArmadillo Rhdf5lib zlibbioc]; }; - ndexr = derive2 { name="ndexr"; version="1.4.1"; sha256="067x2sj3pnq3hrxjpw4y4qp9gimgymxik9zdqjkirix77h817682"; depends=[httr igraph jsonlite plyr tidyr]; }; - nem = derive2 { name="nem"; version="2.56.0"; sha256="02j5rm0h9bjghgba244k0acshbnhrr38ghvx6cmf8za8fw19k3v2"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; }; - netReg = derive2 { name="netReg"; version="1.6.0"; sha256="01qxq7zlbmvh0mazw069fm6bjw0ks90baj8y5i0jc7m101dsm2qi"; depends=[Rcpp RcppArmadillo]; }; - netSmooth = derive2 { name="netSmooth"; version="1.2.0"; sha256="1cz3rca9ig9jl8ddcadbij129v5rpb86ncfrdmfj4m9qy0krlyac"; depends=[cluster clusterExperiment data_table entropy Matrix scater SingleCellExperiment SummarizedExperiment]; }; - netbenchmark = derive2 { name="netbenchmark"; version="1.14.0"; sha256="1gc8dnma4pr1j9wq422x8xh89mvb15kyvjvv86fhhshvdisihngw"; depends=[c3net corpcor fdrtool GeneNet GENIE3 grndata Matrix minet pracma Rcpp]; }; - netbiov = derive2 { name="netbiov"; version="1.16.0"; sha256="0zg4wkf4z6yi84sdp4h8dg8cq5sm6m04abg15hm68y27vw42prs2"; depends=[igraph]; }; - nethet = derive2 { name="nethet"; version="1.14.0"; sha256="1xp08ad4lsmrjgvqydr85k4y0b57hcaxicndh4hz4plqswzl7qpf"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; }; - netprioR = derive2 { name="netprioR"; version="1.8.1"; sha256="1phdaklcwhv1rv94dvz4mcwi5f1b3gya7bwv7489hsx7pa149sac"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; }; - netresponse = derive2 { name="netresponse"; version="1.42.0"; sha256="16hgcjzvbsx1lj2aq8jkam926ykb06im06rr62z705x6hna8k4g0"; depends=[dmt ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz]; }; - networkBMA = derive2 { name="networkBMA"; version="2.22.0"; sha256="12pl1hl1r2j3kvbr061xzzv5fmkh1g60j5ihvzi14gy8chvjk7wk"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; }; - nnNorm = derive2 { name="nnNorm"; version="2.46.0"; sha256="0fslid2ywqbx4d3c2gvhhsmkkkidgjnlr8jsd61qralcdln494wv"; depends=[marray nnet]; }; - nondetects = derive2 { name="nondetects"; version="2.12.0"; sha256="1wsckq31y6cxlgyg579zh6yk1sa1s0lczkvx29dbvy11hjnsgkm6"; depends=[arm Biobase HTqPCR limma mvtnorm]; }; - normalize450K = derive2 { name="normalize450K"; version="1.10.0"; sha256="0ab9g0k0y8lzqx8vvfwxy8yjmal4lgxf64fnz0923jss98czvk21"; depends=[Biobase illuminaio quadprog]; }; - normr = derive2 { name="normr"; version="1.8.0"; sha256="1yj9nnfzj522yr5nw0sm9l6cvk21w4vpxn0bayggs2wx5g03pbsj"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; }; - npGSEA = derive2 { name="npGSEA"; version="1.18.0"; sha256="199n898qn6799p6zk46vlz192zj0z10f9q0xfc129ickfa7zk6gf"; depends=[Biobase BiocGenerics GSEABase]; }; - nuCpos = derive2 { name="nuCpos"; version="1.0.1"; sha256="0waac65n10izn8a6r2rlgi1xwjdc1yxa0pwlnriwkzdg9hpszbdd"; depends=[]; }; - nucleR = derive2 { name="nucleR"; version="2.14.0"; sha256="19y2ars61gbzglqvfzj2xq08iw34vnjm3fzn4dx67r0ivnxncs34"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; }; - nucleoSim = derive2 { name="nucleoSim"; version="1.10.0"; sha256="09mls6rv9qw9w1g3avgj57pi2avg4pnlbcbg29da0szz0dbbb7yn"; depends=[IRanges S4Vectors]; }; - occugene = derive2 { name="occugene"; version="1.42.0"; sha256="0sqmnr571rx18mh9m9ivjp79bqn6dydzhh3h4xc7xxwqwwp0l4fa"; depends=[]; }; - odseq = derive2 { name="odseq"; version="1.10.0"; sha256="0936n8qzxcaxlqwpzh3dc2gnzh7q5cyrk4cif3vxb4hrlix8b1bv"; depends=[kebabs mclust msa]; }; - oligo = derive2 { name="oligo"; version="1.46.0"; sha256="1j9p22chnb09fp26xnlx5zmrxccg0q56ywgxfvbmm0s2jnr02nam"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; }; - oligoClasses = derive2 { name="oligoClasses"; version="1.44.0"; sha256="03kdxgrznx204y7pma1ca4bjgrhhhwfz2ia9radgkl70m447hz13"; depends=[affyio Biobase BiocGenerics BiocManager Biostrings DBI ff foreach GenomicRanges IRanges RSQLite S4Vectors SummarizedExperiment]; }; - omicRexposome = derive2 { name="omicRexposome"; version="1.4.1"; sha256="0jfyin051mwif6sxng7y51pc4gc1wxshfpy09zcj33j9cx2yabcw"; depends=[Biobase ggplot2 ggrepel gridExtra isva limma MultiDataSet omicade4 PMA rexposome SmartSVA stringr SummarizedExperiment sva]; }; - omicade4 = derive2 { name="omicade4"; version="1.22.0"; sha256="1bwfbzkq7p9h1njgaj15hk69cw9649kq5hwf2k8jf3spnbirp114"; depends=[ade4 made4]; }; - omicplotR = derive2 { name="omicplotR"; version="1.2.1"; sha256="1dj2n3y6rhrhiy36hpmmy468zbjcibq0f36lymz217iklh93m0lh"; depends=[ALDEx2 compositions knitr matrixStats rmarkdown shiny vegan zCompositions]; }; - omicsPrint = derive2 { name="omicsPrint"; version="1.2.1"; sha256="0ri8is6d9vl44l1l8hizxa7ysc0inq81kqjjdxr8x09q4xp2hyw0"; depends=[MASS matrixStats MultiAssayExperiment RaggedExperiment SummarizedExperiment]; }; - oncomix = derive2 { name="oncomix"; version="1.4.0"; sha256="00pwd0nbbdlv35p85h5kqybvvzz2833qx2jgprffg2bhmxvaky8w"; depends=[ggplot2 ggrepel mclust RColorBrewer SummarizedExperiment]; }; - oneSENSE = derive2 { name="oneSENSE"; version="1.4.1"; sha256="0hipmgwy8wy7i8mc35vdkgfbqz6g2wcqczl78x9i41av4dacpqz1"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; }; - onlineFDR = derive2 { name="onlineFDR"; version="1.0.0"; sha256="1738wy4px32jzinj9311hvng887ys61dqqs3m3zi5cqkpwcs19hd"; depends=[]; }; - ontoProc = derive2 { name="ontoProc"; version="1.4.0"; sha256="08sgf142b8l4gdsap44b75jcxvwlcz19saqjrw9sg0307h509n77"; depends=[AnnotationDbi Biobase ontologyIndex S4Vectors shiny]; }; - openCyto = derive2 { name="openCyto"; version="1.20.2"; sha256="0fa39bpi26civ7dabxf7py6lydmkhss5gff6ykrbmwp85h9d2nsh"; depends=[Biobase BiocGenerics clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; }; - openPrimeR = derive2 { name="openPrimeR"; version="1.4.1"; sha256="0cmixmj1mnalr89c32ih5hf4v73qf4x73hzvbiw0mnz8niizaqgz"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr tinytex uniqtag XML]; }; - openPrimeRui = derive2 { name="openPrimeRui"; version="1.4.1"; sha256="163a8frs637yvm6vqhi7sxashkbdc61m8mb5lc6n0i98zicmaj4p"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; }; - oposSOM = derive2 { name="oposSOM"; version="2.0.0"; sha256="190sg040nxjja0phmw9k81s139756qsnk1pac3cby21ml6hwbr0j"; depends=[ape Biobase biomaRt fastICA fdrtool igraph pixmap Rcpp RcppParallel scatterplot3d tsne]; }; - oppar = derive2 { name="oppar"; version="1.10.0"; sha256="012ypy3z2dgm6ddmbrq3vyyf5yk9ac18gs733s70jv61z2bd1rlw"; depends=[Biobase GSEABase GSVA]; }; - pRoloc = derive2 { name="pRoloc"; version="1.22.2"; sha256="14psqkyiwghv51irngrc1r0h47dh8cjz4z1b9x6nas3a1wzbicc2"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class coda dendextend e1071 FNN ggplot2 gtools hexbin kernlab knitr LaplacesDemon lattice MASS mclust mixtools MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; }; - pRolocGUI = derive2 { name="pRolocGUI"; version="1.16.0"; sha256="13z6zd7m7hsjvm52lgy9v8ypkr6gs190c26qs0yzq7s4vfq48db2"; depends=[Biobase dplyr DT ggplot2 MSnbase pRoloc scales shiny]; }; - paircompviz = derive2 { name="paircompviz"; version="1.20.0"; sha256="1iraq8n5q24zz3xdv15wiyhd5avz0yr6hh1mzygypp8bmhkgcixv"; depends=[Rgraphviz]; }; - pandaR = derive2 { name="pandaR"; version="1.14.0"; sha256="0jm5xxxynrh08l0iz0wj7jl120a6vsglppryjhl4mgv7cs5pdx9w"; depends=[Biobase BiocGenerics ggplot2 hexbin igraph matrixStats plyr reshape RUnit]; }; - panelcn_mops = derive2 { name="panelcn.mops"; version="1.4.0"; sha256="1ib6v4zkgj7qc5ncnjgsx0rwb7awbisd64p7zxah175zds33gxph"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; - panp = derive2 { name="panp"; version="1.52.0"; sha256="1vv7i3zykv48s0v4nvxaziixkkdl660166cg9fgvbxb8689c2cw7"; depends=[affy Biobase]; }; - parglms = derive2 { name="parglms"; version="1.14.0"; sha256="0mzd1x8xj6sjjm98dahip663zq3k3bm9jn2j60hsyvr18win2bkx"; depends=[BatchJobs BiocGenerics doParallel foreach]; }; - parody = derive2 { name="parody"; version="1.40.0"; sha256="14rzpmmcdq9j19ydb9qksga6l06zdnb29qn13wjxlbn9l7mbfzy4"; depends=[]; }; - pathRender = derive2 { name="pathRender"; version="1.50.0"; sha256="17q2vs878nmjs1k2f11l66wmkjz8zxy9wbhsyg8aal83yzr65hkc"; depends=[AnnotationDbi cMAP graph RColorBrewer Rgraphviz]; }; - pathVar = derive2 { name="pathVar"; version="1.12.0"; sha256="09ncdyamlhs24yyg7fnb77vchqxpxh6asmj32pxhpvkkkgq106p4"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; }; - pathifier = derive2 { name="pathifier"; version="1.20.0"; sha256="064q5nbxgyz4hx6h4f92w7vyd77pndmxadwa8cw9y5qzh9g29a5m"; depends=[princurve R_oo]; }; - pathprint = derive2 { name="pathprint"; version="1.12.0"; sha256="06lv35nx0d098idjnlcr5bziilwnpapbbcsdfrwglcibgqis9hzh"; depends=[]; }; - pathview = derive2 { name="pathview"; version="1.22.3"; sha256="1dw87ldd3awc8br61012iaifznby5qq3i8v333blqspfb4mnmjyy"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; - paxtoolsr = derive2 { name="paxtoolsr"; version="1.16.0"; sha256="0sa680x51kcsbmlrb54z8m1qn1pjyzx7k26pni17mfdzaw1q9jki"; depends=[httr igraph jsonlite plyr R_utils readr rJava rjson XML]; }; - pcaExplorer = derive2 { name="pcaExplorer"; version="2.8.1"; sha256="1af9yf4nnsn3wb93zb0agn2vr04ianhm85326fl6qm51pmjljswh"; depends=[AnnotationDbi biomaRt d3heatmap DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats IRanges knitr limma NMF pheatmap plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; - pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.26.0"; sha256="0rdj9043zdvfh2gwas13i6787kw01m1cr998prgf12n9l107v68s"; depends=[AnnotationDbi Biostrings ellipse]; }; - pcaMethods = derive2 { name="pcaMethods"; version="1.74.0"; sha256="0ik82s9bsdj4a1mmv0a3k6yisa92mxx7maf3dvip1r8gqlm3dyng"; depends=[Biobase BiocGenerics MASS Rcpp]; }; - pcot2 = derive2 { name="pcot2"; version="1.50.0"; sha256="0rj3wd9a917p20kr28cc8si7yjqdh9ddc3n58aih7f96v6qxzq4i"; depends=[amap Biobase]; }; - pcxn = derive2 { name="pcxn"; version="2.4.0"; sha256="0a4hs1rc3p3lx9r188fgfhly60l570qna5ydmkixci5pjvnijv4b"; depends=[pcxnData pheatmap]; }; - pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.46.0"; sha256="1fwkfyazqq9i51fq965xvxqmidmnzg9xxfk74abfaz8y0w4jamak"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; - pepStat = derive2 { name="pepStat"; version="1.16.0"; sha256="1msy1wcvp1d2sdddygnqkgzgldgpb6481wj0q0qvb8f2g47lghb7"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; }; - pepXMLTab = derive2 { name="pepXMLTab"; version="1.16.1"; sha256="03szrw113d90aigy1hr6ylxwc3ccqxinkznfxb3nrw1fzipqz6c4"; depends=[XML]; }; - perturbatr = derive2 { name="perturbatr"; version="1.2.1"; sha256="17dbgj2g4c2bzi3sljh1zsx6azfb02hs3fiha6k01x92fwi83vik"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; }; - pgca = derive2 { name="pgca"; version="1.6.1"; sha256="1j55i52lz6k6bmvxw8vvbynmka43bcd857rl2dc5li5h3c04ympg"; depends=[]; }; - phantasus = derive2 { name="phantasus"; version="1.2.1"; sha256="0nd4zfazkbny94s7jnvj8flnxdvhlv4878w0hklf0fnsyzgc9am9"; depends=[assertthat Biobase ccaPP fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix Matrix_utils opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; }; - phenoTest = derive2 { name="phenoTest"; version="1.30.0"; sha256="0m9ginyg2jda48ihkvalzs89xpn3bshnyli26s0mb91hhdjcn55c"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach HTSanalyzeR limma mgcv SNPchip survival xtable]; }; - phenopath = derive2 { name="phenopath"; version="1.6.7"; sha256="1bx7v90r180kb8rybhlh26zmq7n3110z7xqyy3cczzp6jrlwycr8"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; }; - philr = derive2 { name="philr"; version="1.8.1"; sha256="1rdgz4x54m2wlqrhr4nn26q28gzmlivsppzjj8h8g6h1gy7iqsj5"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; - phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.6.0"; sha256="186580zsbbvjz1nck1nrnp81yfyll0rzpbfij127h26ghq49lccc"; depends=[matrixStats plyr]; }; - phyloseq = derive2 { name="phyloseq"; version="1.26.1"; sha256="13ap1jj6rh82f5x6x2cb29c6p3q3rfg86i0dzmj2f0lvsnhr9spw"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; }; - piano = derive2 { name="piano"; version="1.22.0"; sha256="0fkimnbgmsh3x1r138855glml876al9fbzzz03xw5cybh0rk1ghx"; depends=[Biobase BiocGenerics fgsea gplots igraph marray relations]; }; - pickgene = derive2 { name="pickgene"; version="1.54.0"; sha256="0lsyh1hlpnn7vxqh3ga69qs72wlsrn8hxnzvlv03ga9124kfmnr9"; depends=[MASS]; }; - pint = derive2 { name="pint"; version="1.32.0"; sha256="0ppb7hghv0152qs6zac4i69r0sjckl9hyw8skbb0ksqv785yxpxh"; depends=[dmt Matrix mvtnorm]; }; - pkgDepTools = derive2 { name="pkgDepTools"; version="1.48.0"; sha256="0bsrr3jya1nn694znbsq3zi4h099ak1jsak9fyyccd3icmcmk2x2"; depends=[graph RBGL]; }; - plateCore = derive2 { name="plateCore"; version="1.40.1"; sha256="15ffs6j5p8dfs75hc21rp3ngcrm3265h5a28vzax28p3850c3dy7"; depends=[Biobase flowCore flowStats flowViz lattice latticeExtra MASS robustbase]; }; - plethy = derive2 { name="plethy"; version="1.20.0"; sha256="1018bn55hppwrvj6i5yyzy7fscy1w5v616smpghmplbbycxv3gpi"; depends=[Biobase BiocGenerics DBI ggplot2 IRanges plyr RColorBrewer reshape2 RSQLite S4Vectors Streamer]; }; - plgem = derive2 { name="plgem"; version="1.54.1"; sha256="1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"; depends=[Biobase MASS]; }; - plier = derive2 { name="plier"; version="1.52.0"; sha256="1xg9c232z3vlaa356g1c7b4ysx2bkck5ywb57kim9d5bgbvbk83p"; depends=[affy Biobase]; }; - plotGrouper = derive2 { name="plotGrouper"; version="1.0.1"; sha256="0cshh7dm559w5bmlly293vzndbzq16vkfml3siy8g8w480i0nfxj"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; }; - plrs = derive2 { name="plrs"; version="1.22.0"; sha256="1xr6z9fdbdj8qyjlr1fw2mx30iqz1bcxcqs7snarc34qdzr088m5"; depends=[Biobase BiocGenerics CGHbase ic_infer marray quadprog Rcsdp]; }; - plw = derive2 { name="plw"; version="1.42.0"; sha256="1kbn1hhqnf2cmqxjvq4whaj4h7i4v7cbcybcspafy4wvmysjsjvd"; depends=[affy MASS]; }; - plyranges = derive2 { name="plyranges"; version="1.2.0"; sha256="12cc8pnlq1rq01dwia0994chflm184mp2yb983lz973fp0kpbhd2"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyr tidyselect]; }; - pmm = derive2 { name="pmm"; version="1.14.0"; sha256="1ld7bcw6vphm48k8sy07j3j02pxfz6wiwqbz94jblc93s121b3z7"; depends=[lme4]; }; - podkat = derive2 { name="podkat"; version="1.14.0"; sha256="0df21vdia2zl70niajwqfswbicwb2agarak7dyd7arp29xz9ivvf"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rsamtools]; }; - pogos = derive2 { name="pogos"; version="1.2.1"; sha256="1y0v5r3f75qy67pz96siahxi0xdrilqz04v9qjl1ry866nfzjlkg"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; }; - polyester = derive2 { name="polyester"; version="1.18.0"; sha256="0acwamzwhqbavv0pxah20230mlanncc71lwbbxwki948j1qvg3rp"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; }; - powerTCR = derive2 { name="powerTCR"; version="1.2.0"; sha256="16x8kzidv6d2zm61jw47dgr047ijfkm18xddkk70qxgkrqc0gdpa"; depends=[cubature doParallel evmix foreach magrittr purrr tcR truncdist vegan VGAM]; }; - ppiStats = derive2 { name="ppiStats"; version="1.48.0"; sha256="1aclxj5y32rca97qv5gqfgsq2aly35gs12jxbvwikwbw6hwvi6pn"; depends=[Biobase Category graph lattice ppiData RColorBrewer ScISI]; }; - pqsfinder = derive2 { name="pqsfinder"; version="1.10.1"; sha256="061105p51shc8ipwrrjflaxdqsyna3hi1ivk1yx5878msvv9pkkx"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; - prada = derive2 { name="prada"; version="1.58.1"; sha256="0hasynlsbyvircf3njss8kvijkmrc0h7i5cch9x1c7zlsvz9ai6s"; depends=[Biobase BiocGenerics MASS RColorBrewer rrcov]; }; - prebs = derive2 { name="prebs"; version="1.22.1"; sha256="0b9x855sqrpiz1rdkl1hrflsg0x6fbdcakkh7602zf14fbbdvdyd"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; - predictionet = derive2 { name="predictionet"; version="1.28.0"; sha256="0hhxdvc30pdrpc96i4jvdn4q8gycdlk6hi9p8xdgmfin6pp375rk"; depends=[catnet igraph MASS penalized RBGL]; }; - preprocessCore = derive2 { name="preprocessCore"; version="1.44.0"; sha256="0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j"; depends=[]; }; - primirTSS = derive2 { name="primirTSS"; version="1.0.1"; sha256="05qi4dhazxfgqr5hzcbbbnlzh4ffqqz266bdxgwpmmi9ri3jw7gc"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg38 dplyr GenomicRanges GenomicScores Gviz IRanges JASPAR2018 phastCons100way_UCSC_hg38 purrr R_utils rtracklayer S4Vectors shiny stringr TFBSTools tibble tidyr]; }; - proBAMr = derive2 { name="proBAMr"; version="1.16.1"; sha256="0bsg3g0vqmv5xqn98z9bfj6hjpcfs6zzpaiiih8y5yq8wdbsi3np"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; }; - proFIA = derive2 { name="proFIA"; version="1.8.1"; sha256="1y9d57nrd5zbdnis0wqzk6k1p74f2i8qidjn3rl5xydpvnbqdfh5"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; }; - procoil = derive2 { name="procoil"; version="2.10.0"; sha256="0bv9kq1jsviyxvnclsc47lfjpxwlvsk479bk65zg0qbi397a3cwl"; depends=[Biostrings kebabs S4Vectors]; }; - profileScoreDist = derive2 { name="profileScoreDist"; version="1.10.0"; sha256="0xfnava0bqpsqwzzw5nkwqkcajzacvifd3b2jm3qg5579myjprx4"; depends=[BiocGenerics Rcpp]; }; - progeny = derive2 { name="progeny"; version="1.4.1"; sha256="02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7"; depends=[Biobase]; }; - prot2D = derive2 { name="prot2D"; version="1.20.0"; sha256="0ljggyj557zmbf51cgvq3sl42xqgqh3a2wayyd6s8501ww1xk7fg"; depends=[Biobase fdrtool impute limma MASS Mulcom qvalue samr st]; }; - proteinProfiles = derive2 { name="proteinProfiles"; version="1.22.0"; sha256="1jjricjdc9l2lk7m48x3isrzmn8jxsy8x865ijnmqz9zlzgzz8zs"; depends=[]; }; - proteoQC = derive2 { name="proteoQC"; version="1.18.1"; sha256="0p2wc5lp7ls80lkjcr5f0zjiq0y9xdallg8yjhprb1cicwxdnd5g"; depends=[dplyr ggplot2 MSnbase Nozzle_R1 plotly plyr reshape2 rmarkdown rpx rTANDEM seqinr tidyr VennDiagram XML]; }; - psichomics = derive2 { name="psichomics"; version="1.8.2"; sha256="15v0vi348n2xjv0mxis5vbh3a7qzzsgl5ah597xb06dxqxn4q795"; depends=[AnnotationDbi AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools org_Hs_eg_db pairsD3 plyr R_utils Rcpp recount reshape2 shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; }; - psygenet2r = derive2 { name="psygenet2r"; version="1.14.0"; sha256="11vsh96pmbf4ypyszgz3yqr0y3q7rxxd61hx2xhwy4v82fq8il2f"; depends=[BgeeDB Biobase BiocManager biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; - puma = derive2 { name="puma"; version="3.24.0"; sha256="1mjl2zkf6kxcadb0pcp157hhq4dgrxzjvs5i5s8mfxx54d7i80ih"; depends=[affy affyio Biobase mclust oligo oligoClasses]; }; - pvac = derive2 { name="pvac"; version="1.30.0"; sha256="0r92vrsbvbmyqajcldnjfnyigq5ppsh3bgm5h1i299sr4q7m85iv"; depends=[affy Biobase]; }; - pvca = derive2 { name="pvca"; version="1.22.0"; sha256="0s45j854parwwp5f173p5m8f58n18fqdn4z4z7x2ap5f733fr483"; depends=[Biobase lme4 Matrix vsn]; }; - pwOmics = derive2 { name="pwOmics"; version="1.14.0"; sha256="0v5gsk82899i98b8kv95mj4qry0j8plbj7qb1qsl5k51hz79i5pz"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; }; - qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.0.4"; sha256="06scrbiwzz3nbl1lbhbrh9fgwv064h8ja05bl308931jlxr9fpgc"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr GenomicRanges ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer statmod stringr tibble tidyr]; }; - qcmetrics = derive2 { name="qcmetrics"; version="1.20.1"; sha256="0v09i2njk3l1am3vgmhn48hii7h4kzwdqz6hyb1ix8n9zc423rzs"; depends=[Biobase knitr Nozzle_R1 pander S4Vectors xtable]; }; - qpcrNorm = derive2 { name="qpcrNorm"; version="1.40.0"; sha256="0m67a0b3i5nmd2lxx9ga0p6223y9x0bpz2j8gvqzsjnkh4ix1z0g"; depends=[affy Biobase limma]; }; - qpgraph = derive2 { name="qpgraph"; version="2.16.0"; sha256="110krd6sf87qai60qf9ixgkc43i51xvfiqnzdmwk1na2qhda2sp8"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; - qrqc = derive2 { name="qrqc"; version="1.36.0"; sha256="1pdadzlfx5kbsyp79iqxdliilsnhvx1d9j4dj89pl8hgz4n1zyvz"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rsamtools testthat xtable]; }; - qsea = derive2 { name="qsea"; version="1.8.0"; sha256="0m6h75fvzg7chi2sasaqrddxgl27qymxim7j7j3wg0gizhm2w59l"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; }; - quantro = derive2 { name="quantro"; version="1.16.0"; sha256="1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib"; depends=[Biobase doParallel foreach ggplot2 iterators minfi RColorBrewer]; }; - quantsmooth = derive2 { name="quantsmooth"; version="1.48.0"; sha256="0s7dwf4xkj6ab12ra0ibkn9myif174s476s8nkaz8x8a8yxlzmjn"; depends=[quantreg]; }; - qusage = derive2 { name="qusage"; version="2.16.1"; sha256="1jdslydj6nrwbysmjdp96iga93f5z56m2ilqgwwpcizzhlid25i3"; depends=[Biobase limma lsmeans nlme]; }; - qvalue = derive2 { name="qvalue"; version="2.14.1"; sha256="0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"; depends=[ggplot2 reshape2]; }; - r3Cseq = derive2 { name="r3Cseq"; version="1.28.0"; sha256="00gx50wlnq3dxybsj8fiwb0qmlyk9f9fddya7wckgs4yjb0y9lv4"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges IRanges qvalue RColorBrewer Rsamtools rtracklayer sqldf VGAM]; }; - rBiopaxParser = derive2 { name="rBiopaxParser"; version="2.22.0"; sha256="1zy72y9wiskwr4nymka3p9cw0zbgg0883422ysiijqkywz5cvawn"; depends=[data_table XML]; }; - rCGH = derive2 { name="rCGH"; version="1.12.0"; sha256="0ydd8685ly3kgvry09d0dc8lm6zl9355361bi7y6ra2v7sz4rvbj"; depends=[aCGH affy AnnotationDbi DNAcopy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges lattice limma mclust org_Hs_eg_db plyr shiny TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; - rDGIdb = derive2 { name="rDGIdb"; version="1.8.0"; sha256="0rwgcra484hpbch4pxnqa7x0vw5kzabilr308w1f4vdi6ydrz3gk"; depends=[httr jsonlite]; }; - rGADEM = derive2 { name="rGADEM"; version="2.30.0"; sha256="1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"; depends=[Biostrings BSgenome IRanges seqLogo]; }; - rGREAT = derive2 { name="rGREAT"; version="1.14.0"; sha256="0fpi797byvplg73hinsnm07nqgknwb4cbcn0wdw3q178jmksb5j0"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; }; - rHVDM = derive2 { name="rHVDM"; version="1.48.0"; sha256="0mf74pi9p7kfl9c2hjkmvfzsdfq7sp6gpbxlinj3k3vlbavpkgyg"; depends=[affy Biobase minpack_lm R2HTML]; }; - rMAT = derive2 { name="rMAT"; version="3.32.0"; sha256="1305v5gsbwvy2z7r0gg4gq48xn9yxgbyk4jpjfxaqza49l5sf283"; depends=[affxparser Biobase BiocGenerics IRanges]; }; - rRDP = derive2 { name="rRDP"; version="1.16.1"; sha256="0wahgg5l640nyiznjx10gc6xds0bssw7cpapk844a7i9d7l8my2f"; depends=[Biostrings]; }; - rSFFreader = derive2 { name="rSFFreader"; version="0.30.0"; sha256="14x6xdhdavfrz3ylkys3dlzr8hwshc6v43lccvl4lfhc3jq8xhj5"; depends=[Biostrings IRanges S4Vectors ShortRead XVector]; }; - rTANDEM = derive2 { name="rTANDEM"; version="1.22.1"; sha256="1nfh0423jfzf44acqn3jlnl3561lkxwjxv6i7y3h5j4zi3309q2z"; depends=[data_table Rcpp XML]; }; - rTRM = derive2 { name="rTRM"; version="1.20.0"; sha256="1alz54x6vxsm7mhsasn1cviad0gbg3vlrzm3m5mf9rj61nlz6zgd"; depends=[AnnotationDbi DBI igraph RSQLite]; }; - rTRMui = derive2 { name="rTRMui"; version="1.20.0"; sha256="09rc2kvcpi7c0b0dmq07byrd5208szwm4nvisdr8xhnhcsxq8f51"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; }; - rWikiPathways = derive2 { name="rWikiPathways"; version="1.2.1"; sha256="090mf50r9r1xwvirxwr1p9cv410q8h5pawv9v5kbnmwqi2b6qvzd"; depends=[caTools httr RJSONIO XML]; }; - rain = derive2 { name="rain"; version="1.16.0"; sha256="02grbm9c8q34np24218myzv0zgkq4p37mynpkm6c6xncywijgcsi"; depends=[gmp multtest]; }; - rama = derive2 { name="rama"; version="1.56.0"; sha256="0ns6dczyj8zglrfni1i0sfiqhpcii5h6hdv8yjg0hkm29g2qjzd0"; depends=[]; }; - ramwas = derive2 { name="ramwas"; version="1.6.0"; sha256="19iqh994x28mninyfay6rkjib947w9wjhsz1ac528w9paqjyk0ha"; depends=[BiocGenerics biomaRt Biostrings digest filematrix GenomicAlignments glmnet KernSmooth Rsamtools]; }; - randPack = derive2 { name="randPack"; version="1.28.0"; sha256="03vi35c3mglpiqrkzgnspgxj42bz952ms9bq0cvy5sp6lh9f6l3l"; depends=[Biobase]; }; - rbsurv = derive2 { name="rbsurv"; version="2.40.0"; sha256="08sd8i68zgbbd8anh828yjdl9j19l7m66wdrpqsmgns4n2gwpg80"; depends=[Biobase survival]; }; - rcellminer = derive2 { name="rcellminer"; version="2.4.0"; sha256="1r627fhzzjvjzdj8y0cxr65csj023c1jwl04jnj2i3g2g4pzcicl"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; }; - readat = derive2 { name="readat"; version="1.8.0"; sha256="0sg4dccxkyl7arlfhd0qmq1kx5f1sykvi822ssh0brp8yjj1hx53"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx reshape2 stringi SummarizedExperiment testthat tidyr]; }; - reb = derive2 { name="reb"; version="1.60.0"; sha256="1a62sfl0hw9nqw25b7hv76m9bn5l56d0sin1ii9s4qa2hj67nwxy"; depends=[Biobase idiogram]; }; - recount = derive2 { name="recount"; version="1.8.2"; sha256="0cnvbbpgijx30p7ma2gi508nvi8w7cli29p9af6lvn3q395fs9ya"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; }; - recoup = derive2 { name="recoup"; version="1.10.1"; sha256="0s4lhxffaai3l0rs4h62zcn0y5kxnmqxvcdnin726q3sc75b7h7l"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; }; - regionReport = derive2 { name="regionReport"; version="1.16.1"; sha256="1c4yf6nda4i9h4mapskfnxrrzgv5ic8bkbwyssd650vx840agj99"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; }; - regioneR = derive2 { name="regioneR"; version="1.14.0"; sha256="19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; - regsplice = derive2 { name="regsplice"; version="1.8.1"; sha256="1b5byldkilqshrhdqzgryjasz0m7545x4pa7vy1gk8h91amk52g8"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; }; - restfulSE = derive2 { name="restfulSE"; version="1.4.1"; sha256="00l2j1plx5bfjici3zp3v7yl8dzhdrkjpqi3wbf39y1l816wmpxx"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; }; - rexposome = derive2 { name="rexposome"; version="1.4.0"; sha256="1i0c97lfl18s647l36y0wpjd516viysfcybyp6fpkn8j04v7zxg6"; depends=[Biobase circlize corrplot FactoMineR ggplot2 ggrepel glmnet gplots gridExtra gtools Hmisc imputeLCMD lme4 lsr mice pryr reshape2 S4Vectors scales scatterplot3d stringr]; }; - rfPred = derive2 { name="rfPred"; version="1.20.0"; sha256="07fw3y7jsk6yzqsq521r2d7mckyn7b167y9sc9r6zqsixj9g3fa1"; depends=[data_table GenomicRanges IRanges Rsamtools]; }; - rgsepd = derive2 { name="rgsepd"; version="1.14.1"; sha256="1my5mhja9qvxl1kwxynf77vawgnk4hmnl4hdrry3x325hpyd2sir"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots hash org_Hs_eg_db SummarizedExperiment]; }; - rhdf5 = derive2 { name="rhdf5"; version="2.26.2"; sha256="10zkw3k13wmvyif417gplyf6rwp2gpkjasw97lhwv2f9i32rry9l"; depends=[Rhdf5lib]; }; - rhdf5client = derive2 { name="rhdf5client"; version="1.4.1"; sha256="1pbdwrzwa7r65wkcw821khnvcjy1rbx4vm8rln5srkra5zgmjjhx"; depends=[DelayedArray httr R6 rjson S4Vectors]; }; - riboSeqR = derive2 { name="riboSeqR"; version="1.16.0"; sha256="1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; }; - rnaSeqMap = derive2 { name="rnaSeqMap"; version="2.40.1"; sha256="13fa822z9mmidq30b4ar7xqj7qjkkdp6ih8j0rn6hc5gjhsqy6sh"; depends=[Biobase DBI DESeq edgeR GenomicAlignments GenomicRanges IRanges Rsamtools]; }; - rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.12.0"; sha256="0n4jpd9aqbc14wsi8k1vqhdaz7gp6nn7qr3nk3s783q293rjq1m1"; depends=[RColorBrewer]; }; - roar = derive2 { name="roar"; version="1.18.0"; sha256="15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; }; - rols = derive2 { name="rols"; version="2.10.1"; sha256="02cqiwbrxrhdc3pbq8vr1aasbark51gyf6y7i5z6lxng20sx2l1b"; depends=[Biobase BiocGenerics httr jsonlite progress]; }; - ropls = derive2 { name="ropls"; version="1.14.1"; sha256="1g1r96qmc4j1ynsscglfznm51598m95aiwc2qcawv50g02byzsbv"; depends=[Biobase]; }; - rpx = derive2 { name="rpx"; version="1.18.1"; sha256="14w96lwrx0h1v7pijva2gxwwxsb2lq4cnjaf26wx6wbjw28cni1l"; depends=[RCurl xml2]; }; - rqt = derive2 { name="rqt"; version="1.8.0"; sha256="08kics4hq4y23ydilafylm2rmbnh88hj02rrd5bbl5685as724vn"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; - rqubic = derive2 { name="rqubic"; version="1.28.0"; sha256="0va7263mxij13qyjmqrv9hxbgxig17hjw1617v0gzrcprs978735"; depends=[biclust Biobase BiocGenerics]; }; - rsbml = derive2 { name="rsbml"; version="2.40.0"; sha256="04brk985cdf6psr8ixkqahg9nmb7lrv1jfy0j1c84l2znskya77f"; depends=[BiocGenerics graph]; }; - rtracklayer = derive2 { name="rtracklayer"; version="1.42.2"; sha256="1c76g6h9lx2nm7dvb2zp9dmrpk3vanx3zaz6q9clggpj7yj5lmjd"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; }; - runibic = derive2 { name="runibic"; version="1.4.0"; sha256="1s1zbcbfxbchrh8h9602n5gh8ji8zqll9kfd4wg3w3668ckv7vx3"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; - sRAP = derive2 { name="sRAP"; version="1.22.0"; sha256="0qgskdizjh8z15qx4lvrdy5rg7h20hdg454n2wqvpmrk6wvp0ylp"; depends=[gplots pls qvalue ROCR WriteXLS]; }; - sSeq = derive2 { name="sSeq"; version="1.20.1"; sha256="08f59qg96qkndrlkdyk3i495i00gcx5kj1jcdy6zqkm9j7km88y2"; depends=[caTools RColorBrewer]; }; - safe = derive2 { name="safe"; version="3.22.0"; sha256="0is94jnljq0lsqiyvy91bzkv7xig35q97cjwziszxr9gacizyqay"; depends=[AnnotationDbi Biobase SparseM]; }; - sagenhaft = derive2 { name="sagenhaft"; version="1.52.0"; sha256="0rx7vkm19m18wvyawypp20m1ib7wi8yrmrpj1fg0f15yf9nfiwjg"; depends=[SparseM]; }; - samExploreR = derive2 { name="samExploreR"; version="1.6.1"; sha256="0qgqjd0s4j722z621gi6nggg1m2a123k1rmmxrad01hpwya5magd"; depends=[edgeR ggplot2 RNAseqData_HNRNPC_bam_chr14 Rsubread]; }; - sampleClassifier = derive2 { name="sampleClassifier"; version="1.6.1"; sha256="07aj8rmyvckxngy8y54qqzb85jn6k76l63n0jmdy2c50cizw53l5"; depends=[annotate e1071 ggplot2 MGFM MGFR]; }; - sangerseqR = derive2 { name="sangerseqR"; version="1.18.0"; sha256="1dw3s011w0pir3i9zz3b62qx4frwkw541k569w1qhl0z66qidmgz"; depends=[Biostrings shiny]; }; - sapFinder = derive2 { name="sapFinder"; version="1.20.1"; sha256="1yg99gibx8nc8r873y26cbcm5bjh008rhszxykpdbbgl8xfsclv3"; depends=[pheatmap Rcpp rTANDEM]; }; - savR = derive2 { name="savR"; version="1.20.0"; sha256="13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"; depends=[ggplot2 gridExtra reshape2 scales XML]; }; - scDD = derive2 { name="scDD"; version="1.6.1"; sha256="0dp2awajd5281dwpbs0wb8ij2pq9l60p0b80xhxrb41m5qybcri8"; depends=[arm BiocParallel EBSeq fields ggplot2 mclust outliers S4Vectors scran SingleCellExperiment SummarizedExperiment]; }; - scFeatureFilter = derive2 { name="scFeatureFilter"; version="1.2.1"; sha256="04bk4kzs42mi022qr8whngkqxapngnvpxifd0m60r57skz3v6yqa"; depends=[dplyr ggplot2 magrittr rlang tibble]; }; - scPipe = derive2 { name="scPipe"; version="1.4.1"; sha256="1kl1ik1wd3cq7h2njzdnzs9r26qnim4r63c86pfbfymz23n4aqns"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase rtracklayer S4Vectors scales SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; }; - scater = derive2 { name="scater"; version="1.10.1"; sha256="0rijhy7g5qmcn927y1wyd63la1fhyar9fv1hccsqd23jd98yc55a"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dplyr ggbeeswarm ggplot2 Matrix plyr Rcpp reshape2 Rhdf5lib S4Vectors SingleCellExperiment SummarizedExperiment viridis]; }; - scde = derive2 { name="scde"; version="2.10.1"; sha256="1n1r08wqx1bds7lwz2bbksw5l084cmcbgs03jr8s2l92z43kqmm6"; depends=[BiocParallel Cairo edgeR extRemes flexmix MASS mgcv nnet pcaMethods quantreg RColorBrewer Rcpp RcppArmadillo rjson RMTstat Rook]; }; - scfind = derive2 { name="scfind"; version="1.4.1"; sha256="07lzjqxvdjjzli8ibqvlndgf9n1x477q1pniv91ynrh6jc8dz8cb"; depends=[bit dplyr hash Rcpp reshape2 SingleCellExperiment SummarizedExperiment]; }; - scmap = derive2 { name="scmap"; version="1.4.1"; sha256="1nil8kylf2px6nqjh4lg3fm2mw7j0isynvc6w0lycwj34rzjx3q4"; depends=[Biobase BiocGenerics dplyr e1071 ggplot2 googleVis matrixStats proxy randomForest Rcpp RcppArmadillo reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; }; - scmeth = derive2 { name="scmeth"; version="1.2.2"; sha256="19z26ld4fa22ry2pc8nrwx6042im1w4wpkfi9hmgp6bi92aa0vs5"; depends=[AnnotationHub annotatr Biostrings BSgenome bsseq DelayedArray DT GenomeInfoDb GenomicRanges HDF5Array knitr reshape2 rmarkdown SummarizedExperiment]; }; - scone = derive2 { name="scone"; version="1.6.1"; sha256="0l1x4cjnfjbpx6k55sjqx03555daa6v63rq0rg6b7jpz8xxzwa7p"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; }; - scoreInvHap = derive2 { name="scoreInvHap"; version="1.4.0"; sha256="03d7pny3qkcs279869yry8rkw7js3xyrc8b7p4i7hlpzd44x25a3"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; }; - scran = derive2 { name="scran"; version="1.10.2"; sha256="07mgilr3gq3lnrm1fjm9zhz4w7970bjhsykln1drqy9gkzj5sn7g"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel DelayedArray DelayedMatrixStats dynamicTreeCut edgeR igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; }; - scruff = derive2 { name="scruff"; version="1.0.3"; sha256="0ckqlmdclpfbm4y32h9625wzh7g1bx6gx2n460m2kqig9r17cfkl"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools rtracklayer S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; }; - scsR = derive2 { name="scsR"; version="1.18.0"; sha256="11mf5kv8mk1nlfxd081a7dx1v60yf94cg46b5bjflidp3qhrsi9g"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; }; - segmentSeq = derive2 { name="segmentSeq"; version="2.16.0"; sha256="0pljd8hn2vxcsh22wmv53a7wkw3cdxpdv8q4ksfj5mvasa2mmkvi"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; }; - semisup = derive2 { name="semisup"; version="1.6.0"; sha256="0lizf5x3abv4g8j4jxmsbbdiqj4f4gybc3jvw7zz12bd3fsj3c1i"; depends=[SummarizedExperiment VGAM]; }; - seq2pathway = derive2 { name="seq2pathway"; version="1.14.0"; sha256="1zr6z9kgsvlcvb6fw2r39kx4jm3dxlyv7z5l9p0lkdykfnm313y8"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; }; - seqCAT = derive2 { name="seqCAT"; version="1.4.1"; sha256="1qn5l66qipclmcdnfy569px5wrji0mzmfgg2h6ngi94333649lxv"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges lazyeval S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; - seqCNA = derive2 { name="seqCNA"; version="1.28.0"; sha256="1qf76zslj54g6bxll5bi9kqkph1hb5b1b2yg9qr34ywiq4cw7i8i"; depends=[adehabitatLT doSNOW GLAD seqCNA_annot]; }; - seqLogo = derive2 { name="seqLogo"; version="1.48.0"; sha256="022vr9ydwcivs7rw7kwj73gfk5gc7ckwa1q66vhd4kw9ylh70v68"; depends=[]; }; - seqPattern = derive2 { name="seqPattern"; version="1.14.0"; sha256="0di83qi83mrlw7i12khsq55d03hlazcywaa9m9pki1sfhafpq733"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; }; - seqTools = derive2 { name="seqTools"; version="1.16.0"; sha256="0dcql2pmgpaa5vin1zzhx472qm90rw962pd3pw32ispn02yw0f2l"; depends=[zlibbioc]; }; - seqbias = derive2 { name="seqbias"; version="1.30.0"; sha256="0jwlwqa1z2scnaqkrz5hmmakrjaajf4dwd875s7pswvacygiy859"; depends=[Biostrings GenomicRanges Rsamtools zlibbioc]; }; - seqcombo = derive2 { name="seqcombo"; version="1.4.1"; sha256="0046www9rl5lswcjn6friijd5plj0p7bfg0y0qzqsz7gqpm3nj58"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr rvcheck]; }; - seqplots = derive2 { name="seqplots"; version="1.20.1"; sha256="0hp3x8gdw65wc73hc1rcxbaqypq2zd50axsvcviqfgdv2dcb2ph7"; depends=[BiocManager Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; }; - seqsetvis = derive2 { name="seqsetvis"; version="1.2.1"; sha256="0x5410b3qwqn34lzs1x75ldlv6xmvdbjyxg8ja0gyg4hz5bc4vaj"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; }; - sesame = derive2 { name="sesame"; version="1.0.0"; sha256="01qxdnpkilxv18fpl3rizxri2l7crs62z8nd7ywhxfm6g4ch5l1z"; depends=[DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore R6 randomForest S4Vectors sesameData wheatmap]; }; - sevenC = derive2 { name="sevenC"; version="1.2.0"; sha256="1p2xkv0n8hl9s4dlg54wgry73vnnlzylwximhan2ymnp3hgbg4j0"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; }; - sevenbridges = derive2 { name="sevenbridges"; version="1.12.5"; sha256="15rvjlv7abcic06sbvhyy4ii6cccc06xiyk45qk638n279ixl7aa"; depends=[curl docopt dplyr httr jsonlite objectProperties S4Vectors stringr uuid yaml]; }; - shinyMethyl = derive2 { name="shinyMethyl"; version="1.18.0"; sha256="0dzg1idkdy4x9h3z5yashrb03ad8ncjxz5j05jlaxx6k4aa7z8j8"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; }; - shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.20.1"; sha256="0lz4jr96g20fbrd34f9km6rj08yb2y09gp7zxnm0inlpdkvb4dby"; depends=[mixtools rTANDEM shiny xtable]; }; - sigFeature = derive2 { name="sigFeature"; version="1.0.0"; sha256="0kjf4ss0baq4p7nn305szpvpdssagndxjmggdgfm6mfjsgfi5nj1"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; }; - sigPathway = derive2 { name="sigPathway"; version="1.50.0"; sha256="0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"; depends=[]; }; - sigaR = derive2 { name="sigaR"; version="1.30.0"; sha256="1vlmd6rqdhz9vzvjidxrq7k9vbbp1c82qspkmdxd9nkycyjjp5cg"; depends=[Biobase CGHbase corpcor igraph limma marray MASS mvtnorm penalized quadprog snowfall]; }; - siggenes = derive2 { name="siggenes"; version="1.56.0"; sha256="0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"; depends=[Biobase multtest]; }; - sights = derive2 { name="sights"; version="1.8.1"; sha256="14xch1qaqs4wcwgpys916r2ih3c150my1fqg9qr9qws9m1gbf7mn"; depends=[ggplot2 lattice MASS qvalue reshape2]; }; - signeR = derive2 { name="signeR"; version="1.8.0"; sha256="1qpaa8ag8lv9s7340fdk3k3qc2jyq4r8268rvxb038zdrv7nzvv4"; depends=[BiocGenerics Biostrings class GenomicRanges nloptr NMF PMCMR Rcpp RcppArmadillo VariantAnnotation]; }; - signet = derive2 { name="signet"; version="1.2.3"; sha256="1qzj0mn5jlijrnk9wi5mqq3xj4c8jmb5vjm7q4ww8wiqmzaq41mm"; depends=[graph igraph RBGL]; }; - sigsquared = derive2 { name="sigsquared"; version="1.14.0"; sha256="1y6h3z5mnww2f26hw4a09qiwpgij89bixf3ak5b253apkwd4bpi9"; depends=[Biobase survival]; }; - similaRpeak = derive2 { name="similaRpeak"; version="1.14.0"; sha256="0wf24nk2vibspqdkgw1a55xhnxs1ygshi548ms0lswkprrqcllg2"; depends=[R6]; }; - simpleaffy = derive2 { name="simpleaffy"; version="2.58.0"; sha256="0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s"; depends=[affy Biobase BiocGenerics gcrma genefilter]; }; - simulatorZ = derive2 { name="simulatorZ"; version="1.16.0"; sha256="19xjhrjwxlpygvv7xs752jsvdnqwzj742jkwzsz2nzwkixkw41hf"; depends=[Biobase BiocGenerics CoxBoost gbm GenomicRanges Hmisc SummarizedExperiment survival]; }; - sincell = derive2 { name="sincell"; version="1.14.1"; sha256="0id0m6pkx7myg32m5ydwjhmhw5ighlzpi2hksp23sb0ji02y7iyv"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; }; - singleCellTK = derive2 { name="singleCellTK"; version="1.2.3"; sha256="1n0gxrj7wshzxpqwsmsicrhdf4q45afywqdc59yy2fxm440s0w50"; depends=[AnnotationDbi ape Biobase circlize cluster colourpicker ComplexHeatmap data_table DelayedArray DESeq2 DT enrichR ggplot2 ggtree gridExtra GSVA GSVAdata limma MAST matrixStats multtest plotly RColorBrewer reshape2 Rtsne S4Vectors shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SummarizedExperiment sva]; }; - singscore = derive2 { name="singscore"; version="1.2.2"; sha256="0a32k23l26vjgag7vgv21n9vl8qjy6asrq7ms22wiw9lmg2qkyyc"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel ggsci GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape SummarizedExperiment tidyr]; }; - sizepower = derive2 { name="sizepower"; version="1.52.0"; sha256="082hfzw8348fra6fr1gli5cqjnrg3bgyx28ccy66jzxvrijm2qfl"; depends=[]; }; - skewr = derive2 { name="skewr"; version="1.14.0"; sha256="09132dwp8h3wdrf0agyc0vmby5z7c2hd3px4jrp9vgi2x1849mvn"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; }; - slalom = derive2 { name="slalom"; version="1.4.1"; sha256="0kb4y590cdph90k27av45jy889i3s1jarlhj57lyg8g14sr9sxq6"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; }; - slingshot = derive2 { name="slingshot"; version="1.0.0"; sha256="0nrqzsjwyk78cahw21x4i5lqac7h85k6nrq045nq4jmxyc977li3"; depends=[ape clusterExperiment igraph matrixStats princurve rgl SingleCellExperiment SummarizedExperiment]; }; - slinky = derive2 { name="slinky"; version="1.0.2"; sha256="1bjs41p3a7ggk6brj2hih84p4qi8qd398xzrh1r8lrdwjy1cm6yl"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; }; - snapCGH = derive2 { name="snapCGH"; version="1.52.0"; sha256="15fx1ryc6ab1aia768wpp8zhggfz2l9vildhkjh8chwaam1qd610"; depends=[aCGH cluster DNAcopy GLAD limma tilingArray]; }; - snm = derive2 { name="snm"; version="1.30.0"; sha256="1qjd7g6c03rygp95cpry1m3yi83lyd57zp94whaymfriz39dx2i9"; depends=[corpcor lme4]; }; - snpStats = derive2 { name="snpStats"; version="1.32.0"; sha256="1pplx4pf9bqi7v5v1l74yknc1s61carvbqkf327ky7vbvp0bck33"; depends=[BiocGenerics Matrix survival zlibbioc]; }; - soGGi = derive2 { name="soGGi"; version="1.14.0"; sha256="0v0hvxadqsmscb8h0zy8xi4336pxha2vj5xk03ms81734jaj6adj"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.6.1"; sha256="1znhv5j4dijwiq5rdslvgrmzdh0cbc6mnx41a5njx9zkfgrfkw6j"; depends=[MASS MCMCpack optparse tmvtnorm]; }; - sparsenetgls = derive2 { name="sparsenetgls"; version="1.0.1"; sha256="01apq9p2hqivc0va5rpl3k90ipgr1i9a228r6b8wygxxy62dqphw"; depends=[glmnet huge MASS Matrix parcor]; }; - specL = derive2 { name="specL"; version="1.16.1"; sha256="12g6hp2x89ydv1ip88dmn48wgawhrpn39sfyrf59pw638gy4g4fl"; depends=[DBI protViz RSQLite seqinr]; }; - spikeLI = derive2 { name="spikeLI"; version="2.42.0"; sha256="055zbrbh6wf3vvnc9p8px2ffz9wdhdg0h96260r7c72ax3v6wi5g"; depends=[]; }; - spkTools = derive2 { name="spkTools"; version="1.38.0"; sha256="0rm2vlzid3wjm1g1kzmjklga1gcf852aznhxb1xr50v8drivkkz9"; depends=[Biobase gtools RColorBrewer]; }; - splatter = derive2 { name="splatter"; version="1.6.1"; sha256="1kw9shzqwph44q2fksgp79mrjq23j3806clc4xydw3ys2w4kspj8"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; }; - spliceSites = derive2 { name="spliceSites"; version="1.30.0"; sha256="1j40awy9irx53d1cdsx52pnxirjrrvgsj9zx5qhl2556ca65l26n"; depends=[Biobase BiocGenerics Biostrings doBy IRanges seqLogo]; }; - splicegear = derive2 { name="splicegear"; version="1.54.0"; sha256="0phpkgjkc4c8lfr8xsciqyz7imsjpc3sxwsh95glxhrsm7i2mnip"; depends=[annotate Biobase XML]; }; - splineTimeR = derive2 { name="splineTimeR"; version="1.10.0"; sha256="15dzhijkhpy7d8hwif59bic83fk6fnyjpp4qi7y7vwq139j6yaj2"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; }; - splots = derive2 { name="splots"; version="1.48.0"; sha256="0s10ha17p4yf6id0h0r0a2fk992jp4ah7v8ani689zy6pcc0w34d"; depends=[RColorBrewer]; }; - spotSegmentation = derive2 { name="spotSegmentation"; version="1.56.0"; sha256="06b4dwjll21i13ag5f2si5499gc6h63b5rnlz372pg95idwxsqbh"; depends=[mclust]; }; - srnadiff = derive2 { name="srnadiff"; version="1.2.1"; sha256="1cm2xjj0wd6ll45aa1gq4lzg49sr4v3zni3x0mgma6pkj2prcbwf"; depends=[BiocParallel BiocStyle DESeq2 devtools GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - sscore = derive2 { name="sscore"; version="1.54.0"; sha256="0anpfqvv6as5i28bb0i2h86p51m42ch4gzap5lcxia97lzvxh210"; depends=[affy affyio]; }; - sscu = derive2 { name="sscu"; version="2.12.0"; sha256="0y41krw0r0kmlp32b7cmlwf5qpncha8j357mx9sr3zvm52dphlpp"; depends=[BiocGenerics Biostrings seqinr]; }; - ssize = derive2 { name="ssize"; version="1.56.0"; sha256="13bc5hbnqqxr16pqw0waq29mpgrf4sys4kg63np2a4hpc6l2nrqk"; depends=[gdata xtable]; }; - ssviz = derive2 { name="ssviz"; version="1.16.1"; sha256="01wq3y9xf4g5d2df6j2cckwk9rm1y6ya39g33c0m13jk3xrxvcwi"; depends=[Biostrings ggplot2 RColorBrewer reshape Rsamtools]; }; - staRank = derive2 { name="staRank"; version="1.24.1"; sha256="08pac19nsyb8cfwbsc31m8daiig8p1px4y4rjc00ypvari2hnl2c"; depends=[cellHTS2]; }; - stageR = derive2 { name="stageR"; version="1.4.0"; sha256="063mprdjjvys09cxlgrd930r96i470z30h00pf0h15g5h4w02jak"; depends=[SummarizedExperiment]; }; - statTarget = derive2 { name="statTarget"; version="1.12.1"; sha256="19b8b00kcd6p9b7g4n3jaf8z80fz6y5d7bil8m8bj7ldr2l8dqr0"; depends=[impute pdist pls plyr randomForest ROC rrcov]; }; - stepNorm = derive2 { name="stepNorm"; version="1.54.0"; sha256="16sn793zj06dh69cwzx3vfjkx4gs3dy6x0apyh01vwhnqkani4vl"; depends=[marray MASS]; }; - strandCheckR = derive2 { name="strandCheckR"; version="1.0.0"; sha256="0pmw6iwynpy6mdfh8mb939100715mpwy458i6w6sw1pjghlykrzq"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; - subSeq = derive2 { name="subSeq"; version="1.12.1"; sha256="151fa343n1w7mbrhqcf2f2bhh0s8km0a8lcx534avi1mnp539ql9"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; - supraHex = derive2 { name="supraHex"; version="1.20.0"; sha256="0p27h8xg104ip8lwasvac74hjj9582xc85q06q0n8lr660chfx2b"; depends=[ape hexbin MASS]; }; - survcomp = derive2 { name="survcomp"; version="1.32.0"; sha256="1f6vz8fbifa5lsywxcqdak5gb7fvz6rvds5a7bvdginjy1zindw9"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; - sva = derive2 { name="sva"; version="3.30.1"; sha256="0czja4c5jxa0g3fspi90nyajqmvzb29my4ykv2wi66h43f5dlwhq"; depends=[BiocParallel genefilter limma matrixStats mgcv]; }; - swfdr = derive2 { name="swfdr"; version="1.8.0"; sha256="0hib9mb1yrfl3hqddkqws32ninyc8ylzw8gd4a0sv06l16ks8b4m"; depends=[dplyr ggplot2 reshape2]; }; - switchBox = derive2 { name="switchBox"; version="1.18.0"; sha256="1s49vi0vyh0bmrc6marn69hi9ln12j3kyjkkm2z5fpvv3rvxhgw7"; depends=[gplots pROC]; }; - switchde = derive2 { name="switchde"; version="1.8.1"; sha256="1ydc9h62iyfz0786c5zhz3189p2f7sf3z6fjlvqwjqxva5j0f12b"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; }; - synapter = derive2 { name="synapter"; version="2.6.1"; sha256="19rf8kkqf070ldhnrdi3xl23j2slv4qadw9cx8wvc4p994f2abj9"; depends=[Biobase Biostrings cleaver knitr lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; }; - synergyfinder = derive2 { name="synergyfinder"; version="1.8.0"; sha256="1idc0lnjw8zx6nih1hrzfq9h40zkbdv0iv9si214wx4ynf0w18iv"; depends=[drc ggplot2 gplots gridBase lattice nleqslv reshape2 SpatialExtremes]; }; - synlet = derive2 { name="synlet"; version="1.12.1"; sha256="13rghqqbkxni121ds0slf6cnj2g5zbm3sbbcli95z7mxy2wn3syg"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; }; - systemPipeR = derive2 { name="systemPipeR"; version="1.16.1"; sha256="0qzydz87rld2nhwzbfgrw5jfgh8maa9y54mjx9c4285m11qj2shq"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; }; - tRNA = derive2 { name="tRNA"; version="1.0.0"; sha256="1kzl79q0zim9y7px0dirk41qay96nl2bz8sw76nx56pr1d5jh245"; depends=[assertive BiocGenerics Biostrings GenomicRanges ggplot2 IRanges S4Vectors scales stringr XVector]; }; - tRNAdbImport = derive2 { name="tRNAdbImport"; version="1.0.0"; sha256="0b6h2xzxyl3kh1h8fijm5l0cqy7364p5l0s604fvhnaxa6n3y1ds"; depends=[assertive Biostrings GenomicRanges httr IRanges S4Vectors stringr tRNA xml2]; }; - tRNAscanImport = derive2 { name="tRNAscanImport"; version="1.2.0"; sha256="1pcnwlxbw2g4398y4q94m6z7xsl492hik4z57xgjcri35y3ma06x"; depends=[assertive BiocGenerics Biostrings GenomeInfoDb GenomicRanges rtracklayer S4Vectors stringr tRNA]; }; - tRanslatome = derive2 { name="tRanslatome"; version="1.20.0"; sha256="0aa2gd1mp5lzp62vl0556i7q761jyi02ls04nw175fbq6381l2vy"; depends=[anota Biobase DESeq edgeR GOSemSim gplots Heatplus limma org_Hs_eg_db plotrix RankProd sigPathway topGO]; }; - tenXplore = derive2 { name="tenXplore"; version="1.4.1"; sha256="18bg0wc7y8lafi38mq83qqhrd03wyyk856fa2axinixgn2qid3pq"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; }; - ternarynet = derive2 { name="ternarynet"; version="1.26.0"; sha256="0xar386wy1viks44s2gyiakmvy5d1k2qc422zn74nc0wwgky0jmc"; depends=[igraph]; }; - tigre = derive2 { name="tigre"; version="1.36.0"; sha256="1hyl4d1111bs6bgjpy3dwkfj9yi11r07hwsf2jn4iqcmr9l6g0rz"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; }; - tilingArray = derive2 { name="tilingArray"; version="1.60.0"; sha256="0ak32w49adrrh6xaf20g48xnsxr33d3irng3lbv03y2al812wpha"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; }; - timecourse = derive2 { name="timecourse"; version="1.54.0"; sha256="1cpmcbjwsh2mn4c0bgpvcq5da4cngsznfvz7r6cpma7iivqam1jz"; depends=[Biobase limma marray MASS]; }; - timescape = derive2 { name="timescape"; version="1.6.0"; sha256="0wnk4iwy8ji4xn1cyh257byxfvh5njd9z08hl5f74k1ni94llkp6"; depends=[dplyr gtools htmlwidgets jsonlite stringr]; }; - tkWidgets = derive2 { name="tkWidgets"; version="1.60.0"; sha256="17z04pqys4nhs0c6phffkwj2yw34cajpfbgx70jsd0dba125pzh7"; depends=[DynDoc widgetTools]; }; - tofsims = derive2 { name="tofsims"; version="1.10.1"; sha256="0wgpl4az21zbixjl3ngwpxq81i86yhd41lhhnphrvrwnl7n7gk8x"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; }; - topGO = derive2 { name="topGO"; version="2.34.0"; sha256="1j1jcd16j564kr6qz28140fzmnh9xasi84v1c1fi98sqv30zq9bh"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; }; - topdownr = derive2 { name="topdownr"; version="1.4.1"; sha256="19v8m0lr1y69x1b3k01vlimfi6nzqgjg83ifc7xvzzqfsl45z09w"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR ProtGenerics S4Vectors]; }; - trackViewer = derive2 { name="trackViewer"; version="1.18.3"; sha256="1i64px5f3iymaz933998b63wf6flal7cbr36v3i7w5xr9p2fnp04"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; }; - tracktables = derive2 { name="tracktables"; version="1.16.0"; sha256="160zh73yripvd150jfwm1xpk1amrg1qqjcyl8wwclpss0ks04ayb"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; }; - transcriptR = derive2 { name="transcriptR"; version="1.10.1"; sha256="17m1i36jj7fdh4qqd29zia68q7yjhxgh47xndcbgbik78pfnnig7"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; }; - transcriptogramer = derive2 { name="transcriptogramer"; version="1.4.1"; sha256="1qd447glnwk3ysxnfjyn5i2smyq79mn6qgsa0klrgr3v1909ib57"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; }; - transite = derive2 { name="transite"; version="1.0.2"; sha256="1xrkk7n6zgch24q1hx4fxj2z8ii5pfpakjmf5696v1w1d153415m"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; }; - traseR = derive2 { name="traseR"; version="1.12.0"; sha256="1bf2cblagqkwsc66l9820kb7yh05bk62k0rplnqznnl36i5fw428"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; }; - treeio = derive2 { name="treeio"; version="1.6.2"; sha256="0fvyj3m8yzq94cs2nhmmq6qvf7qqccxan2qkq764a9qlfrrpwa2c"; depends=[ape dplyr jsonlite magrittr rlang rvcheck tibble tidytree]; }; - trena = derive2 { name="trena"; version="1.4.2"; sha256="1rrbkjizc4glp4ql30wn6ijmym4vxl3xda3ffy02maab1vg07mjp"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMariaDB RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr]; }; - triform = derive2 { name="triform"; version="1.24.0"; sha256="12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"; depends=[BiocGenerics IRanges yaml]; }; - trigger = derive2 { name="trigger"; version="1.28.0"; sha256="0wi8lk1ld21h1i0i31c858a0sgisg4ak11kyxjmsh9lyhfzayvwq"; depends=[corpcor qtl qvalue sva]; }; - trio = derive2 { name="trio"; version="3.20.0"; sha256="0fz74p4xj19mp2bbrlcrn2gr0yg7hhk0d1a2dy2k2shg7vwr15lj"; depends=[]; }; - triplex = derive2 { name="triplex"; version="1.22.0"; sha256="1fh7446v07bdhj7babj3gjq4n4zk1y7r37fs30r2cgc9lhqyccr9"; depends=[Biostrings GenomicRanges IRanges S4Vectors XVector]; }; - tspair = derive2 { name="tspair"; version="1.40.0"; sha256="1anz7by0hg51ywk9q49xjaqm8agiqdwd6rnf1mp6axph1wjfhkjm"; depends=[Biobase]; }; - tweeDEseq = derive2 { name="tweeDEseq"; version="1.28.1"; sha256="0imnscn9yf79jciq7zdzasdf777cq4sqvhnhvsy6y69vzmhi5952"; depends=[cqn edgeR limma MASS]; }; - twilight = derive2 { name="twilight"; version="1.58.0"; sha256="16vj02kxlfii0r8cdvbd4q6yqm54znn2i0697dmdfmrqbvn9rjky"; depends=[Biobase]; }; - twoddpcr = derive2 { name="twoddpcr"; version="1.6.0"; sha256="1j4xb6y2hnrvaspv7lpirx62801rq0y0gkqdgy87qkphqsf4n44z"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; - tximeta = derive2 { name="tximeta"; version="1.0.3"; sha256="10fxda9hn1nfz93mni0fv2snpqkr48x73ffjkd5hv4bwqv26cma8"; depends=[AnnotationDbi BiocFileCache ensembldb GenomeInfoDb GenomicFeatures jsonlite rappdirs S4Vectors SummarizedExperiment tibble tximport]; }; - tximport = derive2 { name="tximport"; version="1.10.1"; sha256="16wp09dm0cpb4mc00nmglfb8ica7qb4a55vm8ajgzyagbpfdd44l"; depends=[]; }; - uSORT = derive2 { name="uSORT"; version="1.8.1"; sha256="1z6vlcgs83pc7388c6jwpm9dgv9rr95gsksqy5gaiyy0pa0bga8j"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; - unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.18.0"; sha256="110kb1g1kkfgk3nw099wyaww8l2jk3kk41bsz3gmbb2jni9v0ykx"; depends=[BiocGenerics HTqPCR]; }; - universalmotif = derive2 { name="universalmotif"; version="1.0.22"; sha256="016r859xn2306zsckg0xpwv3ssngngw7drc27h7jhikmf5wkvbv1"; depends=[ape BiocGenerics Biostrings ggplot2 ggseqlogo ggtree gtools processx Rcpp Rdpack]; }; - variancePartition = derive2 { name="variancePartition"; version="1.12.3"; sha256="1ssb41g22440xcv05c3ggfzawjkl3mp74b58spjg5wcwp1rx3xyi"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest progress reshape2 scales]; }; - vbmp = derive2 { name="vbmp"; version="1.50.0"; sha256="08iyryhmahmm1p93c0kgvknf9gkd7i4l4jd3b9a234vwx5xy0zx2"; depends=[]; }; - vidger = derive2 { name="vidger"; version="1.2.1"; sha256="1gz2v4zg6ry06msmxrr3f47i4gc2sfijrbkd0l5x7crp8a2mkcm3"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; }; - viper = derive2 { name="viper"; version="1.16.0"; sha256="0pi9s37xw03pkqmsyqnigzfjmq9llk0gwh92ply07mbppldssrwc"; depends=[Biobase e1071 KernSmooth mixtools]; }; - vsn = derive2 { name="vsn"; version="3.50.0"; sha256="1g6qkpykw99jm2wv2i61dg2ffwk0n8fm4s5pm2q4c024vw5c9b69"; depends=[affy Biobase ggplot2 lattice limma]; }; - vtpnet = derive2 { name="vtpnet"; version="0.22.0"; sha256="03f96286lvhy7wlpi39awf5fjx1b40jzjp5mslfgpwx9gvk0kzdw"; depends=[doParallel foreach GenomicRanges graph gwascat]; }; - vulcan = derive2 { name="vulcan"; version="1.4.0"; sha256="0w9cmfn7m2yn98jrgf1ixkchd2jmfinpbxhcycdfmq2yihla3l3v"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; }; - wateRmelon = derive2 { name="wateRmelon"; version="1.26.0"; sha256="0ymchg3nk89dm92hqksq7cmvwr2a7fxr7z4ymfigj6ifw2r4575s"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; }; - wavClusteR = derive2 { name="wavClusteR"; version="2.16.1"; sha256="1lxi7yn2l9gifqx08mkfc7mswb1lvca5di48g5w6pghf1jdp0rkp"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; }; - waveTiling = derive2 { name="waveTiling"; version="1.24.0"; sha256="023d329nk0w7wm8zplhqw7qwc8jwlscxkf8kbafjljrzpzwvh8an"; depends=[affy Biobase Biostrings GenomeGraphs GenomicRanges IRanges oligo oligoClasses preprocessCore waveslim]; }; - weaver = derive2 { name="weaver"; version="1.48.0"; sha256="1hys2gjr353lb798anamfg6mhv8hadh90qs9sc99zi96ps6c24hf"; depends=[codetools digest]; }; - webbioc = derive2 { name="webbioc"; version="1.54.0"; sha256="16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"; depends=[affy annaffy Biobase BiocManager gcrma multtest qvalue vsn]; }; - widgetTools = derive2 { name="widgetTools"; version="1.60.0"; sha256="0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"; depends=[]; }; - wiggleplotr = derive2 { name="wiggleplotr"; version="1.6.1"; sha256="12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; }; - xcms = derive2 { name="xcms"; version="3.4.4"; sha256="073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; }; - xmapbridge = derive2 { name="xmapbridge"; version="1.40.0"; sha256="1a93vxrv9brfwv64wpiriwak1chlz6rg25dhcb9hyk2b8j8ky3ag"; depends=[]; }; - xps = derive2 { name="xps"; version="1.42.0"; sha256="0x391j5rlihp64k5wslghlrw6vi4xwwjphskvl1k3iffda5yqknb"; depends=[]; }; - yamss = derive2 { name="yamss"; version="1.8.1"; sha256="13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; }; - yaqcaffy = derive2 { name="yaqcaffy"; version="1.42.0"; sha256="192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"; depends=[simpleaffy]; }; - yarn = derive2 { name="yarn"; version="1.8.1"; sha256="0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; }; - zFPKM = derive2 { name="zFPKM"; version="1.4.1"; sha256="0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; }; - zinbwave = derive2 { name="zinbwave"; version="1.4.2"; sha256="1gsh4wgbdb021hqscm8j4mln55xxwrnqkmnllxn3vvbyf4c6zb08"; depends=[BiocParallel copula edgeR genefilter glmnet Matrix SingleCellExperiment softImpute SummarizedExperiment]; }; - zlibbioc = derive2 { name="zlibbioc"; version="1.28.0"; sha256="0bjvzy24kab7ank02cc1qk2ikcz4dllgf66wpsdl0d3zp4gn3l2h"; depends=[]; }; + ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.16.0"; sha256="128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; }; + ABSSeq = derive2 { name="ABSSeq"; version="1.40.0"; sha256="12w2mcx3ammwc4ryqy3zhlw0jn4lfii5b7ll265wvlcs8g4r4yv7"; depends=[limma locfit]; }; + ABarray = derive2 { name="ABarray"; version="1.54.0"; sha256="0i84vyykvs2fgsqpzhybg5hgy7df7ic4l1fkbcfzzdwvnscwws98"; depends=[Biobase multtest]; }; + ACE = derive2 { name="ACE"; version="1.4.0"; sha256="1wvfl7qv1mifx6l72zfc47wsg8vgqpwqprm4hrbmwi0k6d77iivd"; depends=[Biobase GenomicRanges ggplot2 QDNAseq]; }; + ACME = derive2 { name="ACME"; version="2.42.0"; sha256="1bh2c216f5l5w0jv6axm73rc8dsi1kgwr9lk69xdxr2y54bgdqz3"; depends=[Biobase BiocGenerics]; }; + ADAM = derive2 { name="ADAM"; version="1.2.0"; sha256="0rq17wzy42g305zm50c40spl1lvyma4xn932nkcikwfd9b6mdmc6"; depends=[dplyr DT GO_db KEGGREST knitr pbapply Rcpp stringr SummarizedExperiment]; }; + ADAMgui = derive2 { name="ADAMgui"; version="1.2.0"; sha256="1i1dqxz742gknmsy8xxisjfbxxhhp61fjsdcb11sd11giacm2s8j"; depends=[ADAM colorRamps data_table dplyr DT ggplot2 ggpubr ggrepel ggsignif GO_db gridExtra knitr RColorBrewer reshape2 shiny shinyjs stringi stringr testthat varhandle]; }; + ADaCGH2 = derive2 { name="ADaCGH2"; version="2.26.0"; sha256="0q17mn205ymrnijsy2ygkjqzk9qll7vps6mya37p3154g4km4l7d"; depends=[aCGH bit cluster DNAcopy ff ffbase GLAD snapCGH tilingArray waveslim]; }; + AGDEX = derive2 { name="AGDEX"; version="1.34.0"; sha256="0c5nxgbq0vc11jml9qlmdmyxpf3irwbffavgm72bpb6q3q9gmkvr"; depends=[Biobase GSEABase]; }; + AIMS = derive2 { name="AIMS"; version="1.18.0"; sha256="0lqgm9sm310nj3lw8n6xnmnfqsvdq3lrbzz8jbwqppj801z9viav"; depends=[Biobase e1071]; }; + ALDEx2 = derive2 { name="ALDEx2"; version="1.18.0"; sha256="04a5lrvpbp4ygjidapxvfhdc8psd4h6zdv7kwxpg6q4awsa0ni6r"; depends=[BiocParallel GenomicRanges IRanges multtest S4Vectors SummarizedExperiment]; }; + ALPS = derive2 { name="ALPS"; version="1.0.0"; sha256="1hjpvsnqb17nkb8qlz4hkmr193m5v262g7kq1mqj4k4zchh2ffbc"; depends=[assertthat BiocParallel ChIPseeker corrplot data_table dplyr genefilter GenomicRanges GGally gghalves ggplot2 ggseqlogo Gviz magrittr org_Hs_eg_db plyr reshape2 rtracklayer stringr tibble tidyr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + AMARETTO = derive2 { name="AMARETTO"; version="1.2.0"; sha256="0wfmrk5v0sgsk7hbw3v5nydg0js9r3p6aya5ls8bd5cqia4pbbnx"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; }; + AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.12.0"; sha256="08lpjcyrcd698zqvajqqnmnghp5rbcalijnzmgfszicbhcp3pzwl"; depends=[]; }; + ANF = derive2 { name="ANF"; version="1.8.0"; sha256="1rf027kgzp36k8wb0jg7xcf5rwykm0cyykqsn8z416v1wwgxmggb"; depends=[Biobase igraph MASS RColorBrewer survival]; }; + APAlyzer = derive2 { name="APAlyzer"; version="1.0.0"; sha256="01iqqirbv3pljgrbzygc7hbzp48bgglpwhnka832hrdql7fz7l94"; depends=[DESeq GenomicAlignments GenomicFeatures GenomicRanges Rsubread SummarizedExperiment]; }; + ARRmNormalization = derive2 { name="ARRmNormalization"; version="1.26.0"; sha256="0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1"; depends=[ARRmData]; }; + ASAFE = derive2 { name="ASAFE"; version="1.12.0"; sha256="0jf0n0z21n113dwfmyfxgwmyl80hrhg0bibbydaclgcqp34bi8rk"; depends=[]; }; + ASEB = derive2 { name="ASEB"; version="1.30.0"; sha256="1nvgszvpac44y3bbmxafhp6ii6l5iffwgxah4hn30adr3hfd5qrr"; depends=[]; }; + ASGSCA = derive2 { name="ASGSCA"; version="1.20.0"; sha256="1f8v87qf5yvymddvzyrllp8c7wjcim93s046jkcxl3mqzqlc778h"; depends=[MASS Matrix]; }; + ASICS = derive2 { name="ASICS"; version="2.2.0"; sha256="0h0yw8v164mc8xnypmmg1h2856mk6iapppqzvcd81djm2cr9v145"; depends=[BiocParallel ggplot2 gridExtra Matrix PepsNMR plyr quadprog ropls SummarizedExperiment TSdist zoo]; }; + ASSET = derive2 { name="ASSET"; version="2.4.0"; sha256="04mld0rhv5zbp7dcln6nn6zlvnl2rlak5zbgp2hfdvkzaqdk9r2l"; depends=[MASS msm rmeta]; }; + ASSIGN = derive2 { name="ASSIGN"; version="1.22.0"; sha256="1m9n7r2zx8rl60ypfg7jfnbybjznzcpa40z0p763061rbdh94fzq"; depends=[ggplot2 gplots msm Rlab sva yaml]; }; + ASpediaFI = derive2 { name="ASpediaFI"; version="1.0.0"; sha256="1nzjjjyjjjsk09mi3gb9ijdim078vra2w4lp21zkj74cvzzqmwsr"; depends=[BiocParallel biomaRt dplyr DRaWR e1071 fgsea GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz igraph IRanges IVAS limma Matrix mGSZ reshape2 ROCR Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; }; + ASpli = derive2 { name="ASpli"; version="1.12.0"; sha256="0xs8l130kscmjscm88787b83fvzrlgysifrl0v651zkzdkjd0y5d"; depends=[AnnotationDbi BiocGenerics BiocStyle edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rsamtools S4Vectors]; }; + ATACseqQC = derive2 { name="ATACseqQC"; version="1.10.3"; sha256="18zf90iksglbs13cwr4jjwsv332a19lf4bpdmy69jz8bpwrklv22"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno edgeR GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; }; + AUCell = derive2 { name="AUCell"; version="1.8.0"; sha256="1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky"; depends=[BiocGenerics data_table GSEABase mixtools R_utils S4Vectors shiny SummarizedExperiment]; }; + AWFisher = derive2 { name="AWFisher"; version="1.0.1"; sha256="1m10l1xg9x0kxj25hrcb89wbhq7pf6k7iyhi9a0ap0az4rk6lph0"; depends=[edgeR limma]; }; + AffiXcan = derive2 { name="AffiXcan"; version="1.4.0"; sha256="0sl3cvjwxfy2lm5lc132gwvba1c0yvqnv3q1cwhf594dm8hi52a3"; depends=[BiocParallel crayon MultiAssayExperiment SummarizedExperiment]; }; + AffyCompatible = derive2 { name="AffyCompatible"; version="1.46.0"; sha256="10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks"; depends=[Biostrings RCurl XML]; }; + AffyExpress = derive2 { name="AffyExpress"; version="1.52.0"; sha256="0w78kl0r57iacbaaiic5yhbpi18cpay95hhcap16ii75pr7k3yx7"; depends=[affy limma]; }; + AffyRNADegradation = derive2 { name="AffyRNADegradation"; version="1.32.0"; sha256="18pa7jjlx68d9rwrc2mc54hqlm7xqs7jh2a3zwfqyhnwvmqmr08a"; depends=[affy]; }; + AgiMicroRna = derive2 { name="AgiMicroRna"; version="2.36.0"; sha256="0k7bb7qfp6dqpaqx5542zgxhhnnlpnkqc9hpz21d0krsav29jjx2"; depends=[affy affycoretools Biobase limma preprocessCore]; }; + AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.24.0"; sha256="0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; }; + AlphaBeta = derive2 { name="AlphaBeta"; version="1.0.0"; sha256="19vf0rzn168rinl8xn4idhf3ng4aj7zp930pvpfjggyfbbhb3wpa"; depends=[BiocParallel data_table dplyr expm gtools optimx stringr]; }; + AnalysisPageServer = derive2 { name="AnalysisPageServer"; version="1.20.0"; sha256="0hjw26178y771pk1m2agkhdbg8k76hx5bmfb78w9h49s5sr6036k"; depends=[Biobase graph log4r rjson]; }; + Anaquin = derive2 { name="Anaquin"; version="2.10.0"; sha256="1859c7mwji2j0kcw4cawk34fi83fcfvb8h7d3j82k6hg6g1gd1yi"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; }; + AneuFinder = derive2 { name="AneuFinder"; version="1.14.0"; sha256="054m9scwnw0snk9vw3f2a1r1zrd9qqs05khd9n7i7jmivnzx5qrb"; depends=[AneuFinderData bamsignals BiocGenerics Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust ReorderCluster reshape2 Rsamtools S4Vectors]; }; + AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.48.0"; sha256="09piz1f0xpbb4amskx4ilby6lfrn27hhwk75il2c4lq6m3hr4w8s"; depends=[Biobase BiocGenerics DBI IRanges RSQLite S4Vectors]; }; + AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.10.0"; sha256="1l9sxhlvnwn6327vgg02h11ppmqr2zr07ff8wmcng0i1jbqwa8q5"; depends=[GenomicRanges lazyeval]; }; + AnnotationForge = derive2 { name="AnnotationForge"; version="1.28.0"; sha256="0h2r60v339ajk5r6xq4iwwcpihdvf12fi8255byr2dhglzrd8xl7"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; + AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.36.0"; sha256="0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq"; depends=[AnnotationDbi DBI]; }; + AnnotationHub = derive2 { name="AnnotationHub"; version="2.18.0"; sha256="19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; }; + AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.16.0"; sha256="1a982rjpd5gnyas1af7x3xabryz9whgbl8k4jm5639bvmq668zmm"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; }; + ArrayExpress = derive2 { name="ArrayExpress"; version="1.46.0"; sha256="1853akd4rsa312gqlm0imxqhwscifd69swxyrlxp4fifaiv30qw4"; depends=[Biobase limma oligo XML]; }; + ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.36.0"; sha256="05w0w5q1bb0qay6m18bigq5l4q1kycv72pli5g8gpbn6x13dqaar"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer Rhtslib rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; }; + ArrayTV = derive2 { name="ArrayTV"; version="1.24.0"; sha256="1x5kclva72wlblndh4gynb9v22932xas46km13fhdf1k47a8rb1a"; depends=[DNAcopy foreach IRanges oligoClasses S4Vectors]; }; + ArrayTools = derive2 { name="ArrayTools"; version="1.46.0"; sha256="1zs3p81ah7pp605vrfq86cykhapgszf3ba6qmm6npd229007n1ap"; depends=[affy Biobase limma xtable]; }; + AssessORF = derive2 { name="AssessORF"; version="1.4.0"; sha256="081rzjnx4zb5gq5rsm4n6309xf393dpzq79qzy3rqhyblffk3c6z"; depends=[Biostrings DECIPHER GenomicRanges IRanges]; }; + Autotuner = derive2 { name="Autotuner"; version="1.0.1"; sha256="044msxwrnqwvxk3nd436dz2n6jwa70bdn368kxrpx3cxcggr9r90"; depends=[assertthat cluster devtools dplyr entropy MSnbase mzR plyr RColorBrewer rlang scales]; }; + BAC = derive2 { name="BAC"; version="1.46.0"; sha256="0ww3am5kcqmgvxhgp9pxq86p24v3bbjx1hshkdwf9ixcg7aygxjx"; depends=[]; }; + BADER = derive2 { name="BADER"; version="1.24.0"; sha256="01p8hsv49n7x6nrg831889ffc5p8np3hsjflqbgvgxckfs67q9zi"; depends=[]; }; + BAGS = derive2 { name="BAGS"; version="2.26.0"; sha256="04a33ja70q9gv4cmz2vg85lh1h7v9l4j87nnc3p6sdcxlviq2k4x"; depends=[Biobase breastCancerVDX]; }; + BANDITS = derive2 { name="BANDITS"; version="1.2.2"; sha256="1kiync2v1bkc8qqhhxksfkyz04hxhsxzb61sxcmn2vf04lzm5l6m"; depends=[BiocParallel data_table doParallel doRNG DRIMSeq foreach ggplot2 MASS Rcpp RcppArmadillo]; }; + BASiCS = derive2 { name="BASiCS"; version="1.8.1"; sha256="1q9dlvh63795x7zz9x8rgf9fcpd7ipq0260r5slr8rnm0w8yfrag"; depends=[Biobase BiocGenerics coda cowplot data_table ggExtra ggplot2 KernSmooth MASS Matrix matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment viridis]; }; + BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.16.0"; sha256="0a21rgp3ph1gwmj053xhs8y0g25p3sadl79nxsnzyzxiwmk9l3h0"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; }; + BCRANK = derive2 { name="BCRANK"; version="1.48.0"; sha256="0l2ap0y0ab5vv1l0pdqlf2zjqgvp8xx8951fz3bc5mm5ccgvip5l"; depends=[Biostrings]; }; + BDMMAcorrect = derive2 { name="BDMMAcorrect"; version="1.4.0"; sha256="0yb0zv4i62s91adnrm06v7d5zvv8vkl35v0b5zj4yxz2va8hhxkv"; depends=[ape ellipse ggplot2 Rcpp RcppArmadillo RcppEigen SummarizedExperiment vegan]; }; + BEARscc = derive2 { name="BEARscc"; version="1.6.0"; sha256="0q6az6blgc4b27i2m1jrcdrs85nqx6i9lzbwbxq7xkmxslxj04iq"; depends=[data_table ggplot2 SingleCellExperiment]; }; + BEAT = derive2 { name="BEAT"; version="1.24.0"; sha256="0wnlvg5wilrrzzi5kcm768f9qkpyirssgblyyysdhyxjvzkw5cy0"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; }; + BEclear = derive2 { name="BEclear"; version="2.2.0"; sha256="1h9qq8mchkx0yw6ff2irg5afznjpclcw9064l9v1jpfsgg1w6rww"; depends=[abind BiocParallel data_table futile_logger Matrix outliers Rcpp Rdpack]; }; + BGmix = derive2 { name="BGmix"; version="1.46.0"; sha256="1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683"; depends=[KernSmooth]; }; + BHC = derive2 { name="BHC"; version="1.38.0"; sha256="1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh"; depends=[]; }; + BLMA = derive2 { name="BLMA"; version="1.10.0"; sha256="1r9sydwn0rwikf6c652amxjn89c4m2zjk2mabpv3wx3dnw39pvlg"; depends=[Biobase graph GSA limma PADOG ROntoTools]; }; + BPRMeth = derive2 { name="BPRMeth"; version="1.12.0"; sha256="1qpa7i82dydy58b51wgj9bcwi4m3y46q9jylll48wyr28jcqgymq"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; }; + BRAIN = derive2 { name="BRAIN"; version="1.32.0"; sha256="1qag7c6f87kwyklbqn45c4kjs6c3im4rp8w176nym1q13h38dc5p"; depends=[Biostrings lattice PolynomF]; }; + BSgenome = derive2 { name="BSgenome"; version="1.54.0"; sha256="0nn1b3h4hmnx5whf2cmzmyxdrcf4myj8c38rwr0sw4rc07xfzndy"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; }; + BUMHMM = derive2 { name="BUMHMM"; version="1.10.0"; sha256="0980vrhx1wral8cyfk314i9ada94v3qnksp5l0yr6xnm4cprgamz"; depends=[Biostrings devtools gtools IRanges stringi SummarizedExperiment]; }; + BUS = derive2 { name="BUS"; version="1.42.0"; sha256="0x2v0lar4frlrgdf7gqg1ixq2g16267xh4vw0sjp62cig7amf87b"; depends=[infotheo minet]; }; + BUScorrect = derive2 { name="BUScorrect"; version="1.4.0"; sha256="1kf016afc4haj01hcarjw0b9zakjjjl46sp3vh4m5445fgq8mkm1"; depends=[gplots SummarizedExperiment]; }; + BUSpaRse = derive2 { name="BUSpaRse"; version="1.0.0"; sha256="06a7zjijr6vgkr4r4wldapjr5vpq41sxn6fra3z0p3dlpri06hv7"; depends=[AnnotationDbi AnnotationFilter BH biomaRt Biostrings BSgenome data_table dplyr ensembldb GenomeInfoDb GenomicFeatures GenomicRanges magrittr Matrix plyranges Rcpp RcppArmadillo RcppParallel RcppProgress S4Vectors stringr tibble tidyr zeallot]; }; + BaalChIP = derive2 { name="BaalChIP"; version="1.12.0"; sha256="09xcdw658m810f9641rbmkjdyj7pgm3g70rdv31jaiz2h16z9l75"; depends=[coda doBy doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges reshape2 Rsamtools scales]; }; + BadRegionFinder = derive2 { name="BadRegionFinder"; version="1.14.0"; sha256="0kpb1mw9894zdx2yl5r95fkm11n9qra59dlp5d09yd1fsyr6p4z0"; depends=[biomaRt GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; + BaseSpaceR = derive2 { name="BaseSpaceR"; version="1.30.0"; sha256="0z59pzywnm5dpflaa32r6l51xzvv1mb93rn4bj6p8vzq39v2wbcw"; depends=[RCurl RJSONIO]; }; + Basic4Cseq = derive2 { name="Basic4Cseq"; version="1.22.0"; sha256="0dbmnz2c8f729imnabxpj442l7bqsidv4kfaz1ggda9i3j3z514n"; depends=[Biostrings BSgenome_Ecoli_NCBI_20080805 caTools GenomicAlignments GenomicRanges RCircos]; }; + BasicSTARRseq = derive2 { name="BasicSTARRseq"; version="1.14.0"; sha256="0lr0zpsykrnss3z1hfhymsd33wjvcg8mmzqm8zf29vfmpyn37km9"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges S4Vectors]; }; + BatchQC = derive2 { name="BatchQC"; version="1.14.0"; sha256="18b7sfy73i7m4i876pkmw1vadcb8vllld98jafd2bxs6vis3dc6a"; depends=[corpcor d3heatmap ggvis gplots knitr limma Matrix matrixStats MCMCpack moments pander reshape2 rmarkdown shiny sva]; }; + BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.12.0"; sha256="0b4p2d2dvrzanjgxx3f15wq5355li6wq1f7l1irniwiabjm03w2n"; depends=[Biobase]; }; + BayesPeak = derive2 { name="BayesPeak"; version="1.38.0"; sha256="1w5b8zma5xw1v71j67b8gr5bh14vs799dg9vbbs1yhkn42zbiyrr"; depends=[IRanges]; }; + BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.38.0"; sha256="0i46cs2w6s8zyhda5s56m870cma7b05430qcqavg8cv8ycr0fh4c"; depends=[]; }; + BgeeDB = derive2 { name="BgeeDB"; version="2.12.1"; sha256="1fpbjsrbhb4jmwyjjga7bzjd1qng7gyg2grqzdn1nyhpqlfpxciv"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; }; + BiFET = derive2 { name="BiFET"; version="1.6.0"; sha256="0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k"; depends=[GenomicRanges poibin]; }; + BiGGR = derive2 { name="BiGGR"; version="1.22.0"; sha256="1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; }; + BiRewire = derive2 { name="BiRewire"; version="3.18.0"; sha256="1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q"; depends=[igraph Matrix slam tsne]; }; + BiSeq = derive2 { name="BiSeq"; version="1.26.0"; sha256="1wvaijskay6zgnn9b4l0jxqp89lw3nbz3rprhg2vlhrsdi80ki6j"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; }; + BicARE = derive2 { name="BicARE"; version="1.44.0"; sha256="1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs"; depends=[Biobase GSEABase multtest]; }; + BioCor = derive2 { name="BioCor"; version="1.10.0"; sha256="1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl"; depends=[BiocParallel GSEABase Matrix]; }; + BioMM = derive2 { name="BioMM"; version="1.2.0"; sha256="1q1ajzc2f457g9ah3ypd3lymhwdl8l0i63m0b2x89jxwfxvcnbig"; depends=[BiocParallel CMplot e1071 ggplot2 glmnet lattice nsprcomp pROC ranger rms variancePartition vioplot]; }; + BioMVCClass = derive2 { name="BioMVCClass"; version="1.54.0"; sha256="0lpjm3igcq3qkiqq627bix9dsxa4q9xxkbf27h79wbkng8b0prkf"; depends=[Biobase graph MVCClass Rgraphviz]; }; + BioNet = derive2 { name="BioNet"; version="1.46.0"; sha256="1p50ijx73vp53svky3sw8fdxmf0xwfik4ks1mzydhlb47z7gdm9i"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; + BioNetStat = derive2 { name="BioNetStat"; version="1.6.0"; sha256="15lx3zxrd9x1s7hw5d62s7pngyby3cpbpbm2vad54a5qcabpp710"; depends=[BiocParallel ggplot2 Hmisc igraph knitr pathview pheatmap plyr psych RColorBrewer RJSONIO shiny shinyBS whisker yaml]; }; + BioQC = derive2 { name="BioQC"; version="1.14.0"; sha256="0c8qmxvqwws5fdzy23zmj6r3aa2yy3rjxxhxvys63dzyh9s0728v"; depends=[Biobase edgeR Rcpp]; }; + BioSeqClass = derive2 { name="BioSeqClass"; version="1.44.0"; sha256="1a7xrd7p84sqk11bpv8xqmzzzkh8wm09nixbj6gks4sbi5k6b0hd"; depends=[Biobase Biostrings class e1071 foreign ipred klaR nnet party randomForest rpart scatterplot3d tree]; }; + BioTIP = derive2 { name="BioTIP"; version="1.0.0"; sha256="14xvlb3bba8y7ha7b7373qcaihhv94lnxl0vyixzfhkyh4w4phw8"; depends=[cluster GenomicRanges igraph psych stringr]; }; + Biobase = derive2 { name="Biobase"; version="2.46.0"; sha256="1gx41083dqlm59vwqdxvc4ny31x91j48mda9n3scg0f2zwasvqgl"; depends=[BiocGenerics]; }; + BiocCaseStudies = derive2 { name="BiocCaseStudies"; version="1.48.0"; sha256="1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd"; depends=[Biobase]; }; + BiocCheck = derive2 { name="BiocCheck"; version="1.22.0"; sha256="1qnvl5yajgh67ijkq6gdsafri1k5hyw5gzn2ccqk9ymx6i2xd80g"; depends=[BiocManager biocViews codetools graph httr knitr optparse stringdist]; }; + BiocFileCache = derive2 { name="BiocFileCache"; version="1.10.2"; sha256="0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6"; depends=[curl DBI dbplyr dplyr httr rappdirs RSQLite]; }; + BiocGenerics = derive2 { name="BiocGenerics"; version="0.32.0"; sha256="1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn"; depends=[]; }; + BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.4.2"; sha256="1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6"; depends=[BiocParallel Matrix Rcpp RcppAnnoy RcppHNSW S4Vectors]; }; + BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.6.0"; sha256="0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; }; + BiocParallel = derive2 { name="BiocParallel"; version="1.20.1"; sha256="0g0znb4whsvb9hpwx9xaasdi5n4vjqw8cpdyqgrdrjm91rls1h21"; depends=[BH futile_logger snow]; }; + BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.4.6"; sha256="0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr rappdirs RBGL readr rex rlang rvest stringr tibble tidyr tidyselect xml2]; }; + BiocSet = derive2 { name="BiocSet"; version="1.0.1"; sha256="1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9"; depends=[AnnotationDbi dplyr KEGGREST plyr rlang rtracklayer tibble]; }; + BiocSingular = derive2 { name="BiocSingular"; version="1.2.2"; sha256="1282fdwxrpga87y8xflr0sl8ajwawgn2i9i65my8mbg5vrixs407"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors]; }; + BiocSklearn = derive2 { name="BiocSklearn"; version="1.8.1"; sha256="1s5bfslw7ja0i9nvx196gbphb9gfp4jzp3bz0ggp5nh4b588xdq9"; depends=[BBmisc knitr reticulate SummarizedExperiment]; }; + BiocStyle = derive2 { name="BiocStyle"; version="2.14.4"; sha256="1x71in059zql40f4c87bd1gf96r945kdvwbq61jmch9d3d8nwxbb"; depends=[BiocManager bookdown knitr rmarkdown yaml]; }; + BiocVersion = derive2 { name="BiocVersion"; version="3.10.1"; sha256="0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f"; depends=[]; }; + BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.12.1"; sha256="0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6"; depends=[BiocStyle bookdown git2r httr knitr rmarkdown rstudioapi stringr usethis]; }; + Biostrings = derive2 { name="Biostrings"; version="2.54.0"; sha256="0pq7g2hflx2cjlpwdj6mscw9hnxvlf5y50dxf48lbrf9r3q9kmyp"; depends=[BiocGenerics IRanges S4Vectors XVector]; }; + BitSeq = derive2 { name="BitSeq"; version="1.30.1"; sha256="05mxbmwgkv12a4i06s19rgpzrbl6jwbjwfn60z6wrhk4kh8fjj2l"; depends=[IRanges Rhtslib Rsamtools S4Vectors]; }; + BrainStars = derive2 { name="BrainStars"; version="1.30.0"; sha256="0k0s5720b0bi27jk3x6j2p4qw6gwmw5jpyjn838lqcszw5v10dh9"; depends=[Biobase RCurl RJSONIO]; }; + BridgeDbR = derive2 { name="BridgeDbR"; version="1.20.3"; sha256="0ypyhhsjz9i12dkah8iajrmwhk30jdy7yj6y9ab7hjsqnv3l20x5"; depends=[RCurl rJava]; }; + BrowserViz = derive2 { name="BrowserViz"; version="2.8.0"; sha256="0607namgkd0cy0hxmannhbcc59x95piaw03vcs76mns0qi5hsl2d"; depends=[BiocGenerics httpuv jsonlite]; }; + BubbleTree = derive2 { name="BubbleTree"; version="2.16.0"; sha256="0bz2ycj4v8vqyci5894xmld9zjwjd45ljgldjma9g3v2rb2k5z14"; depends=[Biobase BiocGenerics BiocStyle biovizBase dplyr e1071 GenomicRanges ggplot2 gridExtra gtable gtools IRanges limma magrittr plyr RColorBrewer WriteXLS]; }; + BufferedMatrix = derive2 { name="BufferedMatrix"; version="1.50.0"; sha256="1wngrsw8fylahrvghz57pajpq9gpi6dq8w71kvx5mfxapy9gs9ld"; depends=[]; }; + BufferedMatrixMethods = derive2 { name="BufferedMatrixMethods"; version="1.50.0"; sha256="1896gh2hmh4ml4c3k6s3swx8rh2ks43zkzvq93fdl08vsx63bqxq"; depends=[BufferedMatrix]; }; + CAFE = derive2 { name="CAFE"; version="1.22.0"; sha256="1rhmhk0fkd83s84rmj44r8dspch88b1ry2gaxdrsh1c72698hx1a"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; }; + CAGEfightR = derive2 { name="CAGEfightR"; version="1.6.0"; sha256="1r99m3km4y5006plmj9xi9jbq29hy39c6wds518h9302zl31x2jn"; depends=[assertthat BiocGenerics BiocParallel GenomeInfoDb GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges grr Gviz InteractionSet IRanges Matrix Matrix_utils pryr rtracklayer S4Vectors SummarizedExperiment]; }; + CAGEr = derive2 { name="CAGEr"; version="1.28.0"; sha256="1257yz4rn6lysvmdabapw2aai4axdybdd7dlzxfb6vls2mw2cikw"; depends=[beanplot BiocGenerics BiocParallel BSgenome data_table DelayedArray formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; + CALIB = derive2 { name="CALIB"; version="1.52.0"; sha256="00nnnnwgapbhy32wryd3zv9lrl18gs3cvzi87zvzakx5a5wanqc6"; depends=[limma]; }; + CAMERA = derive2 { name="CAMERA"; version="1.42.0"; sha256="0hv1p317wk6fqfwly10s23844s766bs5xis5q6a81iwbd87vba13"; depends=[Biobase graph Hmisc igraph RBGL xcms]; }; + CAMTHC = derive2 { name="CAMTHC"; version="1.4.0"; sha256="1skzp08iq91qr931fpmwljhnfy595igpm57gd5cng4azs6nkmy4n"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF nnls pcaPP rJava SummarizedExperiment]; }; + CATALYST = derive2 { name="CATALYST"; version="1.10.3"; sha256="15qndbxlnrh18x4n14az19xh48gghn7z5df9ihray2f3bk48b35l"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus cowplot data_table dplyr drc DT flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra htmltools limma magrittr Matrix matrixStats nnls plotly purrr RColorBrewer reshape2 Rtsne S4Vectors scales scater shiny shinyBS shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; }; + CAnD = derive2 { name="CAnD"; version="1.18.0"; sha256="0a99v7c7j673pmahvg13qf5m6rkqhc5frkaxgklv1kbif7k2chch"; depends=[ggplot2 reshape]; }; + CCPROMISE = derive2 { name="CCPROMISE"; version="1.12.0"; sha256="0p1yyav0ajhl8qxvcjhv5bmndz6imn0bxg28ka9pmf29h989fxrh"; depends=[Biobase CCP GSEABase PROMISE]; }; + CEMiTool = derive2 { name="CEMiTool"; version="1.10.2"; sha256="1mhjzhwa47jiimg71ikkra1bz8dhfnv3xlvqdq8a99xq1fdapd6s"; depends=[clusterProfiler data_table dplyr DT fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; }; + CFAssay = derive2 { name="CFAssay"; version="1.20.0"; sha256="0n4xci4rq7ylwc20h88p5d6znzys0jayzf8vrgv8vvkjsr5ww3nb"; depends=[]; }; + CGEN = derive2 { name="CGEN"; version="3.22.0"; sha256="1mh9a2r3y184ad83x4y4d7kdd42jiwqgb410x9khmf8hgdi4yhrv"; depends=[mvtnorm survival]; }; + CGHbase = derive2 { name="CGHbase"; version="1.46.0"; sha256="0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x"; depends=[Biobase marray]; }; + CGHcall = derive2 { name="CGHcall"; version="2.48.0"; sha256="1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s"; depends=[Biobase CGHbase DNAcopy impute snowfall]; }; + CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.40.0"; sha256="0vixpy271m2j80a9fqr0siqkd0w31ym7vzghpgnnhjr1m3qk38wd"; depends=[Biobase CGHbase CGHcall]; }; + CGHregions = derive2 { name="CGHregions"; version="1.44.0"; sha256="1q4xg4xs80n3dz0y0wwdyykga03jymga0qx74a91k1jf1jpkgdm9"; depends=[Biobase CGHbase]; }; + CHARGE = derive2 { name="CHARGE"; version="1.6.0"; sha256="1bzbsjkkavhjx5xqb2b5gwhywpcn70si3702hbw7yl62icigjywb"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats plyr SummarizedExperiment]; }; + CHETAH = derive2 { name="CHETAH"; version="1.2.0"; sha256="1b4laxj5arc7cpyz263q09bc9m6k2rrr3s8ll7ans4civhzzqa4z"; depends=[bioDist corrplot cowplot dendextend ggplot2 gplots pheatmap plotly reshape2 S4Vectors shiny SingleCellExperiment SummarizedExperiment]; }; + CHRONOS = derive2 { name="CHRONOS"; version="1.14.0"; sha256="14qk2fckk3zq5rii3cdi5pzx35c1nkaprw9hk6cybnvrl8w4a93v"; depends=[biomaRt circlize doParallel foreach graph igraph openxlsx RBGL RCurl XML]; }; + CINdex = derive2 { name="CINdex"; version="1.14.0"; sha256="1b192pd91bi2a0f1vrfijxzadgmm62fhbia3a2yvy0zpndfcjzh2"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; }; + CMA = derive2 { name="CMA"; version="1.44.0"; sha256="07pcrzwdvrx9wk6xxc55mh8xw4vvap69x8fwqgiwzjq0fcckv1pn"; depends=[Biobase]; }; + CNAnorm = derive2 { name="CNAnorm"; version="1.32.0"; sha256="1z0lsrgp7i20v7lhmq6428nisv3rqslyxp7k6s1360gv7sajhn4i"; depends=[DNAcopy]; }; + CNEr = derive2 { name="CNEr"; version="1.22.0"; sha256="0d7q7kdpd6bpg6xqqp07gq98ffazfn1saxiyig1yn8w2mz1vjkzv"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; }; + CNORdt = derive2 { name="CNORdt"; version="1.28.0"; sha256="006v3wvnhr5hm7y6ljfcps43ahwh4byw33ifaaawk4s4n0qvnqhv"; depends=[abind CellNOptR]; }; + CNORfeeder = derive2 { name="CNORfeeder"; version="1.26.0"; sha256="15b62ky0pzjc3q3f5fd4a0kgw13vk0956y79q7xlch876yc2hnwm"; depends=[CellNOptR graph]; }; + CNORfuzzy = derive2 { name="CNORfuzzy"; version="1.28.0"; sha256="044fg9hl73icm1x4y1xdhxly4w75xs80in2h5cjlvg2kjvbsq0za"; depends=[CellNOptR nloptr]; }; + CNORode = derive2 { name="CNORode"; version="1.28.0"; sha256="18k5bk20f4kdyb963va7aabrc0i84h02m608nsz4dwjm6bkna0al"; depends=[CellNOptR genalg]; }; + CNTools = derive2 { name="CNTools"; version="1.42.0"; sha256="0cvkwafz0g1nlhajdwgz2y3y3h1dq1r24548rcj6m8fz6jwcxdjj"; depends=[genefilter]; }; + CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.18.0"; sha256="05ac5b6pzbm60isw1diabyb8zpbbwxidn88vzlhkcm3jb74c312h"; depends=[exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; + CNVRanger = derive2 { name="CNVRanger"; version="1.2.2"; sha256="045hznxd87bbjfqhfsqcwmc0al1nnsifissn0avr0i0sv6l52z3x"; depends=[BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; }; + CNVfilteR = derive2 { name="CNVfilteR"; version="1.0.4"; sha256="0m3cy2pqld41g6hrjl040912r80x4v651d0wff1nqdas2wnpjbqp"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; }; + CNVrd2 = derive2 { name="CNVrd2"; version="1.24.0"; sha256="0dgl73zvxm843vg34nhdpm4hax5y9chjy1j86x98kqdg1wpy4yjq"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; }; + CNVtools = derive2 { name="CNVtools"; version="1.80.0"; sha256="1f0p58w7kj8sc6awp742s8x5fmlv1f8zmd11bf2ki3rndf3drhfy"; depends=[survival]; }; + COCOA = derive2 { name="COCOA"; version="2.0.0"; sha256="0fq96b8m8vy4801s1pv7wyy0z60mafvhkibih0hld3rv19ammzk7"; depends=[Biobase BiocGenerics ComplexHeatmap data_table fitdistrplus GenomicRanges ggplot2 IRanges MIRA S4Vectors simpleCache tidyr]; }; + CODEX = derive2 { name="CODEX"; version="1.18.0"; sha256="1bpph4c3hw01dwjs3rr1jlb8a01hd31q0yrxg5q4srrcgp2854pf"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; }; + COHCAP = derive2 { name="COHCAP"; version="1.32.0"; sha256="1h18fp6d59a4hp39b9d1gvw9k2x66v46scqym25n4p936jp3dmc8"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; }; + COMPASS = derive2 { name="COMPASS"; version="1.24.1"; sha256="12gnsazjbc233l3nxap4m3rgs14dqr4c433q3vd4gwjiwlc511g8"; depends=[abind BiocStyle clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; }; + CONFESS = derive2 { name="CONFESS"; version="1.14.0"; sha256="1mfah67rnq4wylivd43azcjmybk1nppvlj3lwkzr99igcp67km7y"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; }; + CORREP = derive2 { name="CORREP"; version="1.52.0"; sha256="0fnkjcfcnjc6rnp9xqfj429l5y6a84750xhxjsga4db8lddr6143"; depends=[e1071]; }; + COSNet = derive2 { name="COSNet"; version="1.20.0"; sha256="1qwzmjhiz4v6b8pz51dm9d8yn1k6waprw183z4bzw3vc51ivsvcc"; depends=[]; }; + CRISPRseek = derive2 { name="CRISPRseek"; version="1.26.0"; sha256="1fs17b479hmgh7i1z9ds3pyrg3yc8428xmv2mvq1mmn677k0zj8v"; depends=[BiocGenerics BiocParallel Biostrings BSgenome data_table hash IRanges S4Vectors seqinr]; }; + CRImage = derive2 { name="CRImage"; version="1.34.0"; sha256="1kfgb6hwxsb4v6ls7y08vrbr16aihi2blap8mbll6zfdjhwji47d"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; }; + CSAR = derive2 { name="CSAR"; version="1.38.0"; sha256="1kb200kp3mv89ml3b5gdd2lsaparg5w98aycn2npb7r6811xlckw"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; + CSSP = derive2 { name="CSSP"; version="1.24.0"; sha256="0ccariwsgkqxcnlavl605bihkqsdh3d9bz86bvggqahf3w6ycx2k"; depends=[]; }; + CTDquerier = derive2 { name="CTDquerier"; version="1.5.0"; sha256="1p8vx60gmjv2n74xd1v52r8rkmfpinjy1a5lmxg96dxx8j5xqj1k"; depends=[BiocFileCache ggplot2 gridExtra igraph rappdirs RCurl S4Vectors stringdist stringr]; }; + CVE = derive2 { name="CVE"; version="1.11.2"; sha256="1jlgx707c8mb4il5mf0y4wqqqijh2jfngrp52nfz55xifjx10v93"; depends=[ape ConsensusClusterPlus ggplot2 gplots jsonlite plyr RColorBrewer RTCGAToolbox shiny tidyverse WGCNA]; }; + CancerInSilico = derive2 { name="CancerInSilico"; version="2.6.0"; sha256="07qdrl6l6c5pxf1siahmwiv7l3inaljcm5kzb34k11xksj48lrg7"; depends=[BH Rcpp]; }; + CancerMutationAnalysis = derive2 { name="CancerMutationAnalysis"; version="1.28.0"; sha256="020qxf0102dhv3340rgl7bsabfjypdb3402minmfig6bycibj99p"; depends=[AnnotationDbi limma qvalue]; }; + CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.12.0"; sha256="022515wbm5fsfkrb4bfi6lixlm5ca2mlz7hw2rasc3vf6k45gfq5"; depends=[cluster ConsensusClusterPlus iCluster impute limma NMF sigclust SNFtool survival]; }; + Cardinal = derive2 { name="Cardinal"; version="2.4.0"; sha256="177inzm4i1nyfrnb5790w75m33lxg9afzdry1y2vm2kwrfdznny8"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr Matrix matter mclust nlme ProtGenerics S4Vectors signal sp viridisLite]; }; + Category = derive2 { name="Category"; version="2.52.1"; sha256="0ga0ij9hyzsxa5pavwmv35i8xggia2wygrk4m4z8an0qcvgy3v5g"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; }; + CausalR = derive2 { name="CausalR"; version="1.18.0"; sha256="1kihi3yq8992p94g7a1r5jp7lm7s5bgjl68fpxmz8nzn436mamfx"; depends=[igraph]; }; + CellBench = derive2 { name="CellBench"; version="1.2.0"; sha256="0a4y2wibr0qnci0xg2bpp73idvh3aip87b6rfmxsq17762r8npb8"; depends=[BiocFileCache BiocParallel dplyr glue lubridate magrittr memoise purrr rappdirs rlang SingleCellExperiment tibble tidyr]; }; + CellMapper = derive2 { name="CellMapper"; version="1.12.0"; sha256="028vv2pzyighvjdc9b1160qw7wyaih8jqn72i78c404vg30k2vri"; depends=[S4Vectors]; }; + CellMixS = derive2 { name="CellMixS"; version="1.2.5"; sha256="02gvjcq45zc2blhxiffdlbxgk0mh1azd04vnzdyp11kcbllv4jk5"; depends=[BiocGenerics BiocNeighbors BiocParallel cowplot dplyr ggplot2 ggridges kSamples listarrays magrittr purrr scater SingleCellExperiment SummarizedExperiment tidyr viridis]; }; + CellNOptR = derive2 { name="CellNOptR"; version="1.32.0"; sha256="1r3njwmljyg0wp23qb5g0ys15niwi85lj5bksdrvjd4w1nqdkxfz"; depends=[ggplot2 graph hash igraph RBGL RCurl Rgraphviz stringi stringr XML]; }; + CellScore = derive2 { name="CellScore"; version="1.6.0"; sha256="1jrshfgmbyw1yvrqramix3bv2gldhzjg6r481vkba48pqx4cq3pn"; depends=[Biobase gplots lsa RColorBrewer squash]; }; + CellTrails = derive2 { name="CellTrails"; version="1.4.0"; sha256="197y5lcdvmbzvvwjlpr916lg8cij0yinlb6a7p1p5h3s400amwr3"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; }; + CexoR = derive2 { name="CexoR"; version="1.24.0"; sha256="0m5mcrax6qm9swigmsjij091dh5khzy3gxch22qsbklqr2j50z6p"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; }; + ChAMP = derive2 { name="ChAMP"; version="2.16.1"; sha256="1iy4mgrq0ibnnzxhgjs32hg8ccd9f30afw0g4n9axjgywfz5m94v"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel DT FEM GenomicRanges ggplot2 globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva kpmt limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; }; + ChIC = derive2 { name="ChIC"; version="1.6.0"; sha256="1mvix82v7prqs21xmpyai3g0kq18r4m3cvzjd86am1hagggr9bp5"; depends=[BiocGenerics caret caTools ChIC_data GenomicRanges IRanges progress S4Vectors spp]; }; + ChIPComp = derive2 { name="ChIPComp"; version="1.16.0"; sha256="0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; }; + ChIPQC = derive2 { name="ChIPQC"; version="1.22.0"; sha256="11g0s0hgacg5hs7gdllh69y58awxyi47nsvn9728c4cvbsiml0wk"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; + ChIPSeqSpike = derive2 { name="ChIPSeqSpike"; version="1.6.0"; sha256="0krqnq3bvn6mfpk12ysqhy883dnjcjmwvyjbngjrx83cl2a4zass"; depends=[BiocGenerics corrplot GenomicRanges ggplot2 IRanges LSD Rsamtools rtracklayer S4Vectors seqplots stringr]; }; + ChIPXpress = derive2 { name="ChIPXpress"; version="1.30.0"; sha256="025knahsx0b978g2kdgibf3z1jwjqaqb0ls9yipckzrf09a96h18"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; }; + ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.8.0"; sha256="1ghz5bdpaird9d4dlrkqwjdjpmbnq86gkiyc3kqbigrq7a0hwbna"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; }; + ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.10.0"; sha256="044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; + ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.20.1"; sha256="0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager biomaRt Biostrings BSgenome DBI DelayedArray ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GO_db graph idr IRanges limma matrixStats multtest RBGL regioneR Rsamtools rtracklayer S4Vectors seqinr SummarizedExperiment VennDiagram]; }; + ChIPseeker = derive2 { name="ChIPseeker"; version="1.22.1"; sha256="04ahwmch3a12xj2mv91znhdmkj84mbyw7imlln40m9gfs0k6j04l"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene]; }; + ChIPseqR = derive2 { name="ChIPseqR"; version="1.40.0"; sha256="1vdwp3qnpsrvrhxq6ynyp1cvi9zm02b19j119335z4bp0r17f0li"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; }; + ChIPsim = derive2 { name="ChIPsim"; version="1.40.0"; sha256="100zwbg88zqcp4g8bsndl4j70wc0g6hchnrrnkmz8k11dl2b24q7"; depends=[Biostrings IRanges ShortRead XVector]; }; + ChemmineOB = derive2 { name="ChemmineOB"; version="1.24.0"; sha256="0i9a9w57lj6jkyw34ni6mzgdc1r3008407ahawdap33n013ql5kz"; depends=[BH BiocGenerics Rcpp zlibbioc]; }; + ChemmineR = derive2 { name="ChemmineR"; version="3.38.0"; sha256="1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga"; depends=[base64enc BH BiocGenerics DBI digest DT ggplot2 gridExtra png Rcpp RCurl rjson rsvg]; }; + Chicago = derive2 { name="Chicago"; version="1.14.0"; sha256="09m06y08vf3cnvg3k85gigijwyqx9fc09jks3mpvf3bq3ggdi58a"; depends=[data_table Delaporte Hmisc MASS matrixStats]; }; + ChromHeatMap = derive2 { name="ChromHeatMap"; version="1.40.0"; sha256="0q2ib9xw69a4q74hpjmw8hxjn42ns7gfbc0sh4879zb3z1ay1r0q"; depends=[annotate AnnotationDbi Biobase BiocGenerics GenomicRanges IRanges rtracklayer]; }; + ClassifyR = derive2 { name="ClassifyR"; version="2.6.1"; sha256="1s2ncf5q2bmrr8vbhaznyzc5w09c619ijl3rc9drnzswpfxbsvqr"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; }; + Clomial = derive2 { name="Clomial"; version="1.22.0"; sha256="15zf6pkcii7f314fws7ff9ca6prjdvd4j3cg5wrg7y98387p8bgm"; depends=[matrixStats permute]; }; + Clonality = derive2 { name="Clonality"; version="1.34.0"; sha256="16nvnax20s7lyak8fwraxbpnf8zmbw37qjb4sigrsl44dh9552ci"; depends=[DNAcopy]; }; + CluMSID = derive2 { name="CluMSID"; version="1.2.0"; sha256="18n31midv8c23hw7ij24663hjmwq5h1r13jp9mbqhji1zw3s9vrp"; depends=[ape Biobase dbscan GGally ggplot2 gplots MSnbase mzR network plotly RColorBrewer S4Vectors sna]; }; + ClusterJudge = derive2 { name="ClusterJudge"; version="1.8.0"; sha256="1pl1zw631csx4a561mz7bwndjhyviaz8jxq7f9c9majgk9pyr8jm"; depends=[httr infotheo jsonlite lattice latticeExtra]; }; + ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.14.0"; sha256="1ibfhhq9m39h704gryxv331as24jzacs5wfysjcppirnr45cnka5"; depends=[pracma princurve RColorBrewer scatterplot3d]; }; + CoCiteStats = derive2 { name="CoCiteStats"; version="1.58.0"; sha256="03qjwwmqnsrnck44mf0axv8y7c2hxn1xszp9z0z65ia0g8vh2dxb"; depends=[AnnotationDbi org_Hs_eg_db]; }; + CoGAPS = derive2 { name="CoGAPS"; version="3.6.0"; sha256="0nipjgf75g51bsd1mzr72mldd38jiw5zzf2kvwdzpqllxwvd4vw1"; depends=[BiocParallel cluster gplots RColorBrewer Rcpp rhdf5 S4Vectors SingleCellExperiment SummarizedExperiment]; }; + CoRegFlux = derive2 { name="CoRegFlux"; version="1.2.0"; sha256="1zbscr6yscpmhkyacjc856lzbika1w91cpkp26sc50kicaq3zg3i"; depends=[CoRegNet sybil]; }; + CoRegNet = derive2 { name="CoRegNet"; version="1.24.0"; sha256="0glv6sf7ga2j23j2h3n01cx9l5hwz3s3kpr4kbv6jwj3zas2ckj6"; depends=[arules igraph shiny]; }; + CompGO = derive2 { name="CompGO"; version="1.22.0"; sha256="00awn7h4xcy70zlc8ijclhfhs25s4kw4mmii4r814jj3yddih353"; depends=[GenomicFeatures ggplot2 pathview pcaMethods RDAVIDWebService reshape2 Rgraphviz rtracklayer TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="2.2.0"; sha256="1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p"; depends=[circlize clue colorspace GetoptLong GlobalOptions png RColorBrewer]; }; + ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.50.0"; sha256="0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4"; depends=[ALL Biobase cluster]; }; + CopyNumberPlots = derive2 { name="CopyNumberPlots"; version="1.2.3"; sha256="1bixw2cb9b120d7anrkpzgdqzxscrim838m1kjffmadypwigixj3"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges karyoploteR regioneR rhdf5 Rsamtools SummarizedExperiment VariantAnnotation]; }; + CopywriteR = derive2 { name="CopywriteR"; version="2.18.0"; sha256="0llg1zpxg7qnvja5f5w1z1xic0jdg6zc4mfn97h2sm44skxxcyl1"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; }; + CorMut = derive2 { name="CorMut"; version="1.28.0"; sha256="1s3b5g167bd8xf7aivv1yn5a2mvzajnw7c23nmqm9alsw416s491"; depends=[igraph seqinr]; }; + Cormotif = derive2 { name="Cormotif"; version="1.32.0"; sha256="0im6acb1zl8ad7xd37zalzb4qbn37sjv8j86pycwg1dr5wcpnc1j"; depends=[affy limma]; }; + CountClust = derive2 { name="CountClust"; version="1.14.0"; sha256="0ang7ivgw1gnn75135fpjn5p919zn1nkwqymnrhl8vr3l8c0j0w6"; depends=[cowplot flexmix ggplot2 gtools limma picante plyr reshape2 slam SQUAREM]; }; + CoverageView = derive2 { name="CoverageView"; version="1.24.0"; sha256="0s47svs7xnr9jkylq0dxidqrigihdddiprcl0951vjr4w7kmb5nf"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; + CrispRVariants = derive2 { name="CrispRVariants"; version="1.14.0"; sha256="1wjgfhv49nkfhr5i4yf2svdb9v065hbcpbid035il7cy9kkn776q"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; }; + CrossICC = derive2 { name="CrossICC"; version="1.0.0"; sha256="0rrrrd0bsvagy5rjf6fkkry2cf6qhjf2glhdj399jjpfgssb3vjq"; depends=[Biobase cluster ConsensusClusterPlus data_table dplyr limma MASS MergeMaid]; }; + CytoDx = derive2 { name="CytoDx"; version="1.6.0"; sha256="02vj0mf8prbav80pqvbll77akdgxr3g70izgln93c3wjnbz7gq6z"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; + CytoML = derive2 { name="CytoML"; version="1.12.1"; sha256="0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz"; depends=[base64enc BH Biobase corpcor cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite lattice ncdfFlow openCyto plyr RBGL Rcpp RcppParallel Rgraphviz RProtoBufLib RUnit XML yaml]; }; + DAPAR = derive2 { name="DAPAR"; version="1.18.5"; sha256="1c1adakhmpqdcinm6c436ii6q2bww7jyp7iakgiaqwg3v1cbpzbv"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter igraph impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tmvtnorm vioplot visNetwork vsn]; }; + DART = derive2 { name="DART"; version="1.34.0"; sha256="11fl2dmlihafsdrzcsd1p6kcnwigq5gd4cn661dq2d1vy1frg9ng"; depends=[igraph]; }; + DBChIP = derive2 { name="DBChIP"; version="1.30.0"; sha256="1mr5s8j7zn3vbfrw50zd1x2z92x7j6cgn6qkcw8cccj81yivphkv"; depends=[DESeq edgeR]; }; + DChIPRep = derive2 { name="DChIPRep"; version="1.16.0"; sha256="0v1dy0d4yr3iyxasdi4rwhq7dfi44sif07ws4i04cha6yns1nays"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; }; + DECIPHER = derive2 { name="DECIPHER"; version="2.14.0"; sha256="04g6clqq0qgcb8c0i50qva6jc6dc9h9a3hlrdzwacbm75nk2lkbw"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; }; + DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.6.0"; sha256="1xarraz1gyhf7ik3fh4vsayi7qp21xdvqqp2fd5l86iy0541wxl7"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; }; + DEDS = derive2 { name="DEDS"; version="1.60.0"; sha256="0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"; depends=[]; }; + DEFormats = derive2 { name="DEFormats"; version="1.14.0"; sha256="06q341w9bvdkfysmpcx2k9qkxih1c0x7c6ynch1dck7c3x28gyvs"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; }; + DEGraph = derive2 { name="DEGraph"; version="1.38.0"; sha256="1ll3bc4q1rnfq8cn6ya97wcaz3bi7ajwvjsgqfwqgaj4nv2chnjc"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; }; + DEGreport = derive2 { name="DEGreport"; version="1.22.0"; sha256="0hjqj6v19h14ailszr4rgh56fi9hsgmc8p50mvcswqzdn3mjs7dv"; depends=[Biobase BiocGenerics broom circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr lasso2 logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; }; + DEGseq = derive2 { name="DEGseq"; version="1.40.0"; sha256="05rqkx1654k072wb2c04jiq99s81f0ipagwfklgdlicfxsm52fpb"; depends=[qvalue]; }; + DEP = derive2 { name="DEP"; version="1.8.0"; sha256="1xiwr5r6s3mri8birykl77i7q0nw96q1hfhajbij4nn0ca60xa0m"; depends=[assertthat circlize cluster ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; }; + DEScan2 = derive2 { name="DEScan2"; version="1.6.0"; sha256="0zmcmap3acbc618k6jb6sppglz4n7kbnlbbg26wblm9l0qk79xp9"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; }; + DESeq = derive2 { name="DESeq"; version="1.38.0"; sha256="14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; }; + DESeq2 = derive2 { name="DESeq2"; version="1.26.0"; sha256="1lmbhznfs8dz9ipd53z4ccwvwxqwzx1ayw56jlrvlsambaj8fash"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; }; + DEWSeq = derive2 { name="DEWSeq"; version="1.0.4"; sha256="0l6ll3kwdziihn36qrj92fl0s0ln2mjz4a82gy45k1ch4flhy05x"; depends=[BiocGenerics BiocParallel data_table DESeq2 GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment]; }; + DEXSeq = derive2 { name="DEXSeq"; version="1.32.0"; sha256="0sqqb65ckliif2nmvlvc7w49id59z0nvqcdz5gry8l2mn6azrf6a"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; }; + DEqMS = derive2 { name="DEqMS"; version="1.4.0"; sha256="195nnrfw97jr63j8vpil1axny55r6rk3aahsy93w01gm7fgri8im"; depends=[ggplot2 limma]; }; + DEsingle = derive2 { name="DEsingle"; version="1.6.0"; sha256="05ygzpb24swdxipkk5vp1y887xa7ndz113mfi9gxzhrr6y5cgfhq"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; + DEsubs = derive2 { name="DEsubs"; version="1.12.0"; sha256="13hfn8rxf42hz81cdmplki0pfz49685jhbzzw3inccxg2sllkg2j"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; }; + DFP = derive2 { name="DFP"; version="1.44.0"; sha256="0zsnw9nqgfldb378631lp13liyaxrjkhn09j2b6x8ihdf2ny419j"; depends=[Biobase]; }; + DMCFB = derive2 { name="DMCFB"; version="1.0.0"; sha256="0xy2q2wsj20xmbh6wbwy7yqp1zqa32xlga0imqscm0appgzm8z95"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; }; + DMCHMM = derive2 { name="DMCHMM"; version="1.8.0"; sha256="0gnp0jdmazv4imfgzkxc2zandajiaxj9g55brpfzf0b7ygxb5q6j"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; }; + DMRScan = derive2 { name="DMRScan"; version="1.11.0"; sha256="0vjhggyq0r8kab8ykl87js30l4zbavy224sg3in8fddakmijasaf"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; }; + DMRcaller = derive2 { name="DMRcaller"; version="1.18.0"; sha256="1l0675z5kyj8pijnr2iywja4vsi7ia380hwna12xyxxsrzz9kgn2"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; }; + DMRcate = derive2 { name="DMRcate"; version="2.0.7"; sha256="120z0wsx1aab6bjjgikl5kmxbz9lqwz6i7b631xdy5gag9m9c6vl"; depends=[bsseq DSS edgeR ExperimentHub GenomeInfoDb GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors SummarizedExperiment]; }; + DMRforPairs = derive2 { name="DMRforPairs"; version="1.22.0"; sha256="07714d3ky5igxqqfzn2i8n4ghri77d43kx6qrhkc9jb7k18cl8zd"; depends=[GenomicRanges Gviz R2HTML]; }; + DNABarcodeCompatibility = derive2 { name="DNABarcodeCompatibility"; version="1.2.0"; sha256="1ycda02mzcbr53jipj63zkp7kgg2dq7dbbc9yzb8r49xiz6i5fcd"; depends=[DNABarcodes dplyr numbers purrr stringr tidyr]; }; + DNABarcodes = derive2 { name="DNABarcodes"; version="1.16.0"; sha256="0r2r9qc2qvf7rfl1h5ynvv3xd7n444zbc697s85qxqdpr4sxqmfd"; depends=[BH Matrix Rcpp]; }; + DNAcopy = derive2 { name="DNAcopy"; version="1.60.0"; sha256="119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw"; depends=[]; }; + DNAshapeR = derive2 { name="DNAshapeR"; version="1.14.0"; sha256="1blvfzc1xx11017p12p5s2m26gspc4v2s5pr4i7xhixzvircknbi"; depends=[Biostrings fields GenomicRanges Rcpp]; }; + DOSE = derive2 { name="DOSE"; version="3.12.0"; sha256="0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2 S4Vectors]; }; + DRIMSeq = derive2 { name="DRIMSeq"; version="1.14.0"; sha256="1s0f4n78s4ry18x77qb2p02ks7g2wr95q9nfqd78f1ifidn0wq5k"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; }; + DSS = derive2 { name="DSS"; version="2.34.0"; sha256="1j0ywiri9srpp46043cdi02qsb7jijch274vr66fbdmmkkhx3p1k"; depends=[Biobase bsseq DelayedArray]; }; + DTA = derive2 { name="DTA"; version="2.32.0"; sha256="1qp8cn661xj8lzafqpgc1n4ddkrbfq74kirxpf53nhrr15wm5y7l"; depends=[LSD scatterplot3d]; }; + DaMiRseq = derive2 { name="DaMiRseq"; version="1.10.0"; sha256="0gghifpdkq323mgagqicvfc3pfpzh5n9f09gzpl1gc7jj4jpj6q8"; depends=[arm caret corrplot DESeq2 e1071 EDASeq edgeR FactoMineR FSelector ggplot2 Hmisc ineq kknn limma lubridate MASS pheatmap pls plsVarSel randomForest RColorBrewer reshape2 RSNNS SummarizedExperiment sva]; }; + DeMAND = derive2 { name="DeMAND"; version="1.16.0"; sha256="1c2ac14asgkxjwlh0657s2sp54sjxdk0ggc0wf5gc888fw0lyi6w"; depends=[KernSmooth]; }; + DeMixT = derive2 { name="DeMixT"; version="1.2.5"; sha256="0x6sw9c03blm4hraj44ijxjwizq7ms94q2038bsc67isfcl31vb5"; depends=[base64enc ggplot2 KernSmooth knitr matrixcalc matrixStats Rcpp SummarizedExperiment truncdist]; }; + DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.28.0"; sha256="00hcasjypi3ramb90b78h8pvnv11kian2cygvdhljnz8d41pq5x7"; depends=[ggplot2 limSolve pcaMethods]; }; + DeepBlueR = derive2 { name="DeepBlueR"; version="1.12.0"; sha256="06flk1l768zn42dhxjwklsgi8k7addskmg70d19ja80wwzksdixq"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; }; + DelayedArray = derive2 { name="DelayedArray"; version="0.12.2"; sha256="09lackgix5jpm16k0mz2zkibflfb4wzidbz4q32mlxmklf40037q"; depends=[BiocGenerics BiocParallel IRanges Matrix matrixStats S4Vectors]; }; + DelayedDataFrame = derive2 { name="DelayedDataFrame"; version="1.2.0"; sha256="05v3fj3krhc6ihb8jjlzxwdd3f1q5n97m13i02h9c8b6s00v4kbh"; depends=[BiocGenerics DelayedArray S4Vectors]; }; + DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.8.0"; sha256="0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy"; depends=[BiocParallel DelayedArray HDF5Array IRanges Matrix matrixStats S4Vectors]; }; + DepecheR = derive2 { name="DepecheR"; version="1.2.2"; sha256="199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm"; depends=[beanplot doSNOW dplyr FNN foreach ggplot2 gplots MASS matrixStats mixOmics moments Rcpp RcppEigen reshape2 robustbase viridis]; }; + DiffBind = derive2 { name="DiffBind"; version="2.14.0"; sha256="1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2"; depends=[amap BiocParallel DESeq2 dplyr edgeR GenomicAlignments GenomicRanges ggplot2 ggrepel gplots IRanges lattice limma locfit RColorBrewer Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment systemPipeR]; }; + DiffLogo = derive2 { name="DiffLogo"; version="2.10.0"; sha256="0nhj1v7z037ck72pyq2wg1rix7k5fl7qb8m9x2y7d4yz6vif95v8"; depends=[cba]; }; + Director = derive2 { name="Director"; version="1.12.0"; sha256="0cpqqdcr4103mixk00dr4bgbpydicgl1q44plrkc42aqjr62w8vb"; depends=[htmltools]; }; + DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.28.0"; sha256="0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s"; depends=[BiocGenerics IRanges S4Vectors]; }; + DiscoRhythm = derive2 { name="DiscoRhythm"; version="1.2.1"; sha256="0jih8cp69ql5wd6s7il8116in0prgbpafp8v3j7mcnbax0k55g46"; depends=[BiocGenerics BiocStyle broom data_table dplyr DT ggExtra ggplot2 gridExtra heatmaply kableExtra knitr magick matrixStats matrixTests MetaCycle plotly reshape2 rmarkdown S4Vectors shiny shinyBS shinycssloaders shinydashboard shinyjs SummarizedExperiment UpSetR VennDiagram viridis zip]; }; + DominoEffect = derive2 { name="DominoEffect"; version="1.6.0"; sha256="0a5m28asw4mkghgxr4rpyrj2b69hja6a31li29a803flwv5kkzgg"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; + Doscheda = derive2 { name="Doscheda"; version="1.8.1"; sha256="0skwb0dx1xyx4948wgps80l307z0rdh366fsn6vh4s90kff7asc3"; depends=[affy calibrate corrgram d3heatmap drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; }; + DriverNet = derive2 { name="DriverNet"; version="1.26.0"; sha256="1ah4ng7yw5as09gkk3qvvmsxc2v93qbg224rj7jf0mcjxn4gb8z7"; depends=[]; }; + DropletUtils = derive2 { name="DropletUtils"; version="1.6.1"; sha256="1kyx3ssvk49816m9s2pfwl654254y76256k8wz2wpn3q7shacvw7"; depends=[beachmat BH BiocParallel dqrng edgeR HDF5Array Matrix R_utils Rcpp rhdf5 Rhdf5lib S4Vectors SingleCellExperiment]; }; + DrugVsDisease = derive2 { name="DrugVsDisease"; version="2.28.0"; sha256="1h1gha2qxrr8ngzf0an5mm9w264rw8p57fxxcb01nramy0gfw0jm"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt cMap2data DrugVsDiseasedata GEOquery hgu133a_db hgu133a2_db hgu133plus2_db limma qvalue RUnit xtable]; }; + DupChecker = derive2 { name="DupChecker"; version="1.24.0"; sha256="0sqa8m1iiglw3p6d9pvy853p3nzz8krxq34wq5xcsx45gyswycdn"; depends=[R_utils RCurl]; }; + DynDoc = derive2 { name="DynDoc"; version="1.64.0"; sha256="1pii36icj5w6bwzlxnkl431wqjh30b69rmnahjsjld26999kr5lc"; depends=[]; }; + EBImage = derive2 { name="EBImage"; version="4.28.1"; sha256="0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs"; depends=[abind BiocGenerics fftwtools htmltools htmlwidgets jpeg locfit png RCurl tiff]; }; + EBSEA = derive2 { name="EBSEA"; version="1.14.0"; sha256="0jw7ka2ls5a2jzj18cdx7cpwxckpak1xlw36lqs5ny2pygv3ga5w"; depends=[edgeR limma plyr]; }; + EBSeq = derive2 { name="EBSeq"; version="1.26.0"; sha256="0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6"; depends=[blockmodeling gplots testthat]; }; + EBSeqHMM = derive2 { name="EBSeqHMM"; version="1.20.0"; sha256="00n5dlqdzhr01g06a5gffv8p5ii8wdzmh68jdwdr21magmv0psba"; depends=[EBSeq]; }; + EBarrays = derive2 { name="EBarrays"; version="2.50.0"; sha256="063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13"; depends=[Biobase cluster lattice]; }; + EBcoexpress = derive2 { name="EBcoexpress"; version="1.30.0"; sha256="0xjzwsd80qak606d85wjbgvib9zljpl2xjdj79d3fcvwl2ml1vgc"; depends=[EBarrays mclust minqa]; }; + EDASeq = derive2 { name="EDASeq"; version="2.20.0"; sha256="19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj"; depends=[AnnotationDbi aroma_light Biobase BiocGenerics BiocManager biomaRt Biostrings DESeq GenomicFeatures GenomicRanges IRanges Rsamtools ShortRead]; }; + EDDA = derive2 { name="EDDA"; version="1.24.0"; sha256="1pqxynm35dxsw22qb1pmx3vh5mp8s6jg2j2llq9xk37sahj0vgcm"; depends=[baySeq DESeq edgeR Rcpp ROCR snow]; }; + EGAD = derive2 { name="EGAD"; version="1.14.0"; sha256="09hnfvdh4mvhapkm8p3pvrnscw4d0kgq38bp6kkqf2vvcacll1rh"; depends=[affy arrayQualityMetrics Biobase GEOquery gplots igraph impute limma MASS Matrix plyr RColorBrewer RCurl zoo]; }; + EGSEA = derive2 { name="EGSEA"; version="1.14.0"; sha256="0srkfa6c5z5s3a4gvdvciycr5qd6m79mc50prxfpp9givxd96r3d"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; + ELBOW = derive2 { name="ELBOW"; version="1.22.0"; sha256="12nfivvbl9mb5m4vikwl8k72d5ijk7i460xm2q4dllrrxxngi8i6"; depends=[]; }; + ELMER = derive2 { name="ELMER"; version="2.10.0"; sha256="0bhm7f69sfiya4jk4sg8y75g7wb79cjyc0rjb9nlnyaipd7m8qg0"; depends=[biomaRt circlize ComplexHeatmap DelayedArray doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggpubr ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr progress purrr readr reshape rmarkdown rtracklayer rvest S4Vectors scales stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; }; + EMDomics = derive2 { name="EMDomics"; version="2.16.0"; sha256="0w808f1rs4d5ld7zds53wm7bvjj88iirhwsb3bqnm5g54mmzqykr"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; + ENCODExplorer = derive2 { name="ENCODExplorer"; version="2.12.1"; sha256="0brnlj89d6is0pbrwln1zhiiyprsggzr32xm38hxk9xsh8sl202v"; depends=[AnnotationHub data_table dplyr GenomeInfoDb GenomicRanges jsonlite RCurl rtracklayer S4Vectors stringi stringr tidyr]; }; + ENVISIONQuery = derive2 { name="ENVISIONQuery"; version="1.34.0"; sha256="1riv8l6afdqd986w77y6wi5h07awqf0x69q7g71qziag8hkbr8zm"; depends=[rJava XML]; }; + ENmix = derive2 { name="ENmix"; version="1.22.4"; sha256="157n7s3d60q2x1agj5344ig0iyc9d43qsq74sb51mml2imqjzawa"; depends=[AnnotationHub Biobase doParallel dynamicTreeCut ExperimentHub foreach genefilter geneplotter gplots illuminaio impute irr matrixStats minfi preprocessCore quadprog RPMM S4Vectors SummarizedExperiment]; }; + ERSSA = derive2 { name="ERSSA"; version="1.4.0"; sha256="0azj6zgxnf4bjn3n5zigfp0d4nq21zj63v85bjyq677nja3rwiim"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; + EasyqpcR = derive2 { name="EasyqpcR"; version="1.28.0"; sha256="0qjskwbj98iisadjli84y90isc2sxxw7bhvd6yknch5dq5ll7jp6"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; }; + EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.14.0"; sha256="1z9gj437z6z6afb1qpsbkvppai6rahp6rl1vhbs0zq8lqw8bvhb7"; depends=[]; }; + EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.4.0"; sha256="1vyrgj8yd69ji0anfyqfcrzds2w5scl0cg4bdfiild15wg95mkkh"; depends=[ggplot2 ggrepel]; }; + EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.16.0"; sha256="07bkn5a8j2d621qszdp5jsikg4s4qzfwri9ixscks5gsrb9346f8"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; + EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.16.1"; sha256="1c8w68ij9a8p8c4hf4abl51lbrav9zvllh4sifqz1r1lmxka2zrh"; depends=[AnnotationDbi BiocFileCache biocGraph BiocManager ComplexHeatmap edgeR geneplotter GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview rappdirs Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; }; + EpiDISH = derive2 { name="EpiDISH"; version="2.2.2"; sha256="110bcrkrl47h07i9wy11p0ip0lwd0kig5anbgrcvhpwy4rqqdfi2"; depends=[e1071 locfdr MASS matrixStats quadprog stringr]; }; + EventPointer = derive2 { name="EventPointer"; version="2.4.0"; sha256="1xn5r988ynddyaiik3g16pfnh665b8srrwq0jlq4v7hbszvnsh04"; depends=[affxparser Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg38 cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges graph igraph IRanges limma MASS Matrix matrixStats nnls prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment]; }; + ExCluster = derive2 { name="ExCluster"; version="1.4.0"; sha256="15acwm4jnmyqjf0arqh130yakz183pli710xjkzvci8a6k68k7x4"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; + ExiMiR = derive2 { name="ExiMiR"; version="2.28.0"; sha256="1xyvwlf14k9h7mp22h2jinw1qjpixsz5v3jsazhf5hrnkka1kah8"; depends=[affy affyio Biobase limma preprocessCore]; }; + ExperimentHub = derive2 { name="ExperimentHub"; version="1.12.0"; sha256="054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; }; + ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.12.0"; sha256="106jficagk6r3clhijjdb92awkndpz7f7n3iyj5bdmss7si5aay6"; depends=[AnnotationHubData BiocCheck BiocGenerics BiocManager biocViews curl DBI ExperimentHub graph httr S4Vectors]; }; + ExpressionAtlas = derive2 { name="ExpressionAtlas"; version="1.14.0"; sha256="14vqb2l5ra1v90r7ka02d0mir1vm9p6jxsvkgj2v87l7bszkirlb"; depends=[Biobase httr limma S4Vectors SummarizedExperiment XML xml2]; }; + ExpressionView = derive2 { name="ExpressionView"; version="1.38.0"; sha256="1qqcwwps4g2q69wb66m4kvabfd2cchwl4mmz0b67hff14w2bxyk0"; depends=[AnnotationDbi bitops caTools eisa GO_db isa2 KEGG_db]; }; + FCBF = derive2 { name="FCBF"; version="1.4.0"; sha256="1jy8k2cidnwjij3b89z36l4laz9fvixi50xw3xhikds8q522q7ij"; depends=[ggplot2 gridExtra mclust pbapply SummarizedExperiment]; }; + FELLA = derive2 { name="FELLA"; version="1.6.0"; sha256="0fknngg3mvb8yp9rw8bv1583iv32xms2fk694k7825k4zaw7zav0"; depends=[igraph KEGGREST Matrix plyr]; }; + FEM = derive2 { name="FEM"; version="3.14.0"; sha256="0r95q6b9sz9wkd9sq9xnzg0s2p1vn6p5vdh2f7z4cb8i14gavfcv"; depends=[AnnotationDbi BiocGenerics corrplot graph igraph impute limma marray Matrix org_Hs_eg_db]; }; + FGNet = derive2 { name="FGNet"; version="3.20.0"; sha256="0badapighhs9j281pr8g45yy8birsvkiqaclv1dakm9rrzd009cf"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; }; + FISHalyseR = derive2 { name="FISHalyseR"; version="1.20.0"; sha256="0wppdgxfnm96mh9mynvc1hj27cnnsdr5pdvrrl7z3yb45rzdcfmq"; depends=[abind EBImage]; }; + FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.22.0"; sha256="0ka4213mhi9xy4j1m1py45p62qy14rmr8dpgjbwpwpnp9xw3a91s"; depends=[fda MASS]; }; + FamAgg = derive2 { name="FamAgg"; version="1.14.0"; sha256="1pdgs23lrzn91lcy4kk9dmihsn7zk0q2fl6ii96ldq9hggd5vmnd"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; }; + FastqCleaner = derive2 { name="FastqCleaner"; version="1.4.0"; sha256="14shi7mjbl5239pf79sf4f81h7pqkm96sw50wfqiq05nsxzdq5wc"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; }; + FindMyFriends = derive2 { name="FindMyFriends"; version="1.16.0"; sha256="0h4map6xb1aasmmx0dxv452zzvcqpk481sbr64c8hwh203a4m1a7"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; }; + FitHiC = derive2 { name="FitHiC"; version="1.12.0"; sha256="1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc"; depends=[data_table fdrtool Rcpp]; }; + FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.18.0"; sha256="1kkpmnq2446sf8b9isy5vki39vgqmjaf2jh9h36d9xpxf0qfibmc"; depends=[jsonlite RCurl XML]; }; + FlowSOM = derive2 { name="FlowSOM"; version="1.18.0"; sha256="0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5"; depends=[BiocGenerics ConsensusClusterPlus CytoML flowCore flowWorkspace igraph RColorBrewer tsne XML]; }; + FoldGO = derive2 { name="FoldGO"; version="1.4.0"; sha256="0bi805g4q833rpxyxl7gi53cv2gddvl1bgi1j21651sbinapdh5c"; depends=[ggplot2 tidyr topGO]; }; + FourCSeq = derive2 { name="FourCSeq"; version="1.20.0"; sha256="0rnlgvxyi32g6nng8pkdsd13xy4x09lv6zg64m82m9s1zfaksclm"; depends=[Biobase Biostrings DESeq2 fda GenomicAlignments GenomicRanges ggbio ggplot2 gtools LSD Matrix reshape2 Rsamtools rtracklayer SummarizedExperiment]; }; + FunChIP = derive2 { name="FunChIP"; version="1.12.0"; sha256="092sisii6lf4pjsfsy9xnd87d6la4kh7cvwxcrqw89ir7a26igf8"; depends=[doParallel fda foreach GenomeInfoDb GenomicAlignments GenomicRanges RColorBrewer Rcpp Rsamtools shiny]; }; + FunciSNP = derive2 { name="FunciSNP"; version="1.30.0"; sha256="16m2acjhj2y60wbzk07gbzx78j9ryg5ygpn7d5zqn3p7agnrpxv2"; depends=[Biobase BiocGenerics ChIPpeakAnno FunciSNP_data GenomicRanges ggplot2 IRanges plyr reshape Rsamtools rtracklayer S4Vectors scales snpStats TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; + GA4GHclient = derive2 { name="GA4GHclient"; version="1.10.0"; sha256="1kr2nsqm50xhvvdgx5m9fnjk7c8w6rskqx6dn91ppxl858712h6a"; depends=[BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite S4Vectors VariantAnnotation]; }; + GA4GHshiny = derive2 { name="GA4GHshiny"; version="1.8.0"; sha256="11l3mv8a747yidzx656a6xsqhjcfcjkd5jbw9m1ns803r0mm1bhb"; depends=[AnnotationDbi BiocGenerics dplyr DT GA4GHclient GenomeInfoDb GenomicFeatures openxlsx purrr S4Vectors shiny shinyjs shinythemes tidyr]; }; + GAPGOM = derive2 { name="GAPGOM"; version="1.2.0"; sha256="17x14yjai6cs2gms2lf2kkw2yjzw3vd3bp03fg5qi7ysm6h88kmy"; depends=[AnnotationDbi Biobase BiocFileCache data_table dplyr fastmatch GEOquery GO_db GOSemSim graph igraph magrittr Matrix matrixStats org_Hs_eg_db org_Mm_eg_db plyr RBGL]; }; + GARS = derive2 { name="GARS"; version="1.6.0"; sha256="15j1vjldnmiv5kvf5lgf91h77z9i0dj0d5a171jynw3jnhs95fsa"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; }; + GAprediction = derive2 { name="GAprediction"; version="1.12.0"; sha256="0x44n8rqnmvszcjmwn1v2an2s21x7zg1yxvk9qppkpvc4k7zd5vp"; depends=[glmnet Matrix]; }; + GCSscore = derive2 { name="GCSscore"; version="1.0.0"; sha256="1jnd9h1cnp06lg34mcwqfhwcn47w3xi42q1m69qk6yg509vz2mdr"; depends=[affxparser AnnotationForge Biobase BiocManager data_table devtools dplR RSQLite stringr]; }; + GDCRNATools = derive2 { name="GDCRNATools"; version="1.6.0"; sha256="0109cwrdvh6nn6w3vcgk6z1nh30x9lwli21ydyqbp2rip1d4hrcn"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; + GDSArray = derive2 { name="GDSArray"; version="1.6.0"; sha256="1dc8lbwwxpxgyy6qn46hk3wcv9pa809rsg76ar9sjqv9hdvcp94l"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; + GEM = derive2 { name="GEM"; version="1.12.0"; sha256="0287m3ahc0s078vdqgynm8hnwvil75iyzj76803a52mlrrf7lizj"; depends=[ggplot2]; }; + GENESIS = derive2 { name="GENESIS"; version="2.16.1"; sha256="04zriqzzlvpqbw1jl7hnq9x7padbj7qvnxhvjsryx76yrfr0kzb0"; depends=[Biobase BiocGenerics data_table dplyr foreach gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; + GENIE3 = derive2 { name="GENIE3"; version="1.8.0"; sha256="0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l"; depends=[reshape2]; }; + GEOmetadb = derive2 { name="GEOmetadb"; version="1.48.0"; sha256="16c6l5m75x8iypw1lm4psj2hbhadfk5zgw1fs52infpnb82fhsv9"; depends=[GEOquery RSQLite]; }; + GEOquery = derive2 { name="GEOquery"; version="2.54.1"; sha256="0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; }; + GEOsubmission = derive2 { name="GEOsubmission"; version="1.38.0"; sha256="0fji7sli5jl0b4xf8wlrf064b47q49lfdnxhjf8pnph353ymg3yy"; depends=[affy Biobase]; }; + GEWIST = derive2 { name="GEWIST"; version="1.30.0"; sha256="1d3y0xfi8l10k5wv0r9ja5d4yf7kks3jpvahkf4hv75qdjjl96ch"; depends=[car]; }; + GGBase = derive2 { name="GGBase"; version="3.48.0"; sha256="0i5k1id5mh0m38xp8wy3c5lj7xmqwwqcrw7diiz1nkk66qs9mh8l"; depends=[AnnotationDbi Biobase BiocGenerics digest genefilter GenomicRanges IRanges limma Matrix S4Vectors snpStats SummarizedExperiment]; }; + GGtools = derive2 { name="GGtools"; version="5.22.0"; sha256="0axxmiwahvsdjpq07ic9r3q4zvnp08cqksn8xfn06r9862432dkl"; depends=[AnnotationDbi biglm Biobase BiocGenerics Biostrings bit data_table ff GenomeInfoDb GenomicRanges GGBase ggplot2 Gviz hexbin Homo_sapiens IRanges iterators reshape2 ROCR Rsamtools rtracklayer S4Vectors snpStats VariantAnnotation]; }; + GIGSEA = derive2 { name="GIGSEA"; version="1.4.0"; sha256="0z95v410bqpbamfkz74dg3pvlwf6azh1ryd3w92x7iqbwy6570ws"; depends=[locfdr MASS Matrix]; }; + GISPA = derive2 { name="GISPA"; version="1.10.0"; sha256="1j2va0jsgprys8w7a3qbr2sy50jdl5d5m17l9jmqmxz87s1v69x9"; depends=[Biobase changepoint data_table genefilter GSEABase HH lattice latticeExtra plyr scatterplot3d]; }; + GLAD = derive2 { name="GLAD"; version="2.50.0"; sha256="0p4gsy3kfhwdi0ddimswkw7yh2pgbkhcm3fnd77x3i35gm12v86l"; depends=[aws]; }; + GMRP = derive2 { name="GMRP"; version="1.14.0"; sha256="0ykvjdn809gg8l147sflma9g8sjd02l1d2zx7x7ajwc7zdzq1lxv"; depends=[diagram GenomicRanges plotrix]; }; + GNET2 = derive2 { name="GNET2"; version="1.2.0"; sha256="0ijwh22gy33nffs1iy82373ksmxk3gppzbv6kig85fj9ilvfcxxg"; depends=[DiagrammeR ggplot2 matrixStats Rcpp reshape2 SummarizedExperiment xgboost]; }; + GOFunction = derive2 { name="GOFunction"; version="1.34.0"; sha256="1ads9dnwhvdyys6dmscn9yp9fkm2lczqzwj4mb4llr0bv83lgvns"; depends=[AnnotationDbi Biobase DBI GO_db graph Rgraphviz SparseM]; }; + GOSemSim = derive2 { name="GOSemSim"; version="2.12.1"; sha256="1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05"; depends=[AnnotationDbi GO_db Rcpp]; }; + GOSim = derive2 { name="GOSim"; version="1.24.0"; sha256="1k38kzdpp43fdwqbhniq74cz096chp72qxv57v0bl3ca3dck9hfb"; depends=[annotate AnnotationDbi cluster corpcor flexmix GO_db graph Matrix org_Hs_eg_db RBGL Rcpp topGO]; }; + GOTHiC = derive2 { name="GOTHiC"; version="1.22.0"; sha256="0f2rylcc7d5m65ci9ia096wn4h92vn4f16aqikwagl4dy2w4s4y8"; depends=[BiocGenerics BiocManager Biostrings BSgenome data_table GenomeInfoDb GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors ShortRead]; }; + GOexpress = derive2 { name="GOexpress"; version="1.20.0"; sha256="1y0hs8zad74n8fwdgndf1vplv7dq208c4sv6p5q9xf16q9xhc252"; depends=[Biobase biomaRt ggplot2 gplots randomForest RColorBrewer RCurl stringr]; }; + GOfuncR = derive2 { name="GOfuncR"; version="1.6.1"; sha256="1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb"; depends=[AnnotationDbi GenomicRanges gtools IRanges mapplots Rcpp vioplot]; }; + GOpro = derive2 { name="GOpro"; version="1.12.0"; sha256="164fml5m9iclnwc7yb7jkr1kkd78pvmshfq8adz14xpcvhfvivm0"; depends=[AnnotationDbi BH dendextend doParallel foreach GO_db IRanges MultiAssayExperiment org_Hs_eg_db Rcpp S4Vectors]; }; + GOstats = derive2 { name="GOstats"; version="2.52.0"; sha256="19f4gxm3sbprqrnwzvskvywv6j4ibm8xkrbgg4h0fvh2b5331nwc"; depends=[annotate AnnotationDbi AnnotationForge Biobase Category GO_db graph RBGL Rgraphviz]; }; + GOsummaries = derive2 { name="GOsummaries"; version="2.22.0"; sha256="124qpsic8bqdqsz9mdrp12dmlvnjdl4bdqiyq2ld5b727xg8rq9z"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; }; + GRENITS = derive2 { name="GRENITS"; version="1.38.0"; sha256="17g3r1xxwpgl7xdb6w1gx4mlhpwz8n3qabslsknljspglwvaqkmk"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; }; + GRmetrics = derive2 { name="GRmetrics"; version="1.12.0"; sha256="06k5va2d5jzab7ay3glcp5anjdv19vhcarnc371jnwmv9qnljjb3"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; }; + GRridge = derive2 { name="GRridge"; version="1.10.0"; sha256="08nhv5fvqbdx5ahlsvhdijaasqf8548pxawl5b2jiv5jr0nzsbr0"; depends=[glmnet graph Iso mvtnorm penalized survival]; }; + GSALightning = derive2 { name="GSALightning"; version="1.14.0"; sha256="0vil7njz9mjrf2hhb9vmwl6hf1ca3ipwk2yhfpymbjg84cppvja0"; depends=[data_table Matrix]; }; + GSAR = derive2 { name="GSAR"; version="1.20.0"; sha256="16acza67i1sk8jxprkpk8wy2d915cma24q41fx3sn2p12zbkwjaf"; depends=[igraph]; }; + GSCA = derive2 { name="GSCA"; version="2.16.0"; sha256="125r1qa82p56d3cz7z9ml76625yjw8p05hi6y3c1d5ifg8i2ddbv"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; }; + GSEABase = derive2 { name="GSEABase"; version="1.48.0"; sha256="0kcb90sxlf19d5dxhdbqk9x62svky4262cccl0wxarbq6gf3bd57"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; }; + GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.6.4"; sha256="0cqdmnxb78rj1ml1wy5gdnswpfcsqb703wy9ibp13m54lanqw4c6"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO rappdirs S4Vectors SummarizedExperiment]; }; + GSEAlm = derive2 { name="GSEAlm"; version="1.46.0"; sha256="0yf3m0mzv70l8xv2njb7siay8pj1lygk2wq60j4jprk36wpdq000"; depends=[Biobase]; }; + GSRI = derive2 { name="GSRI"; version="2.34.0"; sha256="0zcp48jhn804l882w40kgik8lfc0ffpjwlcyszc8iqnchq7cv0hk"; depends=[Biobase fdrtool genefilter GSEABase les]; }; + GSReg = derive2 { name="GSReg"; version="1.20.0"; sha256="07dyp4m87im2bacsbmycfyx387gk85aqnm86m61zd610kk2y5yms"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; }; + GSVA = derive2 { name="GSVA"; version="1.34.0"; sha256="1lx5lpppidxcxh9i6sq2f639bkcygl4rycagfa01y8gqay0klxam"; depends=[Biobase BiocGenerics geneplotter GSEABase shiny shinythemes]; }; + GUIDEseq = derive2 { name="GUIDEseq"; version="1.16.0"; sha256="1iif5k2phxb0h6wslv9yjacdrdbwb10mg9babapbl96vssgzjqrz"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table GenomeInfoDb GenomicAlignments GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; }; + GWASTools = derive2 { name="GWASTools"; version="1.32.0"; sha256="0mivgzgmgyjazd5hl5hy04gz3rvf9fiwwzvpc0j8xynsvf7gxy79"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; }; + GateFinder = derive2 { name="GateFinder"; version="1.6.0"; sha256="1csgik1a22kg68aghari27si9g3rv46a0pad46ip9j2hb5gk02jn"; depends=[diptest flowCore flowFP mvoutlier splancs]; }; + GenRank = derive2 { name="GenRank"; version="1.14.0"; sha256="02sb6acfz9z4n4mzb8cwa6yna8p5c8f0y7b1fpzdqz2c9l2v392h"; depends=[matrixStats reshape2 survcomp]; }; + GenVisR = derive2 { name="GenVisR"; version="1.18.1"; sha256="0bjxvm1lzd0p076l3hgagnsrzdngkh9kh3pkqr8gq8vxrj8wx24l"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; }; + GeneAccord = derive2 { name="GeneAccord"; version="1.4.0"; sha256="0wz8ys89zxnjbys63xxmil6ny9qm02waqn55zizgr83pfz5139lj"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; }; + GeneAnswers = derive2 { name="GeneAnswers"; version="2.28.0"; sha256="1bzc2fdwr1c8rxxqqxcvysqa0amj226z9ji6rz21xizah045q35y"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; }; + GeneBreak = derive2 { name="GeneBreak"; version="1.16.0"; sha256="1jgp3b1w1fk4d9q4mmjc6iw60xs33n3x41mzzfjj9gdsjvckq126"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; }; + GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.32.0"; sha256="0gfqrcdd5s24axwmvrdjhmfb7jy0kyvf7mlffg71kryq17dc91wn"; depends=[Biobase PGSEA]; }; + GeneGA = derive2 { name="GeneGA"; version="1.36.0"; sha256="0bfc03p4v6nh2054v1h1vcx91j6hn5r7qipfkhvpmskdgbjh0yla"; depends=[hash seqinr]; }; + GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.12.0"; sha256="10d1nhq0kb9dzp0z4bda5128adfinp65qn8dwn7qyr9fc8r49s8c"; depends=[data_table FactoMineR GenomicRanges GGtools igraph IRanges kernlab mvtnorm plspm Rsamtools snpStats]; }; + GeneMeta = derive2 { name="GeneMeta"; version="1.58.0"; sha256="0iiyn5apv4dk1fs89b9xwhyxivc5gvc0ijh1pnq115abn1wb2b2k"; depends=[Biobase genefilter]; }; + GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.28.1"; sha256="1wxp86nqswz2h7h1wdy9kf9kl1l89c5vasv78rsnz1wn2rxbfzda"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; + GeneOverlap = derive2 { name="GeneOverlap"; version="1.22.0"; sha256="155jpv4r4xvkhsw9vrflmy8dyl7hvlki4dz8ccqzwhxxyz3id362"; depends=[gplots RColorBrewer]; }; + GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.42.0"; sha256="0wdrwks3qhiizf2iz4yq2f64jmbpzwlxkk3snwz893cafmnjw9g6"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; }; + GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.30.0"; sha256="1mplx4xlma7n4g1721l4ip9ynlw1f7479lpm57fb5aflmihjmlfn"; depends=[Biobase limma MASS survival]; }; + GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.6.0"; sha256="0bkc3pdbx42yj1jidppwy7mskghg31rg8m9vp2k87713vkd43gnk"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; }; + GeneticsDesign = derive2 { name="GeneticsDesign"; version="1.54.0"; sha256="0lb798m0dbip1v7ala4jdi2ls93p7nj7hv6mpxkwvk882kw8r3f6"; depends=[gmodels gtools mvtnorm]; }; + GeneticsPed = derive2 { name="GeneticsPed"; version="1.48.0"; sha256="14qwq9366ssglh13926ngm8a0jf6n2xcdsmbxrhynx0m3042rm8n"; depends=[gdata genetics MASS]; }; + GenoGAM = derive2 { name="GenoGAM"; version="2.4.0"; sha256="1bfxyyw7akg13mgxg8m4q5bqzyzd3a0sivc7hx9mhjfbl9fxmjsi"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; }; + GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.46.0"; sha256="05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"; depends=[biomaRt]; }; + GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.22.1"; sha256="0phadr67yb4l25x41a9wg4pjy1wbxlk14jhidhz6g5n4z6x45qbm"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; + GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.22.1"; sha256="065xvy4pkda0ajvl1b75iski95k1pnbhxwdq7vkfl8v55915vqh6"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; + GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.10.0"; sha256="1lz88gqdvmzppyinc1n3rs0ycx96fa8w8bmnndh25iyal111g4li"; depends=[dplyr GenomicRanges httr IRanges jsonlite magrittr rappdirs readr rlang S4Vectors SummarizedExperiment tibble xml2]; }; + GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.38.2"; sha256="0dd226kgks50jdx5w35f3wmg95hy8aibi4kcn8p5kmqp5i8j580b"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; + GenomicFiles = derive2 { name="GenomicFiles"; version="1.22.0"; sha256="1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; + GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.20.2"; sha256="0mqb899wah5n7bp2lajhwy2zpqqhi18plza3i3m51rfl9n62smph"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; + GenomicOZone = derive2 { name="GenomicOZone"; version="1.0.0"; sha256="08840yq6y2aclqad26pmd8kagicmbg0rr84h1f0x0pdcwlmaimps"; depends=[biomaRt Ckmeans_1d_dp GenomeInfoDb GenomicRanges ggbio ggplot2 gridExtra IRanges plyr Rdpack S4Vectors sjstats]; }; + GenomicRanges = derive2 { name="GenomicRanges"; version="1.38.0"; sha256="0xdds6ws7jjdfy4x3mb0qhy43kpxdmifmpw0jdk4wgw999zabb50"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; + GenomicScores = derive2 { name="GenomicScores"; version="1.10.0"; sha256="175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj"; depends=[AnnotationHub Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors XML]; }; + GenomicTuples = derive2 { name="GenomicTuples"; version="1.20.0"; sha256="02sglyvr6qhqazwxj6fq9w7g86f6q3nw2jmdni1wb3gdglxbbac2"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; + Genominator = derive2 { name="Genominator"; version="1.40.0"; sha256="15qh2j2s063rahf0z9hgn49pm83kdaj24ncc8gbyac3jn650xm7a"; depends=[BiocGenerics DBI GenomeGraphs IRanges RSQLite]; }; + GladiaTOX = derive2 { name="GladiaTOX"; version="1.2.0"; sha256="1g9ph1vq3hyck8f3i6c4939y0gr8mgcvc745mzqa5n8pnnv53fs9"; depends=[brew data_table DBI ggplot2 ggrepel numDeriv RColorBrewer RCurl RJSONIO RMySQL RSQLite stringr tidyr XML xtable]; }; + Glimma = derive2 { name="Glimma"; version="1.14.0"; sha256="1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r"; depends=[edgeR jsonlite S4Vectors]; }; + GlobalAncova = derive2 { name="GlobalAncova"; version="4.4.0"; sha256="0q9h6vzv8jix5k0jbmkzldkcipq33fszgx5nhrc9bhkfqjzk95dc"; depends=[annotate AnnotationDbi Biobase corpcor dendextend globaltest GSEABase VGAM]; }; + GmicR = derive2 { name="GmicR"; version="1.0.6"; sha256="0d1r99h9acqa9fgwmddmkql41fy8impabf2bg91fk0b37dsjch12"; depends=[AnnotationDbi ape bnlearn Category data_table DT GOstats gRain gRbase GSEABase org_Hs_eg_db org_Mm_eg_db reshape2 shiny WGCNA]; }; + GraphAT = derive2 { name="GraphAT"; version="1.58.0"; sha256="15mmg0hjnw6m147y5i43v76r1mixxb3xrszzq8x8zy15yna81012"; depends=[graph MCMCpack]; }; + GraphAlignment = derive2 { name="GraphAlignment"; version="1.50.0"; sha256="0gljds4ylkr39r79nxkxlhw1m36h05xkci1n54m65131ryjmprzd"; depends=[]; }; + GraphPAC = derive2 { name="GraphPAC"; version="1.28.0"; sha256="1aa7p9h55mvpa908d1jriiyf02das45cr1pib93pwcl6nw8jsgya"; depends=[igraph iPAC RMallow TSP]; }; + GreyListChIP = derive2 { name="GreyListChIP"; version="1.18.0"; sha256="126d5407k90ymph4vrrrgkfxhl4d9af2lmfk7szianrsglz58nnj"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; + Guitar = derive2 { name="Guitar"; version="2.2.0"; sha256="1avwad7mwncil6nlikks1ps3ivkphgab3kzc0y1l792z2c7qx14d"; depends=[AnnotationDbi dplyr GenomicFeatures GenomicRanges ggplot2 knitr magrittr rtracklayer]; }; + Gviz = derive2 { name="Gviz"; version="1.30.3"; sha256="0c9i26h5czm60n1bxzmdxxpywcj0sig6wcj913pb41mr83bbgra3"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; + HCABrowser = derive2 { name="HCABrowser"; version="1.2.0"; sha256="02yyl118abjzp1dk1bpb67rlrq4zd85nl8n4gi59mcrjiwj0q64i"; depends=[BiocFileCache curl dplyr googleAuthR httr jsonlite plyr readr rlang S4Vectors stringr tibble tidygraph tidyr]; }; + HCAExplorer = derive2 { name="HCAExplorer"; version="1.0.0"; sha256="0s0yxs6xic52zv0wl54rg8m55wl2b5inl1ci2f2rq87c7aqbjkf7"; depends=[curl dplyr httr jsonlite plyr rlang S4Vectors tibble tidygraph vctrs]; }; + HDF5Array = derive2 { name="HDF5Array"; version="1.14.3"; sha256="1z153a7nxmlml72pl1saasj2il9g5ahpynkpv3mkhhsvl5kbwbh6"; depends=[BiocGenerics DelayedArray IRanges Matrix rhdf5 Rhdf5lib S4Vectors]; }; + HDTD = derive2 { name="HDTD"; version="1.20.0"; sha256="1qxc2gjixsnrl1111x3jmkl8i78azjfq48igqrbz3b4p0261w7d0"; depends=[Rcpp RcppArmadillo]; }; + HELP = derive2 { name="HELP"; version="1.44.0"; sha256="1j7w7p6waym7qn6vsflf6dlwajbccfw7vhmpl7qzzgxb7aldl8pl"; depends=[Biobase]; }; + HEM = derive2 { name="HEM"; version="1.58.0"; sha256="1bq2a886rp7c28hd6gvk70xdl3fhrqaq73lp2xabxjd5ic7zwq2c"; depends=[Biobase]; }; + HIBAG = derive2 { name="HIBAG"; version="1.22.0"; sha256="1y7049ydj15g0qv5c1n6028cj8zgmvrj6c2g24xs6xy87600f98l"; depends=[]; }; + HIREewas = derive2 { name="HIREewas"; version="1.4.0"; sha256="0m39h8gkmdq6j0b24cbr9ppwbv4qpn729r9pdjkqzqg6k6fr0ph1"; depends=[gplots quadprog]; }; + HMMcopy = derive2 { name="HMMcopy"; version="1.28.1"; sha256="0byhd41f988y9g9383bm0kzl4ampsj7yrgi9wnjjd0am1sylr7sk"; depends=[data_table]; }; + HPAanalyze = derive2 { name="HPAanalyze"; version="1.4.3"; sha256="0xv6d3s5xzxbzw9wsm8xzdkm0l4jxrs7iq3j8bi4mlgqg5njir97"; depends=[dplyr ggplot2 gridExtra openxlsx tibble xml2]; }; + HTSFilter = derive2 { name="HTSFilter"; version="1.26.0"; sha256="14k70chzvkhzp0h5z24lsjrbcz4sa0k59hdv533zmq19hkmw17yq"; depends=[Biobase BiocParallel DESeq DESeq2 edgeR]; }; + HTSanalyzeR = derive2 { name="HTSanalyzeR"; version="2.38.0"; sha256="1dc6avr58g90bq1vyz0pf5llh3pii162f8db12vcsm9v9b1bk4i6"; depends=[AnnotationDbi biomaRt BioNet cellHTS2 graph GSEABase igraph RankProd]; }; + HTSeqGenie = derive2 { name="HTSeqGenie"; version="4.16.0"; sha256="1qadcjwsxc8s1wqw5jf2c5d1ndpnkm3j47ccyfk14qdsq57w807c"; depends=[BiocGenerics BiocParallel Biostrings Cairo chipseq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR hwriter IRanges Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment VariantAnnotation VariantTools]; }; + HTqPCR = derive2 { name="HTqPCR"; version="1.40.0"; sha256="008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx"; depends=[affy Biobase gplots limma RColorBrewer]; }; + Harman = derive2 { name="Harman"; version="1.14.0"; sha256="1bw08fal6v1pjwc5pqjjmwr6msml6w2ywsqvn1rj806v5dkj3h5s"; depends=[Rcpp]; }; + Harshlight = derive2 { name="Harshlight"; version="1.58.0"; sha256="1n7h4s7qawjw4awl8vidc1ynh08v1dkv0igpz1fz8jm2iwhxdxda"; depends=[affy altcdfenvs Biobase]; }; + Heatplus = derive2 { name="Heatplus"; version="2.32.1"; sha256="1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1"; depends=[RColorBrewer]; }; + HelloRanges = derive2 { name="HelloRanges"; version="1.12.0"; sha256="19s9jkjrca14wvska7zaf2i598lyifr3w9nfgfcnphxwz5f5hj9r"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; + HiCBricks = derive2 { name="HiCBricks"; version="1.4.0"; sha256="0aspirx1jl914nyxw9vwhd7v3n8yavsbv91nwb69hrg4k76iq3hp"; depends=[BiocParallel curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges jsonlite R_utils R6 RColorBrewer readr reshape2 rhdf5 S4Vectors scales stringr tibble viridis]; }; + HiCcompare = derive2 { name="HiCcompare"; version="1.8.0"; sha256="0lkzbxipcj2l3gybiqvpby3hvbqjb2mdpi7yi0k0adyf1cpablch"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq rhdf5 S4Vectors]; }; + HiLDA = derive2 { name="HiLDA"; version="1.0.0"; sha256="0c53ppqh1067kb7ma4hvz17fph3hba9ss5bf1fypmxhkjin3z7cb"; depends=[abind BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot forcats GenomicFeatures GenomicRanges ggplot2 R2jags Rcpp S4Vectors stringr tidyr TxDb_Hsapiens_UCSC_hg19_knownGene XVector]; }; + HiTC = derive2 { name="HiTC"; version="1.30.0"; sha256="0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; }; + HilbertCurve = derive2 { name="HilbertCurve"; version="1.16.0"; sha256="0i19lgqlp67554anfmvb15739y6vwdcmf79aj323y3rmwiis20cq"; depends=[circlize GenomicRanges HilbertVis IRanges png polylabelr]; }; + HilbertVis = derive2 { name="HilbertVis"; version="1.44.0"; sha256="0rh666h3542a2ly1nbfx4jqlq8ngp7vnazv472y80nfyj5fmaqar"; depends=[lattice]; }; + HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.44.0"; sha256="1lmf4chpf6di9dqbyqjqyb5f8dmhydb7kzxf58wly02hsm01rqin"; depends=[HilbertVis]; }; + HumanTranscriptomeCompendium = derive2 { name="HumanTranscriptomeCompendium"; version="1.2.0"; sha256="1fczd6qq2fvr202i3dadq43azljxxr7dgnhc8drd9cxi6krr7wjp"; depends=[S4Vectors shiny ssrch SummarizedExperiment]; }; + HybridMTest = derive2 { name="HybridMTest"; version="1.30.0"; sha256="069kvinqmrbdm2igj1a7gr30z9d7i9mx4d52d4fm3lvaf9i28r1l"; depends=[Biobase fdrtool MASS survival]; }; + IHW = derive2 { name="IHW"; version="1.14.0"; sha256="0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; + IMAS = derive2 { name="IMAS"; version="1.10.0"; sha256="05z0ib5p9f690mr2dhsywbkyf2sh5wjkf2f04z036y41d35gxpwm"; depends=[AnnotationDbi BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfortify ggplot2 gridExtra IRanges IVAS lattice lme4 Matrix Rsamtools S4Vectors survival]; }; + IMMAN = derive2 { name="IMMAN"; version="1.6.0"; sha256="1xrp67a9v6k13x86zf4lhx6gwnvf8cm9bw64ihkjsnliwi12ic66"; depends=[Biostrings igraph seqinr STRINGdb]; }; + IMPCdata = derive2 { name="IMPCdata"; version="1.22.0"; sha256="0lvi2rfwp6d67mj5y20plkdwf0xigqh8pkadjprqrsi9972vgc1y"; depends=[rjson]; }; + INDEED = derive2 { name="INDEED"; version="2.0.0"; sha256="0a84785jg223mfyhcghby5ayi7k4smn952imzk084jgjrzn7dm4r"; depends=[devtools glasso igraph visNetwork]; }; + INPower = derive2 { name="INPower"; version="1.22.0"; sha256="1ffprh2x5yg8zlx8w0xsr8ip2yj0x8d9rkjg7ki4k485cxd41y2q"; depends=[mvtnorm]; }; + INSPEcT = derive2 { name="INSPEcT"; version="1.16.3"; sha256="0y4gpvrbmcipdnyz9lz9ywn0317xnpcriiisqvxygin05vgcpilp"; depends=[Biobase BiocGenerics BiocParallel DESeq2 deSolve gdata GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges KernSmooth plgem pROC rootSolve Rsamtools S4Vectors shiny SummarizedExperiment TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + IONiseR = derive2 { name="IONiseR"; version="2.10.0"; sha256="1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; }; + IPO = derive2 { name="IPO"; version="1.12.0"; sha256="11fk095mcd0gm3yjli97x5srza9x7syi9rbv8b1cmwdyapmzjrjj"; depends=[BiocParallel CAMERA rsm xcms]; }; + IPPD = derive2 { name="IPPD"; version="1.34.0"; sha256="1xghzsxdh9ms552av1sxg2c7hv32p8xil7yyw29m8bblircag82s"; depends=[bitops digest MASS Matrix XML]; }; + IRanges = derive2 { name="IRanges"; version="2.20.2"; sha256="1jhnxb9yacmj2z82b6992gihjvj1a0gnjwbjiagyyx03fqnv23kg"; depends=[BiocGenerics S4Vectors]; }; + ISoLDE = derive2 { name="ISoLDE"; version="1.14.0"; sha256="177cbz3wqs7jsc2gcj3ncajnp8cvd9krk0d31r0wp8mcx6kqbx1x"; depends=[]; }; + ITALICS = derive2 { name="ITALICS"; version="2.46.0"; sha256="1qib7ka8ynz6chr36vjy5lbwklb5v28a92ibawwgwrb2wxrqkmg4"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; }; + IVAS = derive2 { name="IVAS"; version="2.6.0"; sha256="02fpqjbsb6d1fzvsrcfwkwwnb1fg78nfqsb2wgiakd6i7rc3sihf"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; }; + IWTomics = derive2 { name="IWTomics"; version="1.10.0"; sha256="10rsjjrkmf6czbpa7w69smf0nmml36c5dczzlvlmhx71ya1dhj89"; depends=[fda GenomicRanges gtable IRanges KernSmooth S4Vectors]; }; + Icens = derive2 { name="Icens"; version="1.58.0"; sha256="0jfz8w0xk4a4q6h2fwd862z48saky3cp387hvdy883b92w1kw9wi"; depends=[survival]; }; + IdMappingAnalysis = derive2 { name="IdMappingAnalysis"; version="1.30.0"; sha256="1pp834kwfv3vgxm4ph7xzzr8hpc3hs80l6bjda6vmmmv4w2avvmc"; depends=[Biobase boot mclust R_oo rChoiceDialogs RColorBrewer]; }; + IdMappingRetrieval = derive2 { name="IdMappingRetrieval"; version="1.34.0"; sha256="0d32a5a4m74bqj78gjifnab2j3dxxy4yhix8idzw5hjz22qngwgl"; depends=[AffyCompatible biomaRt ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; }; + IdeoViz = derive2 { name="IdeoViz"; version="1.22.0"; sha256="0rsz6dawrx5qdrypxs2hgihmx3kbpdg1y73h876yxccgdlabvzil"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; }; + IgGeneUsage = derive2 { name="IgGeneUsage"; version="1.0.0"; sha256="11kdh6a9zs2qqyz7x7w2kd9fdpaa889dnr69wyvhnpbjb16gjvkd"; depends=[Rcpp reshape2 rstan StanHeaders SummarizedExperiment]; }; + Imetagene = derive2 { name="Imetagene"; version="1.16.0"; sha256="1nig0cn8rwh47d2yrlv9k2zz38qmaly4jwrbpjahjlyxgm3j5hq6"; depends=[d3heatmap ggplot2 metagene shiny shinyBS shinyFiles shinythemes]; }; + ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.14.1"; sha256="0lzhx3c62rx4grgpqy5z0jxalj2rinkqksq72aflxaivvx72pb04"; depends=[Biobase curl data_table digest flowCore flowWorkspace ggplot2 gplots heatmaply httr jsonlite pheatmap plotly preprocessCore R6 Rlabkey rmarkdown scales]; }; + ImpulseDE = derive2 { name="ImpulseDE"; version="1.12.0"; sha256="05zbx99bmfvfpig5srrz9v4nx4aii8vcc1rywm9wjc6lkg4lfzpw"; depends=[amap boot]; }; + ImpulseDE2 = derive2 { name="ImpulseDE2"; version="1.10.0"; sha256="1j6aajiccmm77zmdfcsni9qahdyccg6sj6f8vnfhigy5fy4vyxdd"; depends=[Biobase BiocParallel circlize ComplexHeatmap cowplot DESeq2 ggplot2 knitr Matrix S4Vectors SummarizedExperiment]; }; + InPAS = derive2 { name="InPAS"; version="1.18.0"; sha256="148mgbywhbddvb704malij4zspr24f1rjbk2rxpq2v2s7058lmd5"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; }; + InTAD = derive2 { name="InTAD"; version="1.6.0"; sha256="040jqdwbyf3mz4nkaqcnc72zmyj3vs6k404ld6ljink0gzysldi1"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggpubr IRanges mclust MultiAssayExperiment qvalue rtracklayer S4Vectors SummarizedExperiment]; }; + IntEREst = derive2 { name="IntEREst"; version="1.10.2"; sha256="1j3zmqqpgfp4j463l5imggqzhrl7484cfyk7irlm16iwxxrlwz5h"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; }; + InterMineR = derive2 { name="InterMineR"; version="1.8.1"; sha256="1ryja9f1ds10f5lrc00lkad7lnixg2dy1imrh0d21j1wq1lfy1j6"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; }; + InteractionSet = derive2 { name="InteractionSet"; version="1.14.0"; sha256="0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; }; + IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.8.0"; sha256="1lq8v8zbjigm5k9r1l6d87wm83asnq4wm3s1bwprdfaqlk6cq6wx"; depends=[FGNet igraph knitr]; }; + IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="1.4.1"; sha256="1lyagc0v0c1n7b8fqn9lagzb61b9gsjs219a487xlsqcqgyhssnk"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; }; + IsoCorrectoRGUI = derive2 { name="IsoCorrectoRGUI"; version="1.2.0"; sha256="1h1h5s83f8hs01wzh0fqvwvr1i300w1q9ncqvys9vlx7bz8l3b9p"; depends=[IsoCorrectoR readxl tcltk2]; }; + IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.22.0"; sha256="1hckxl6g26z94nqvxxrxnirgczqd9lhm9smkqmag7mwjvvsyg63b"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; }; + IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.8.0"; sha256="0dsss8qvy7hf75krcd7vgpvfzz3jbzfkl8z5lznsxl760kmwa5b5"; depends=[Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer readr reshape2 rtracklayer stringr tximport VennDiagram XVector]; }; + JunctionSeq = derive2 { name="JunctionSeq"; version="1.16.0"; sha256="0nsyql5bq4g5995kya71bh0v29v1lgbi3l0lyscbm6mcax4hajs4"; depends=[Biobase BiocGenerics BiocParallel DESeq2 genefilter geneplotter GenomicRanges Hmisc IRanges locfit plotrix Rcpp RcppArmadillo S4Vectors statmod stringr SummarizedExperiment]; }; + KCsmart = derive2 { name="KCsmart"; version="2.44.0"; sha256="0k8xkbxy7nxnn07wbsdzfad4vdjbgx72qlml8cf7vb2223hd9qr7"; depends=[BiocGenerics KernSmooth multtest siggenes]; }; + KEGGREST = derive2 { name="KEGGREST"; version="1.26.1"; sha256="1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247"; depends=[Biostrings httr png]; }; + KEGGgraph = derive2 { name="KEGGgraph"; version="1.46.0"; sha256="18jvy5lh5r2ikjsvzgv35wxqgbqpq0z5yphv863danlcmdb36gdr"; depends=[graph RCurl XML]; }; + KEGGlincs = derive2 { name="KEGGlincs"; version="1.12.0"; sha256="0ybgm4zcsqsx7paljcbw93qj7arcb9ndzr4rcvaimgjlh60nbngq"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; }; + KEGGprofile = derive2 { name="KEGGprofile"; version="1.28.0"; sha256="1ci4mdcm3pk7v7bhslqwkydwc935mkx296q7a9sz3nwyndr1z2vi"; depends=[AnnotationDbi biomaRt ggplot2 KEGG_db KEGGREST png RCurl reshape2 TeachingDemos XML]; }; + KinSwingR = derive2 { name="KinSwingR"; version="1.4.0"; sha256="1ak2yqrdzkam069361chj7v2bxzhb9ry7m0cfp95jlfhlmr2j34z"; depends=[BiocParallel data_table sqldf]; }; + KnowSeq = derive2 { name="KnowSeq"; version="1.0.0"; sha256="0ms5d5cf4va13jzg42zjy99i6i6lni418b87ja3264lmxl9r2lnc"; depends=[arrayQualityMetrics Biobase biomaRt caret class cqn e1071 edgeR factoextra ggplot2 gplots httr jsonlite kernlab limma mclust multtest pathview praznik quantreg R_utils randomForest RCurl reshape2 rhdf5 stringr sva topGO tximport tximportData XML]; }; + LBE = derive2 { name="LBE"; version="1.54.0"; sha256="0dx43mig5y3dcr2fpvi86rigbh1nxk9a6b2p36fgzfnq6l3dbcha"; depends=[]; }; + LEA = derive2 { name="LEA"; version="2.8.0"; sha256="16fc2b58nggdwvpipzaa2w80g08ka4iahsyjn8ahhmxmxfand0w9"; depends=[]; }; + LINC = derive2 { name="LINC"; version="1.14.0"; sha256="07ffywm538h8m8gyhm25vcmw3xkrxzqhxzsggb9x6ica2zij8k3k"; depends=[ape Biobase clusterProfiler DOSE ggplot2 ggtree gridExtra org_Hs_eg_db png Rcpp ReactomePA reshape2 sva]; }; + LMGene = derive2 { name="LMGene"; version="2.42.0"; sha256="133mzbppywsqkyxkfadcyglg8s3ilkcqhkc7gih2jjiwcxx106dh"; depends=[affy Biobase multtest survival]; }; + LOBSTAHS = derive2 { name="LOBSTAHS"; version="1.12.0"; sha256="1m4y5d1vm8954k16d64kv0v0nz99lgay5fg220x4vj506s91jgy6"; depends=[CAMERA xcms]; }; + LOLA = derive2 { name="LOLA"; version="1.16.0"; sha256="1py2373fkk9mksxl8d48ifczbgpg33ky2npid45wwdkw3mf9zq3a"; depends=[BiocGenerics data_table GenomicRanges IRanges reshape2 S4Vectors]; }; + LPE = derive2 { name="LPE"; version="1.60.0"; sha256="0m26b72nqgac6fzxsxwl8r64qzang06crv5nzr1dmiyvv85d6q8j"; depends=[]; }; + LPEadj = derive2 { name="LPEadj"; version="1.46.0"; sha256="1rpp0g0xafakilgkwfkr9w6zm2hlyx2bnmwrxnidrqvs1z7zc8qr"; depends=[LPE]; }; + LRBaseDbi = derive2 { name="LRBaseDbi"; version="1.4.0"; sha256="1hjl0lpsy7zlncvlr8q09jwpaw9iszndx12ag6ii3wcjlhdlbd9s"; depends=[AnnotationDbi Biobase DBI RSQLite]; }; + LVSmiRNA = derive2 { name="LVSmiRNA"; version="1.36.0"; sha256="0rilrapn432cxybb6jssan6dbn7qfb8b5c5fvn6chm4kmn2hjhdl"; depends=[affy Biobase BiocGenerics limma MASS quantreg SparseM vsn zlibbioc]; }; + LedPred = derive2 { name="LedPred"; version="1.20.0"; sha256="1f53v8aw0ys178kvbsa0cd3kys4271m93dxyk73c2345mv87f8bl"; depends=[akima e1071 ggplot2 irr jsonlite plot3D plyr RCurl ROCR testthat]; }; + LineagePulse = derive2 { name="LineagePulse"; version="1.6.0"; sha256="0m88bkys9vpq7k4qypm70mw5jfb0qvigbm5k9i6ca62xlx3rjxsv"; depends=[BiocParallel circlize ComplexHeatmap ggplot2 gplots knitr Matrix RColorBrewer SingleCellExperiment SummarizedExperiment]; }; + LinkHD = derive2 { name="LinkHD"; version="1.0.0"; sha256="0yym2pxpzarpnfi5gmg99cxdkhq5gg5h6wqzqnvyd1rbgr63rh83"; depends=[cluster data_table emmeans ggplot2 ggpubr gridExtra MultiAssayExperiment reshape2 rio scales vegan]; }; + Linnorm = derive2 { name="Linnorm"; version="2.10.0"; sha256="15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67"; depends=[amap apcluster ellipse fastcluster fpc ggdendro ggplot2 gmodels igraph limma MASS mclust Rcpp RcppArmadillo Rtsne statmod vegan zoo]; }; + LiquidAssociation = derive2 { name="LiquidAssociation"; version="1.40.0"; sha256="13spdphpf3ffk20ds4yrq50wrpiwz9bn2wp9lhrsvx5a5l8cpxag"; depends=[Biobase geepack org_Sc_sgd_db yeastCC]; }; + Logolas = derive2 { name="Logolas"; version="1.10.0"; sha256="0pmpvncbh60xg07a945axv3fnff5djlvvxbx69723hbxp14vkyxh"; depends=[Biostrings ggplot2 gridBase LaplacesDemon SQUAREM]; }; + LoomExperiment = derive2 { name="LoomExperiment"; version="1.4.0"; sha256="0m9y5i9dwm53vwwyxqbmhrp7rga8fhsl2b39g4almmmwg0m4xdp7"; depends=[DelayedArray GenomicRanges HDF5Array Matrix rhdf5 rtracklayer S4Vectors SingleCellExperiment stringr SummarizedExperiment]; }; + LowMACA = derive2 { name="LowMACA"; version="1.16.0"; sha256="0qp6x72yfiqz20frzww33rg34da5x7q4n6b9mvpz5nrmd10cknh4"; depends=[BiocParallel Biostrings cgdsr data_table gridBase httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; }; + LymphoSeq = derive2 { name="LymphoSeq"; version="1.14.0"; sha256="02v9si759hr54vp8dwh529qx5slx0q7gn2sidc7slp91fpma1bfz"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; }; + M3C = derive2 { name="M3C"; version="1.8.0"; sha256="10lpqv4z58s5dlinlhv51mjg3rc0sdv8jpiy6y0vxs2h15j4xgp8"; depends=[cluster corpcor dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust survival umap]; }; + M3D = derive2 { name="M3D"; version="1.20.0"; sha256="0q4aq98cwp6b8mzkjk4iwvllw1d67hm7zvqaf4rb7vb5dpx7yjaj"; depends=[BiocGenerics BiSeq GenomicRanges IRanges Rcpp S4Vectors SummarizedExperiment]; }; + M3Drop = derive2 { name="M3Drop"; version="1.12.0"; sha256="1r49r82gbk7gp0gkp0xh6zk1agh88qj8hkjsrr8jwm8rmihc47r5"; depends=[bbmle gplots Hmisc irlba Matrix matrixStats numDeriv RColorBrewer reldist statmod]; }; + MACPET = derive2 { name="MACPET"; version="1.6.0"; sha256="0zzv6l2arij6xwldwxa209jcyyf1ygwp5a4r1y3h5b3zn76hjs9c"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; }; + MACSQuantifyR = derive2 { name="MACSQuantifyR"; version="1.0.0"; sha256="07czlj54n16fpppqnx8sq2bc68207lvm4lman5k1dm9y2dniyy5l"; depends=[ggplot2 ggrepel gridExtra lattice latticeExtra png prettydoc readxl rmarkdown rvest xml2]; }; + MADSEQ = derive2 { name="MADSEQ"; version="1.12.0"; sha256="0zj3h29l2ay5dhg63hfgjjfbs6v4s9rwz4zar5jgf94ml5kxcky7"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; }; + MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.6.4"; sha256="17i9w335j2jpfwacbincckig1glhyyqii5rhvwrhrryaj3cdss1m"; depends=[Biobase biomaRt clusterProfiler data_table dendextend DOSE enrichplot ggplot2 ggpubr ggrepel ggsci graph gridExtra KEGGgraph KEGGREST msigdbr pathview pheatmap png scales sva XML]; }; + MAIT = derive2 { name="MAIT"; version="1.20.0"; sha256="1iybkaf18xd3598vyz6gjknfrxf4x8h0l6k2gixy8pgdlbcyfv40"; depends=[agricolae CAMERA caret class e1071 gplots MASS pls plsgenomics Rcpp xcms]; }; + MANOR = derive2 { name="MANOR"; version="1.58.0"; sha256="1iyrvdzdcn1530grsfjvckzplnw65vf3z0x27nj2gdqf6akflws0"; depends=[GLAD]; }; + MAST = derive2 { name="MAST"; version="1.12.0"; sha256="1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga"; depends=[abind Biobase BiocGenerics data_table ggplot2 plyr progress reshape2 S4Vectors SingleCellExperiment stringr SummarizedExperiment]; }; + MBASED = derive2 { name="MBASED"; version="1.20.0"; sha256="1w9pc93m5z9smwcxl9pxyjr37y6h94jnb5wx2xmxjika1q9czj0a"; depends=[BiocGenerics BiocParallel GenomicRanges RUnit SummarizedExperiment]; }; + MBAmethyl = derive2 { name="MBAmethyl"; version="1.20.0"; sha256="0dmiahz6m2y429dzsnv0a7bvb9ngllqgmws457in3crq85qq2swp"; depends=[]; }; + MBCB = derive2 { name="MBCB"; version="1.40.0"; sha256="1q7sg5anvdfhd0ya93ifbgnmpgapysn9dbfh40pvv2vymqv39vzg"; depends=[preprocessCore tcltk2]; }; + MBQN = derive2 { name="MBQN"; version="1.0.1"; sha256="1bpxdary7w99r0j2dya4apr5hffy4znji2vbpp0h4yj5gz6xpwia"; depends=[BiocFileCache ggplot2 limma PairedData preprocessCore rappdirs RCurl reshape2 rpx SummarizedExperiment xml2]; }; + MBttest = derive2 { name="MBttest"; version="1.14.0"; sha256="1nfmnc0hwmggi1m10zykhxvdlzmy7fy0lqp9z3snkcmp1n2m6ar2"; depends=[gplots gtools]; }; + MCRestimate = derive2 { name="MCRestimate"; version="2.42.0"; sha256="1d4ahbzq3qpjldyh0w7siqwmghmylak8jjlhrc619y5vd47nijfh"; depends=[Biobase e1071 golubEsets pamr randomForest RColorBrewer]; }; + MCbiclust = derive2 { name="MCbiclust"; version="1.10.0"; sha256="1kyq4ccx1dzl0nld23ippis2x1ds1sj23h2y25h1m04jcw40bsyd"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; }; + MDTS = derive2 { name="MDTS"; version="1.6.0"; sha256="1zzvk5ql4k29aizv52i29zxcpvyzacb4jy1vh11dd4qwrqazvdyv"; depends=[Biostrings DNAcopy GenomicAlignments GenomicRanges IRanges Rsamtools stringr]; }; + MEAL = derive2 { name="MEAL"; version="1.16.0"; sha256="1892wd53h3jh0m11frlv95fn8xxdbwr2wnklgmnfdyd9xyfsmrwr"; depends=[Biobase BiocGenerics DMRcate GenomicRanges ggplot2 Gviz IRanges isva limma matrixStats minfi missMethyl MultiDataSet permute S4Vectors SmartSVA SummarizedExperiment vegan]; }; + MEB = derive2 { name="MEB"; version="1.0.0"; sha256="0x0pbgnbr48g40rf5rv1c8yws1knmfmfyzjh3vh7kb7a1hjdqjc9"; depends=[e1071 SummarizedExperiment]; }; + MEDIPS = derive2 { name="MEDIPS"; version="1.38.0"; sha256="152sakww2q0dpyarh8x3nkgyv7a291cyz758qajv70d6b6izqndy"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; }; + MEDME = derive2 { name="MEDME"; version="1.46.0"; sha256="19daafnhkivwgn4yv1k8cnsgn94fny22mi7n4q3q9i0qrpf2k4qq"; depends=[Biostrings drc MASS]; }; + MEIGOR = derive2 { name="MEIGOR"; version="1.20.0"; sha256="0mwcyln9sqfg7ldl7brgn62qj9dd2l5068wrm39lrnrvaivziv0r"; depends=[CNORode deSolve Rsolnp snowfall]; }; + MGFM = derive2 { name="MGFM"; version="1.20.0"; sha256="0jlyv58nzniya12axm4fm9g66dhxznh2274k6bma57whr2in6sv5"; depends=[annotate AnnotationDbi]; }; + MGFR = derive2 { name="MGFR"; version="1.12.0"; sha256="16zxwxcvg0sgwvabv125z4w6b2pwlngz5dh35cymgp511acwbvf4"; depends=[annotate biomaRt]; }; + MIGSA = derive2 { name="MIGSA"; version="1.10.1"; sha256="07y9cldgywngabnsmgn4k22rpksy8i6a1d3iw3ma21zycvknnah2"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; }; + MIMOSA = derive2 { name="MIMOSA"; version="1.24.0"; sha256="1xd65i046y3r3la0fv0ynvflq7n1rd5y03f53q0789m54hkm1fly"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; }; + MIRA = derive2 { name="MIRA"; version="1.8.0"; sha256="1r08x4d96sf8zj2xyfx9lrh5lrixmq0w1yaj78jp6mvlfzbxrm0h"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; }; + MLInterfaces = derive2 { name="MLInterfaces"; version="1.66.5"; sha256="05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rpart sfsmisc shiny threejs]; }; + MLP = derive2 { name="MLP"; version="1.34.0"; sha256="1plnp99bgjrk7691w4x8xzw7bxkv1d36xzign6ikz6c28c1gjghm"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; }; + MLSeq = derive2 { name="MLSeq"; version="2.4.0"; sha256="0cxmz06c1f62z70pcc5zsf3yhig2z0sw0ss8djsh33n868z40z7c"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; }; + MMAPPR2 = derive2 { name="MMAPPR2"; version="1.0.0"; sha256="0504pmknk6rh8r1b531m19ki8wknbgy0fihgc861dfy4p85bnn2d"; depends=[Biobase BiocGenerics BiocParallel data_table dplyr ensemblVEP GenomeInfoDb GenomicRanges gmapR IRanges magrittr Rsamtools S4Vectors stringr tidyr VariantAnnotation VariantTools]; }; + MMDiff2 = derive2 { name="MMDiff2"; version="1.14.0"; sha256="0586p4z30f6z58l4zk295wn4qwjl5qg9jr8vs1dzrbkwc5hppf0m"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; }; + MMUPHin = derive2 { name="MMUPHin"; version="1.0.0"; sha256="15ysglr1prf298qlm0yj5k5j68zd71iifqmg6n9qyn97mzl3b01b"; depends=[cowplot dplyr fpc ggplot2 igraph Maaslin2 metafor tidyr]; }; + MODA = derive2 { name="MODA"; version="1.12.0"; sha256="07ayd43avgibr3nbrphkmsdammmdmayk6krs9l70qzljnbgj97g2"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; }; + MOFA = derive2 { name="MOFA"; version="1.2.0"; sha256="04vrp406skx1kw4c1b40fnq24b3iafphhrgyvxq9g35hij85amh2"; depends=[Biobase corrplot cowplot doParallel dplyr foreach GGally ggbeeswarm ggplot2 ggrepel MultiAssayExperiment pheatmap RColorBrewer reshape2 reticulate rhdf5 scales]; }; + MOSim = derive2 { name="MOSim"; version="1.0.2"; sha256="0j6vyz9wwpzp1iq8f1406qf19vfkh7m4rj2qsl2dzz2j3zmcyfmh"; depends=[Biobase dplyr ggplot2 HiddenMarkov IRanges lazyeval matrixStats purrr rlang S4Vectors scales stringi stringr tibble tidyr zoo]; }; + MPFE = derive2 { name="MPFE"; version="1.22.0"; sha256="1pyifclijm3lf50580hw3ykpns3344zfg2bsva42dvyaca1yb7mf"; depends=[]; }; + MPRAnalyze = derive2 { name="MPRAnalyze"; version="1.4.0"; sha256="08wh7h27a50y96jg9z90f7fkq56hmdx2s64z1blqygjndx5kv76h"; depends=[BiocParallel progress SummarizedExperiment]; }; + MSGFgui = derive2 { name="MSGFgui"; version="1.20.0"; sha256="18xv8ivgzjbyafhlf9jf57j62lg79h6c1idgc9ncw4nn4nfxczra"; depends=[MSGFplus mzID mzR shiny shinyFiles xlsx]; }; + MSGFplus = derive2 { name="MSGFplus"; version="1.20.0"; sha256="0vy6aylpkd47s4p5c2xl9gfrx25cgh2dbrq2rqb9cyfl51v4r8jd"; depends=[mzID ProtGenerics]; }; + MSnID = derive2 { name="MSnID"; version="1.20.0"; sha256="0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; }; + MSnbase = derive2 { name="MSnbase"; version="2.12.0"; sha256="1z889xkfphqqmv31i8hh5xqyclv660ic26rfck5bjpgk3s2zzwi6"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; }; + MSstats = derive2 { name="MSstats"; version="3.18.5"; sha256="0c3sfk3nlvmr35xz6r7db4dyqwvb44agqkgh8gllymwxp1q73zaj"; depends=[broom data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore purrr reshape2 snow statmod stringr survival tidyr]; }; + MSstatsQC = derive2 { name="MSstatsQC"; version="2.4.0"; sha256="0ns4pcjf1zjbr2c1db8p1h1dxaq3khwxcvqbbliaasbfahskiy00"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics]; }; + MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.6.0"; sha256="16qg0jffahqxhh2g7hm3ykmpfbmwvrnmsr2qx73xd6gpg5lghh24"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly shiny]; }; + MSstatsSampleSize = derive2 { name="MSstatsSampleSize"; version="1.0.1"; sha256="0knmm2950jm873qdh7fvqfh7zv2qmb6f6s88jjan2iv9vlxf744j"; depends=[BiocParallel caret ggplot2 gridExtra MSstats reshape2]; }; + MSstatsTMT = derive2 { name="MSstatsTMT"; version="1.4.5"; sha256="1ji0k0b3h94jar3h81qrd7zfgh5cfjii9vzr3rrfj1z8rzci1f2s"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 statmod tidyr]; }; + MTseeker = derive2 { name="MTseeker"; version="1.3.0"; sha256="182w8w8f6v9vfx5562pr7ypp1fwgm6n6q18j8l1nmsj6352y4p7a"; depends=[Biobase BiocGenerics Biostrings circlize GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR Homo_sapiens IRanges jsonlite Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VariantTools viridis xml2]; }; + MVCClass = derive2 { name="MVCClass"; version="1.60.0"; sha256="188p6w92p2rky62rv4473xf66srvrxnzk6hz4ywqbn4wq0fzkl2x"; depends=[]; }; + MWASTools = derive2 { name="MWASTools"; version="1.10.0"; sha256="0hd5mfnbngcc2vj2wcz8grfa1nr7hgampp4wcbpjmchk66vb0cfg"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; + Maaslin2 = derive2 { name="Maaslin2"; version="1.0.0"; sha256="123ll5lhqdd3vc0cydrsv9xh35qdkia6msj78pplcawlrd4nqg3z"; depends=[biglm car chemometrics cplm data_table dplyr edgeR ggplot2 hash lmerTest logging lpsymphony MASS metagenomeSeq MuMIn optparse pbapply pcaPP pheatmap pscl robustbase vegan]; }; + MantelCorr = derive2 { name="MantelCorr"; version="1.56.0"; sha256="05msf80a5ls59bvwdrjfv5ilyd69kg3v6n4ahbizr07d9ndqwhgj"; depends=[]; }; + MassArray = derive2 { name="MassArray"; version="1.38.0"; sha256="17lcvw4a7zijbii6na2zm66pkx3gwa5znwww473bidqq71hsjvns"; depends=[]; }; + MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.52.0"; sha256="0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7"; depends=[waveslim]; }; + MatrixRider = derive2 { name="MatrixRider"; version="1.18.0"; sha256="13h4yx8knmx2qhh56q4lx0ac4skacrkvd9c6226nms8z7xr6gzdj"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; }; + MaxContrastProjection = derive2 { name="MaxContrastProjection"; version="1.10.0"; sha256="1iwwm07dnbpys76z1rzn0zqs3nid5fg2xvq78rn666ai1xgvp5kl"; depends=[EBImage]; }; + MeSHDbi = derive2 { name="MeSHDbi"; version="1.22.0"; sha256="17nbj474w1hp8dp1l23nms97w8g0wr3jbyl35r8bqwkzrh3wzk9v"; depends=[AnnotationDbi Biobase BiocGenerics RSQLite]; }; + MeasurementError_cor = derive2 { name="MeasurementError.cor"; version="1.58.0"; sha256="0lmkfcr410cjv8yfsm7fnigrzf5i3qxixxrlcv51vqgj7lnxyz3h"; depends=[]; }; + Melissa = derive2 { name="Melissa"; version="1.2.0"; sha256="0cym2wj7m6rnmr9ddw4n9zrsjkkmnw7rch9mdk9xkk5dznzrvchq"; depends=[assertthat BiocStyle BPRMeth clues cowplot data_table doParallel foreach GenomicRanges ggplot2 magrittr matrixcalc MCMCpack mvtnorm ROCR truncnorm]; }; + MergeMaid = derive2 { name="MergeMaid"; version="2.58.0"; sha256="1ykkmsp9m6zs6bgw1sicv50918y7mvjk04rbnbbjrzy0p7rc8m5z"; depends=[Biobase MASS survival]; }; + Mergeomics = derive2 { name="Mergeomics"; version="1.14.0"; sha256="1c2fl8jmmh4qhh6bqqkbzdgzq5ipsscjp0akd3xgvb69nwhraj4w"; depends=[]; }; + MetCirc = derive2 { name="MetCirc"; version="1.16.0"; sha256="0wrf31xxj76alm2xdqmxsdl9ah7p38ysfwra7zhmlvc2xjzvknhy"; depends=[amap circlize ggplot2 MSnbase S4Vectors scales shiny]; }; + MetID = derive2 { name="MetID"; version="1.4.0"; sha256="02f586g5jpr0pbidc61fr6vph6g6i65vzw95lpsh1vsbdcs06x4b"; depends=[ChemmineR devtools igraph Matrix stringr]; }; + MetNet = derive2 { name="MetNet"; version="1.4.2"; sha256="1rdmqlib1mg5sqqmb4f0sqmv4ifkrin14g0pwbsi0qz6gb90g14n"; depends=[BiocParallel bnlearn GENIE3 mpmi parmigene ppcor sna stabs]; }; + MetaCyto = derive2 { name="MetaCyto"; version="1.8.0"; sha256="0kb4dysq0glalq3mvk7ckagdxxx6sd7a6vyjcf5v842dxymwkxan"; depends=[cluster fastcluster flowCore FlowSOM ggplot2 metafor tidyr]; }; + MetaNeighbor = derive2 { name="MetaNeighbor"; version="1.6.0"; sha256="11nkn6lwjbsqhn8yfjxnrnc6hpqrmaby3gr3c9anmgg12aiqfc5w"; depends=[beanplot GenomicRanges gplots Matrix matrixStats RColorBrewer Rcpp SummarizedExperiment]; }; + MetaVolcanoR = derive2 { name="MetaVolcanoR"; version="1.0.1"; sha256="0iq8d0shwrz9wjldqlz4kkcz444i6qd70j2a8c261bgsdsbzqj1v"; depends=[cowplot data_table dplyr ggplot2 htmlwidgets metafor metap plotly rlang tidyr topconfects]; }; + Metab = derive2 { name="Metab"; version="1.20.0"; sha256="00aa531dddz37b234l613r1hzjr04iw2bjrcqhalphxff3hkp1l3"; depends=[pander svDialogs xcms]; }; + MetaboSignal = derive2 { name="MetaboSignal"; version="1.16.0"; sha256="12pq9z8q772kfyj9rvxb8bw2cbicdhh9j7acfssk5bqk3jn1l21s"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; + MethCP = derive2 { name="MethCP"; version="1.0.0"; sha256="0hrsipmzfxqp7j99xq8bkld9qz3yk7ngf4lzf9sn0b28j2kl5hdg"; depends=[bsseq DNAcopy DSS GenomeInfoDb GenomicRanges IRanges methylKit S4Vectors]; }; + MethPed = derive2 { name="MethPed"; version="1.14.0"; sha256="1d42a04lrs5sjk1143kpxkg87laaracbkq2favs2zq4f8dj5j023"; depends=[Biobase randomForest]; }; + MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.18.0"; sha256="1h0cgs3j5rwp91m6qbqch2hqwwnyz4przz44gmqr9pridm5jpn8s"; depends=[Biostrings gplots seqinr stringr]; }; + MethylAid = derive2 { name="MethylAid"; version="1.20.0"; sha256="1inz2dvdx8w3bzif46dp14plqr692idc38syx2wbblmv9v3x0fws"; depends=[Biobase BiocGenerics BiocParallel ggplot2 gridBase hexbin matrixStats minfi RColorBrewer shiny SummarizedExperiment]; }; + MethylMix = derive2 { name="MethylMix"; version="2.16.0"; sha256="04chgiwzc7s18i329wv1zq0nr2hlvdlwfbx1qpr4y0ks6xaa6wvp"; depends=[data_table digest foreach ggplot2 impute limma R_matlab RColorBrewer RCurl RPMM]; }; + MethylSeekR = derive2 { name="MethylSeekR"; version="1.26.0"; sha256="1dgv2hynd4h54srxpxflczfixhb9rsax81bawrswxycw2wv077g3"; depends=[BSgenome geneplotter GenomicRanges IRanges mhsmm rtracklayer]; }; + Mfuzz = derive2 { name="Mfuzz"; version="2.46.0"; sha256="0dh0lznx4cpaw6isx0n4fi01z1gdljv64q8k5aqd2fcpzvpfwhbg"; depends=[Biobase e1071 tkWidgets]; }; + MiChip = derive2 { name="MiChip"; version="1.40.0"; sha256="1kwwb45h17cgg9mynl9mhnhn1qyaxwxc1x8bbc9vywi4nxjbvymy"; depends=[Biobase]; }; + MiPP = derive2 { name="MiPP"; version="1.58.0"; sha256="0iylhrk6s5vwmmxvh4zijb5kixm8vb52m6dp1yj14lgjaaxvyxkb"; depends=[Biobase e1071 MASS]; }; + MiRaGE = derive2 { name="MiRaGE"; version="1.28.0"; sha256="0yf98q7nd0i7xbi2fgy5g3z7dq0b88n4f1i2qga5slqwyyrmly25"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; + MineICA = derive2 { name="MineICA"; version="1.26.0"; sha256="0bbpwfllhigfacfjrlibbjhsp6gbmdry27zds6lw5advsji50xnv"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; }; + MinimumDistance = derive2 { name="MinimumDistance"; version="1.30.0"; sha256="19mrihv5pv5npksr8d6ks96fhlaml9rb6xvsiisrmlwmppriqmmn"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; + Mirsynergy = derive2 { name="Mirsynergy"; version="1.22.0"; sha256="0g1k3i481y62dqjw34nx7g1zqds9dk26avjxsl4mclj9wdgbvidb"; depends=[ggplot2 gridExtra igraph Matrix RColorBrewer reshape scales]; }; + MmPalateMiRNA = derive2 { name="MmPalateMiRNA"; version="1.36.0"; sha256="184ix333q45zrax529r7cqvl8vv175jn2vlw93ljfni3llkkg9l2"; depends=[Biobase lattice limma statmod vsn xtable]; }; + MoPS = derive2 { name="MoPS"; version="1.20.0"; sha256="1l6qwq0yq462kg2iacxnnjnsp319zyr8gkp60pkw1fhd83sn68j6"; depends=[Biobase]; }; + Modstrings = derive2 { name="Modstrings"; version="1.2.1"; sha256="0ki8pj7g6y5n5zpajwbx6vx3qamx2lsi9xw9amajvcp82svbqk9w"; depends=[assertive BiocGenerics Biostrings GenomicRanges IRanges S4Vectors stringi stringr XVector]; }; + MoonlightR = derive2 { name="MoonlightR"; version="1.12.0"; sha256="06pg5mv068i3pfkw8qid47kmrzsfwphvajg3v07h54yv8qzgi77h"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; + MotIV = derive2 { name="MotIV"; version="1.42.0"; sha256="07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k"; depends=[BiocGenerics Biostrings GenomicRanges IRanges lattice rGADEM S4Vectors]; }; + MotifDb = derive2 { name="MotifDb"; version="1.28.0"; sha256="0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc"; depends=[BiocGenerics Biostrings IRanges rtracklayer S4Vectors splitstackshape]; }; + Mulcom = derive2 { name="Mulcom"; version="1.36.0"; sha256="159mcbz1x8vzvd8vwlqgr69wrgplw28i18acfills6vpxpq0q5pl"; depends=[Biobase fields]; }; + MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.12.6"; sha256="174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; }; + MultiDataSet = derive2 { name="MultiDataSet"; version="1.14.0"; sha256="0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; }; + MultiMed = derive2 { name="MultiMed"; version="2.8.0"; sha256="1m5apc88zbk31gf0h6m9lf289i6n3r73am0j1y0acc2v2dmlwyg4"; depends=[]; }; + MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.12.0"; sha256="08715l6swrlccviw7932v5hyrd2x4c6049vy9qnxk0lw3sp1zvsf"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; }; + NADfinder = derive2 { name="NADfinder"; version="1.10.0"; sha256="0awya5rxc6d4rf9m3cpplb12dq0blf182zk81sj9v0ba3g9vjdai"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; + NBAMSeq = derive2 { name="NBAMSeq"; version="1.2.1"; sha256="0k4hvwn76184m3ni12cvvnj7zxb41lkks87w5gkxnwb8m0mlr4z2"; depends=[BiocParallel DESeq2 genefilter mgcv S4Vectors SummarizedExperiment]; }; + NBSplice = derive2 { name="NBSplice"; version="1.4.0"; sha256="1384pfry70v3xjmyc1q0c4s88wyr94v2vkvlyicc6avbp61jlxaz"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; }; + NCIgraph = derive2 { name="NCIgraph"; version="1.34.0"; sha256="1pxdhj5rrmax7xxj938q02vjlq9c0j64fmplzcxaczx8bhnlvy5q"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; }; + NOISeq = derive2 { name="NOISeq"; version="2.30.0"; sha256="1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4"; depends=[Biobase Matrix]; }; + NTW = derive2 { name="NTW"; version="1.36.0"; sha256="1164npd6d597xi9fqr1qichyr8cn4mdazghh20gq2swh3s129d4q"; depends=[mvtnorm]; }; + NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.16.0"; sha256="0naspag7r3a634m2bdn8sihldfm65b37nr52d0gly55z0y28yay9"; depends=[Biobase matrixStats Rcpp]; }; + NanoStringQCPro = derive2 { name="NanoStringQCPro"; version="1.18.0"; sha256="14ny303gd3lrhr92rksbgnm26fbxj95rp9rjzzihsmikl5cghs85"; depends=[AnnotationDbi Biobase knitr NMF org_Hs_eg_db png RColorBrewer]; }; + NarrowPeaks = derive2 { name="NarrowPeaks"; version="1.30.0"; sha256="0ld0w39ky21jvd217kawaqxp5n3m9hhy5b43gn56dr0k9ylnpwrc"; depends=[BiocGenerics CSAR fda GenomeInfoDb GenomicRanges ICSNP IRanges S4Vectors]; }; + NeighborNet = derive2 { name="NeighborNet"; version="1.4.0"; sha256="0lc1rd456fkjcdq0h8z050kz408yhzskh8fbpppmd9yfizbsncsw"; depends=[graph]; }; + NetPathMiner = derive2 { name="NetPathMiner"; version="1.22.0"; sha256="17rldj4yk5bs8zbmg8fvg79r1ml82zpqp7rpph6sc2yznsw88716"; depends=[igraph]; }; + NetSAM = derive2 { name="NetSAM"; version="1.26.0"; sha256="0z10glqwyxvrgavab97mm4vrzq9139isghf1bv2mhljia648msml"; depends=[graph igraph seriation]; }; + NormalyzerDE = derive2 { name="NormalyzerDE"; version="1.4.0"; sha256="1898fakk2mymr4x43z09916q20n219vpb5mdm5iq94k2c6ggfrqm"; depends=[ape Biobase car ggforce ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; }; + NormqPCR = derive2 { name="NormqPCR"; version="1.32.0"; sha256="0j3z4qwr932m0nkzig7kznc3w37nrjii2mjzsa95qxrqyxxmg1km"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; }; + NuPoP = derive2 { name="NuPoP"; version="1.36.0"; sha256="1zalsqfvlqm4abhlqwckcmh8wcq9zpg3zdllpafw1jqwbj21dldz"; depends=[]; }; + OCplus = derive2 { name="OCplus"; version="1.60.0"; sha256="031fnrym8h1n85yl6p6pwmfsqsm55l65ipam69ffm79c09bmxy0a"; depends=[akima multtest]; }; + OGSA = derive2 { name="OGSA"; version="1.16.0"; sha256="0ilv0lhlvmsbn9hv618mmx8gc0z94gjvjhhzbymapm5r5blwyzkf"; depends=[Biobase gplots limma]; }; + OLIN = derive2 { name="OLIN"; version="1.64.0"; sha256="1i75nyq8anawy77yl6nhghblmwi6qa7hrlaaa12cq6pylc3km2sa"; depends=[limma locfit marray]; }; + OLINgui = derive2 { name="OLINgui"; version="1.60.0"; sha256="08pbmn4l2ixqndnjb6dakz0sjj7zbyjxvaflb5y804rj15hc2skr"; depends=[marray OLIN tkWidgets widgetTools]; }; + OMICsPCA = derive2 { name="OMICsPCA"; version="1.4.0"; sha256="1dczdggzl1d2zmfla81z2972zzjz9kvwmbvvyhy6sg2jn3kfsfvx"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; }; + OPWeight = derive2 { name="OPWeight"; version="1.8.0"; sha256="15lac1wfis13nhbniv0lz0d946lzm32s381szba0n5i4lvj31dqz"; depends=[MASS qvalue tibble]; }; + ORFik = derive2 { name="ORFik"; version="1.6.9"; sha256="1ml7p3k5i31wwnanvj3aai49sbrp5l76jnjn039y8adc3jsj7b68"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra IRanges Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + OSAT = derive2 { name="OSAT"; version="1.34.0"; sha256="0imn45bm8bn95i1hzd0gwpldw5cjr3ilpmn0w5ylgnr1scp38xlf"; depends=[]; }; + OTUbase = derive2 { name="OTUbase"; version="1.36.0"; sha256="10gnhlaz8izd6l5c2yja1nxg7bcghivw3mwl0hgvrkqqgbpgbi8j"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; + OUTRIDER = derive2 { name="OUTRIDER"; version="1.4.0"; sha256="0j1p8558h36fqjjzhhwdwdimkcaf2v6j9wp7g76b2m1mz8fsy12d"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 gplots heatmaply IRanges matrixStats pcaMethods pheatmap plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo S4Vectors scales SummarizedExperiment]; }; + OVESEG = derive2 { name="OVESEG"; version="1.2.0"; sha256="1v80fqm9aa59q487rcpsp5r917fp69anff8kgy11ipwfl7m0pzpa"; depends=[BiocParallel fdrtool limma Rcpp SummarizedExperiment]; }; + OmaDB = derive2 { name="OmaDB"; version="2.2.0"; sha256="0b4r88fq2nfn4yix6qhwjk556bfh2qxfyi129p1zz8k4ql38cf58"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; }; + OmicCircos = derive2 { name="OmicCircos"; version="1.24.0"; sha256="0r2p0kr9hf824l2zfk3ampbdbk9d04a7q99cj6bx0hq7bhnh7nvw"; depends=[GenomicRanges]; }; + OmicsLonDA = derive2 { name="OmicsLonDA"; version="1.2.2"; sha256="0zc0r011v4db8svqg986psy2fdlcvckgj61crslm41rgaq0h788j"; depends=[BiocGenerics BiocParallel ggplot2 gss plyr pracma SummarizedExperiment zoo]; }; + OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.18.0"; sha256="1kg5apfvsafc6fczz2b3bn26zmjcar20qfhms0wx3mq6v146ls1x"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; }; + OmnipathR = derive2 { name="OmnipathR"; version="1.0.1"; sha256="0lflk5v6r6w41sj2sascxdl5b81h6dfdkhff7zvx2h5hfvpcbs3p"; depends=[dplyr igraph rlang]; }; + Onassis = derive2 { name="Onassis"; version="1.8.2"; sha256="1h44aly83qzfppbzlzhic990rs5sy70426862ylk06rx985vn0az"; depends=[AnnotationDbi clusteval data_table dendextend DT GEOmetadb ggfortify ggplot2 knitr OnassisJavaLibs RCurl rJava RSQLite Rtsne]; }; + OncoScore = derive2 { name="OncoScore"; version="1.14.0"; sha256="0maqr6rm3xq5qywyvh0xdnkmscya6v7xbwpz41c8i1gki2kaakja"; depends=[biomaRt]; }; + OncoSimulR = derive2 { name="OncoSimulR"; version="2.16.0"; sha256="1937jkxnqkrvxqvpxnz1gv6qghcgs47y3d6vq80ph70sdisnz10l"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph nem RColorBrewer Rcpp Rgraphviz smatr]; }; + OrderedList = derive2 { name="OrderedList"; version="1.58.0"; sha256="1lmbx5cdscc1dfdxx5ncn4nwkxxkgh976v52a17pa1pr5hiwlwsx"; depends=[Biobase twilight]; }; + Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.14.0"; sha256="191bxij92z94cpr1g22dqi4394jsigwz9ljlzm4vwrz7zmqs73a2"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges RSQLite S4Vectors]; }; + OrganismDbi = derive2 { name="OrganismDbi"; version="1.28.0"; sha256="1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; }; + Oscope = derive2 { name="Oscope"; version="1.16.0"; sha256="1r3h695qxhgdlcrdiljcihqrnbrsgwcw3wgr98h3vmmhzgkfsb16"; depends=[BiocParallel cluster EBSeq testthat]; }; + OutlierD = derive2 { name="OutlierD"; version="1.50.0"; sha256="0bw9m2r3jx10hn1ky1a7zpiwcsd46dnn8lryxydi2pwv6d43qh6r"; depends=[Biobase quantreg]; }; + PAA = derive2 { name="PAA"; version="1.20.0"; sha256="0pnqs84sxwmifv19w2mqg6czmdxgw1g1cxd7jbrq331y44lx9z00"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; }; + PADOG = derive2 { name="PADOG"; version="1.28.0"; sha256="0jh3cp5r2xdkavlfvyg8iyf1y8bgh7804m6yk71znwv5ii92wmma"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGG_db KEGGdzPathwaysGEO limma nlme]; }; + PAIRADISE = derive2 { name="PAIRADISE"; version="1.2.0"; sha256="0c5iw230x1sgq463hph6jlggjfhjx4znrcgj87x40d7dn78yb2w1"; depends=[abind BiocParallel nloptr S4Vectors SummarizedExperiment]; }; + PANR = derive2 { name="PANR"; version="1.32.0"; sha256="0sgi8rs7srnjsjwqf6bvq8civ0yjz96cw9z0ibda4zhzx8iwy0qm"; depends=[igraph MASS pvclust RedeR]; }; + PAPi = derive2 { name="PAPi"; version="1.26.0"; sha256="1g2rv2vvby983pzv8737x6bc73h6cxwmpfiz5p01ylskp41w58vg"; depends=[KEGGREST svDialogs]; }; + PAST = derive2 { name="PAST"; version="1.2.8"; sha256="1d49i9h8yfn5frybzhzjk586yin59i6jwnmybxd3ymwxd06xpj36"; depends=[doParallel dplyr foreach GenomicRanges ggplot2 iterators qvalue rlang rtracklayer S4Vectors]; }; + PCAN = derive2 { name="PCAN"; version="1.14.0"; sha256="0fagvnb8x1lrzvvvv3iip1svphnx2wnc7llaka0mf1axcpkpy7c8"; depends=[BiocParallel]; }; + PCAtools = derive2 { name="PCAtools"; version="1.2.0"; sha256="17i0dy6aan6b38v3dbhqjwyjks3c763mzpwnc2rbc94i2waj1rl5"; depends=[beachmat BH BiocParallel BiocSingular cowplot DelayedArray DelayedMatrixStats dqrng ggplot2 ggrepel lattice Matrix Rcpp reshape2]; }; + PCpheno = derive2 { name="PCpheno"; version="1.48.0"; sha256="1w284pqf0crhy2vrf7p6ivxk76xddycvhgpb5jkcwa71caldimg7"; depends=[annotate AnnotationDbi Biobase Category GO_db graph GSEABase KEGG_db ppiData ppiStats ScISI SLGI]; }; + PECA = derive2 { name="PECA"; version="1.22.0"; sha256="1y8r37fqjwn3kf90ykc2yng959mfs81hwdbjgb5pscl0ryq8fd07"; depends=[affy aroma_affymetrix aroma_core genefilter limma preprocessCore ROTS]; }; + PERFect = derive2 { name="PERFect"; version="1.0.0"; sha256="00m5vz936i8x8m2qvq2j67grjq5hml3ambwp1faq4083l5qkh2db"; depends=[fitdistrplus ggplot2 Matrix phyloseq psych sn zoo]; }; + PGA = derive2 { name="PGA"; version="1.16.0"; sha256="1d2yqvzmpvz8w05m4779kpf2sdbwbm4mf3rc0wmqya3b160vdasm"; depends=[AnnotationDbi biomaRt Biostrings customProDB data_table dplyr GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap processx RCurl readr Rsamtools RSQLite rTANDEM rtracklayer S4Vectors seqinr stringr VariantAnnotation]; }; + PGSEA = derive2 { name="PGSEA"; version="1.60.0"; sha256="10ii92rnzfxxgwfw438rh4xpd5cnd7ibfvnx1739n15sgrm9hyc7"; depends=[annaffy AnnotationDbi Biobase GO_db KEGG_db]; }; + PICS = derive2 { name="PICS"; version="2.30.0"; sha256="1bxa6hsgzp0ik7mb9jv64x2c187brdp1czqdnjj5lz1s2qcvp348"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; }; + PING = derive2 { name="PING"; version="2.30.0"; sha256="1flq61048l250cqggz1nqjhrlixxxmiw7p0p7qjki2gg1j59grjn"; depends=[BiocGenerics BSgenome chipseq fda GenomicRanges Gviz IRanges PICS S4Vectors]; }; + PLPE = derive2 { name="PLPE"; version="1.46.0"; sha256="024haa7qr6ljn1f60n9cqr4byp3plh91qrvyawz3lqwxqha19xav"; depends=[Biobase LPE MASS]; }; + POST = derive2 { name="POST"; version="1.10.0"; sha256="1ga6ffc62ck1ssc0yi7vhhlihspzk4vcckbz80ry6y6aq340mgya"; depends=[Biobase CompQuadForm GSEABase Matrix survival]; }; + PPInfer = derive2 { name="PPInfer"; version="1.12.0"; sha256="0z7d84ch6kc1x6w5r768jg88cbi9qj31bi66204vcgqqnlyjqlnz"; depends=[biomaRt fgsea ggplot2 igraph kernlab STRINGdb yeastExpData]; }; + PREDA = derive2 { name="PREDA"; version="1.32.0"; sha256="0plnzbiab4y1lzrjdx7k7ymanlz6213hf6jspi5z49ppr2mmj4cb"; depends=[annotate Biobase lokern multtest]; }; + PROMISE = derive2 { name="PROMISE"; version="1.38.0"; sha256="00wbmf1f7h3409lrdr7c2rs3hfwhm3mdm94x7y8ij8a9rq0scb40"; depends=[Biobase GSEABase]; }; + PROPER = derive2 { name="PROPER"; version="1.18.0"; sha256="08cnnm8nznlk01r0jwcvkpi2qd5b2jfdcl031jvkx4w5dmhpli5r"; depends=[edgeR]; }; + PROPS = derive2 { name="PROPS"; version="1.8.0"; sha256="1hh33smsf69lgs1b5pn0yb6ndxz0x4ihxc09a1ygwnhnw4dcjyqm"; depends=[Biobase bnlearn reshape2 sva]; }; + PROcess = derive2 { name="PROcess"; version="1.62.0"; sha256="0ib263xy6j0r6dc5pl85in5zha4h8gzxi579qpc318jy72ca50sv"; depends=[Icens]; }; + PSEA = derive2 { name="PSEA"; version="1.20.0"; sha256="0vq4h3rx94hzarm38402p787x8mxyqfcj2cz909sm78bsy97khv5"; depends=[Biobase MASS]; }; + PSICQUIC = derive2 { name="PSICQUIC"; version="1.24.0"; sha256="0a5nslzbn1wvlcmlg773hlxb1w6q2qamm86frnkrfsfdfblzh4gn"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; }; + PWMEnrich = derive2 { name="PWMEnrich"; version="4.22.0"; sha256="1a38ma90im0ypy0hqcfmb5n3vqyc5falv9w0rdvqfw9k0j9zkbgv"; depends=[BiocGenerics Biostrings evd gdata seqLogo]; }; + PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.14.0"; sha256="0by4bn740naalaf8sdhd3yaab5y3a92h327g6nksl2djksn297mx"; depends=[FindMyFriends igraph jsonlite pcaMethods shiny]; }; + Path2PPI = derive2 { name="Path2PPI"; version="1.16.0"; sha256="1g9z64aqhx7xdc7fg182v4q82r82421z990vs9hvjfgg0x1hdp2j"; depends=[igraph]; }; + PathoStat = derive2 { name="PathoStat"; version="1.12.0"; sha256="01c81m4bl48swz7w2k6xraqj7317n79q8l1rpl23fcxmj98nna88"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; }; + PathwaySplice = derive2 { name="PathwaySplice"; version="1.10.0"; sha256="0qqv24zpfavbj96n9jvrn3yisgba7ia7lvdxyh6v61ff3kj0czlh"; depends=[annotate AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr EnrichmentBrowser ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq KEGGREST mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; }; + Pbase = derive2 { name="Pbase"; version="0.26.0"; sha256="06n779rjgiy6csdvqa7nrdz5cq0n5w1rwmzrn5xcnzsz2lxv2ws5"; depends=[AnnotationFilter Biobase BiocGenerics BiocParallel biomaRt Biostrings cleaver ensembldb GenomicRanges Gviz IRanges MSnbase mzID mzR Pviz Rcpp rtracklayer S4Vectors]; }; + PepsNMR = derive2 { name="PepsNMR"; version="1.4.0"; sha256="0yava5dcabcvsvh1pqxzz0a0kgcx58jlsvvk7i3pcw0p66393vfk"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; }; + PharmacoGx = derive2 { name="PharmacoGx"; version="1.17.1"; sha256="0h2458gphawx2l47qdkf8z6ixfbi5fai9hy0dab1gkc0c9697xbc"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; }; + PhenStat = derive2 { name="PhenStat"; version="2.22.0"; sha256="0bhf7hhj6bbdszy3w93qk7i5qfyhrz9bai3qy46i93kwh0bmmzby"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; }; + PhyloProfile = derive2 { name="PhyloProfile"; version="1.0.7"; sha256="0r50xjfvh357z83nxajmnicyi2ydn78284v9fxfb148rca26v4jn"; depends=[ape BiocStyle bioDist Biostrings colourpicker data_table DT energy ExperimentHub ggplot2 gridExtra OmaDB pbapply plyr RColorBrewer shiny shinyBS shinyjs xml2 zoo]; }; + Pi = derive2 { name="Pi"; version="1.14.0"; sha256="0ff32k8y5mplg38f8mj7npr84yfm5hcm32jbfkivh6vlldbh3c1y"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice Matrix plot3D randomForest ROCR scales supraHex]; }; + Pigengene = derive2 { name="Pigengene"; version="1.12.0"; sha256="0a0803a6rq8f60ssy5y15gswn6p58ryb2lb3spy1fgpzc2c92s2j"; depends=[bnlearn C50 dplyr gdata GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; }; + PoTRA = derive2 { name="PoTRA"; version="1.2.0"; sha256="0x7n3ri3w4ib64x8rf94lgndm9nkmzn2lcv96vgq9vjkbdvmyvfi"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; }; + Polyfit = derive2 { name="Polyfit"; version="1.20.0"; sha256="15nk16apcb8afhj9l19w6rmz897gs6i412l6z9l34i53zbkqhq62"; depends=[DESeq]; }; + PowerExplorer = derive2 { name="PowerExplorer"; version="1.6.0"; sha256="0ab09fb8dgr9qp7za9d1qm6rcm2qqhbqfnqg4i5i364pcsdqkv6c"; depends=[Biobase BiocParallel data_table DESeq2 ggplot2 gridExtra MASS ROTS S4Vectors SummarizedExperiment vsn]; }; + PrInCE = derive2 { name="PrInCE"; version="1.2.0"; sha256="1bygqabhbyarwpmy7i26v7n43qy22386haizszw6qk3fmcggd64h"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; }; + PrecisionTrialDrawer = derive2 { name="PrecisionTrialDrawer"; version="1.2.1"; sha256="0h71h03wxpykg4sr3zw3ikh18cd41mwjncijwnp9450wln5al6fw"; depends=[BiocParallel biomaRt brglm cgdsr data_table DT GenomicRanges ggplot2 ggrepel googleVis httr IRanges jsonlite LowMACAAnnotation magrittr matrixStats RColorBrewer reshape2 S4Vectors shiny shinyBS stringr XML]; }; + Prize = derive2 { name="Prize"; version="1.16.0"; sha256="0gg950w096ssa3036yrw4q4cm8v4pxh3cx1fya284xiyi87i8i0i"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; }; + Prostar = derive2 { name="Prostar"; version="1.18.6"; sha256="0na2n52r4i3mibp6ixpzz4a9whq61npvj816l9vg6wrf6zp56xc7"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable sass shiny shinyAce shinyBS shinycssloaders shinyjs shinythemes shinyTree shinyWidgets tibble webshot XML]; }; + ProtGenerics = derive2 { name="ProtGenerics"; version="1.18.0"; sha256="1k1ggjgx2la8b21841a4ngkp6xfxwz0czv7x960r7i1jqif8y48z"; depends=[]; }; + ProteoMM = derive2 { name="ProteoMM"; version="1.4.0"; sha256="0xnlsixbgmw9fn227mpi4mh1ia5p1fl4rlsns326p0nnvk7scc1y"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; + ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.16.0"; sha256="1qx335i4l99jvqlbwqqdfjin6c8sq0rrrh0nvl3wjsn03f1fxxdh"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDb MSnbase mzR RCurl]; }; + PureCN = derive2 { name="PureCN"; version="1.16.0"; sha256="0pb0203z3njf3y8ln2j6j5ab5zzwwwzxkwvpqjmnp11yz69vkn12"; depends=[BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; + Pviz = derive2 { name="Pviz"; version="1.20.0"; sha256="01ylwk4qvsj36las4wrqbw5lpcd1lrwd49ipz3v79s96yiazxwiy"; depends=[Biostrings biovizBase data_table GenomicRanges Gviz IRanges]; }; + QDNAseq = derive2 { name="QDNAseq"; version="1.22.0"; sha256="0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq"; depends=[Biobase CGHbase CGHcall DNAcopy future future_apply GenomicRanges IRanges matrixStats R_utils Rsamtools]; }; + QSutils = derive2 { name="QSutils"; version="1.4.0"; sha256="01i71zwc5nj6cqa7fq8zjpcgzlq7wf398i9pcczswh3l2wayf3y8"; depends=[ape BiocGenerics Biostrings psych]; }; + QUALIFIER = derive2 { name="QUALIFIER"; version="1.29.1"; sha256="0z5aid77j8bsisc07j8275s0agq6v47vk7bjiwapphw9zgdvnzbd"; depends=[Biobase data_table flowCore flowViz flowWorkspace hwriter lattice latticeExtra MASS ncdfFlow reshape XML]; }; + QUBIC = derive2 { name="QUBIC"; version="1.14.0"; sha256="0yicyig3qr0y4784rb9zappvrjwrk9gshz4vlfklrl0paijqhj3n"; depends=[biclust Matrix Rcpp RcppArmadillo]; }; + Qtlizer = derive2 { name="Qtlizer"; version="1.0.0"; sha256="1gqjrv9bqdqhw464bdsgglq3flszh2hwcl4a2cmfahi6w7xwskks"; depends=[curl GenomicRanges httr stringi]; }; + QuartPAC = derive2 { name="QuartPAC"; version="1.18.0"; sha256="1wfcf9sqklg6l3r5jydvyyv282my5vk7ws5ry7hxg9kpzvpbricv"; depends=[data_table GraphPAC iPAC SpacePAC]; }; + QuasR = derive2 { name="QuasR"; version="1.26.0"; sha256="07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges IRanges Rbowtie Rhisat2 Rhtslib Rsamtools rtracklayer S4Vectors ShortRead]; }; + QuaternaryProd = derive2 { name="QuaternaryProd"; version="1.20.0"; sha256="13g58xr6f5qwar5bs141a8x05kv85pnnvlwpgai6730z2aff0gzr"; depends=[dplyr Rcpp yaml]; }; + R3CPET = derive2 { name="R3CPET"; version="1.18.0"; sha256="02hhna99z8ybw538mwd6fn7akzy8sxyms80907q287mb1g26amd9"; depends=[BiocGenerics clues clValid data_table GenomeInfoDb GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp RCurl reshape2 S4Vectors]; }; + R453Plus1Toolbox = derive2 { name="R453Plus1Toolbox"; version="1.36.0"; sha256="15z4k3a9kbb0dsq768pc8mwrl0lg3f9giwxdmg1gvcfhf663c13k"; depends=[Biobase BiocGenerics biomaRt Biostrings BSgenome GenomicRanges IRanges R2HTML Rsamtools S4Vectors ShortRead SummarizedExperiment TeachingDemos VariantAnnotation xtable XVector]; }; + R4RNA = derive2 { name="R4RNA"; version="1.14.0"; sha256="1y50i55bmx70nixfvjgbaq4mjzmyl1svfkkczn53gwlchki5761c"; depends=[Biostrings]; }; + RBGL = derive2 { name="RBGL"; version="1.62.1"; sha256="0ixbkdirf08i400db587r262j52sdwdgk3884nxk5xkbhx2m6vg0"; depends=[BH graph]; }; + RBM = derive2 { name="RBM"; version="1.18.0"; sha256="176b2hqmy2njyr0cs8jv846bhv6b9gfkqmj803ic2y2bzlzwrc2b"; depends=[limma marray]; }; + RBioinf = derive2 { name="RBioinf"; version="1.46.0"; sha256="1qys21bw79s74p262lcrbn2fyahfavp3dzdxy37c5441fxi2blwq"; depends=[graph]; }; + RCAS = derive2 { name="RCAS"; version="1.12.0"; sha256="1s3gvvxi1029d1vfwnjh21nnw3mlx08kcwz63891hml9y850cvsn"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; }; + RCASPAR = derive2 { name="RCASPAR"; version="1.32.0"; sha256="1qzwjs8l585dkx6b1vdhlpnqypx6mlfmhvihp0gqfiiv9n053cmy"; depends=[]; }; + RCM = derive2 { name="RCM"; version="1.2.0"; sha256="0h7kwcif953kamaxp6a3z72p726lc8gizwh58933qn34195jv8is"; depends=[alabama edgeR ggplot2 MASS nleqslv phyloseq RColorBrewer reshape2 tensor tseries vegan VGAM]; }; + RCy3 = derive2 { name="RCy3"; version="2.6.3"; sha256="1g05mqs8av6yz826lpldgz0viwm0zq9hzxw11bdv6dq6bbm8vhqb"; depends=[BiocGenerics graph httr igraph R_utils RJSONIO XML]; }; + RCyjs = derive2 { name="RCyjs"; version="2.8.0"; sha256="09hzqf8ppx3fhli28rsnyg22nrsv85vk0k2hw0gw1liz7dd1grwz"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; }; + RDAVIDWebService = derive2 { name="RDAVIDWebService"; version="1.24.0"; sha256="1yq9d71zd533qjda2gd7hrmwz3gj0cvb0447y2hgp0h83dyswv3s"; depends=[Category ggplot2 GO_db GOstats graph RBGL rJava]; }; + RDRToolbox = derive2 { name="RDRToolbox"; version="1.36.0"; sha256="0mq6sh5m0i5b7lb315r9v1hci363dwzihpgldvhyk8iv02lsiymg"; depends=[MASS rgl]; }; + REBET = derive2 { name="REBET"; version="1.4.0"; sha256="1536zl0madigiang9lyxi00sb97b0k6zqzg63fh7cp54124c6zri"; depends=[ASSET]; }; + REDseq = derive2 { name="REDseq"; version="1.32.0"; sha256="15qm9031x9bdywdizwfhpfqvnfrh2pysl8rjxgbbp1ljwkrk39zx"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome BSgenome_Celegans_UCSC_ce2 ChIPpeakAnno IRanges multtest]; }; + REMP = derive2 { name="REMP"; version="1.10.0"; sha256="1isvmnwn08mmivbb4zym6j3v8ig28g96whzsiamwvbzlv02dv55k"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome caret doParallel foreach GenomeInfoDb GenomicRanges impute IRanges iterators kernlab minfi org_Hs_eg_db ranger readr rtracklayer S4Vectors settings SummarizedExperiment]; }; + RGMQL = derive2 { name="RGMQL"; version="1.6.0"; sha256="0da50c4kw87wvajjlbddw3bl3j03i818zdb5g387cif1dkw0gs63"; depends=[BiocGenerics data_table dplyr GenomicRanges glue httr plyr RGMQLlib rJava rtracklayer S4Vectors xml2]; }; + RGSEA = derive2 { name="RGSEA"; version="1.20.0"; sha256="05s3irix9i9w8znzgh3hyjq56qz2iwj0bvfxg6a134hy68db8x84"; depends=[BiocGenerics]; }; + RGalaxy = derive2 { name="RGalaxy"; version="1.30.0"; sha256="1gdczln3gqnmd4w5ycnsc6kk29493q3dfvimlbj40z4vjy98wdgj"; depends=[Biobase BiocGenerics optparse roxygen2 XML]; }; + RGraph2js = derive2 { name="RGraph2js"; version="1.14.0"; sha256="00vafaafnydlrh608k0h87px578c8i0a9s3xzv74xss0gx1h5nkh"; depends=[digest graph rjson whisker]; }; + RIPSeeker = derive2 { name="RIPSeeker"; version="1.26.0"; sha256="1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + RITAN = derive2 { name="RITAN"; version="1.10.0"; sha256="0l76a13jvbx99g3s9iwg1zg1wwbzs75r6hlr2wf032gd5blky38w"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png RColorBrewer reshape2 RITANdata sqldf STRINGdb]; }; + RIVER = derive2 { name="RIVER"; version="1.10.0"; sha256="0lhrrr7qfpka3x19sdsjgvpzr4g94851w80idbzf507k7p31f1v3"; depends=[Biobase ggplot2 glmnet pROC]; }; + RImmPort = derive2 { name="RImmPort"; version="1.14.0"; sha256="1zf21mp5mn0c6prs5z9lmfbgjjka5cd789adw19a3v2n9k530kh0"; depends=[data_table DBI dplyr plyr reshape2 RSQLite sqldf]; }; + RJMCMCNucleosomes = derive2 { name="RJMCMCNucleosomes"; version="1.10.0"; sha256="0yj1l88sfcvb2q695zazxw26jgppx7q7qw3lhskf7p05pz5rpgw7"; depends=[BiocGenerics BiocParallel consensusSeekeR GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; + RLMM = derive2 { name="RLMM"; version="1.48.0"; sha256="02lmszqs4aahxr2n2ni2d3xrcs7bgfm5sr4b44z8zazcacrap189"; depends=[MASS]; }; + RMassBank = derive2 { name="RMassBank"; version="2.14.1"; sha256="12sg68q1i8h2nzi4qf9izqb9qq89vvl9pzzi2nn353vsx0a4m0c3"; depends=[Biobase digest httr MSnbase mzR rcdk Rcpp RCurl rjson S4Vectors XML yaml]; }; + RNASeqPower = derive2 { name="RNASeqPower"; version="1.26.0"; sha256="0gd7bcsg6jd7k7aq2drb86bnvnibzp7asa47qw9wkq5ihz20k44i"; depends=[]; }; + RNASeqR = derive2 { name="RNASeqR"; version="1.4.0"; sha256="1c4c719g4b4xyrkqrfbxxq54ky2vkynrh3ai4jjixj4r8lv2vyj1"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; }; + RNAdecay = derive2 { name="RNAdecay"; version="1.6.0"; sha256="0ymr2xqnz2b39v046qfikai5b2h0w95jqxy85dy8hsppn0r2gnar"; depends=[ggplot2 gplots nloptr TMB]; }; + RNAinteract = derive2 { name="RNAinteract"; version="1.34.0"; sha256="070qy3y532cfhr3v1wiv09pxprgs72dd44igrf5mn77xlbn0xbmy"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; }; + RNAither = derive2 { name="RNAither"; version="2.34.0"; sha256="1d358kkr5vw7a7i9lfbp692py69yhgg5n3xnx1w8vgsgpdc6mhly"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; }; + RNAmodR = derive2 { name="RNAmodR"; version="1.0.2"; sha256="1f7gag9fz9pg0lqxph8xf9xwj5skc6dp20gr7brxp91l2di28wap"; depends=[assertive BiocGenerics BiocParallel Biostrings biovizBase BSgenome colorRamps GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz IRanges matrixStats Modstrings RColorBrewer reshape2 ROCR Rsamtools rtracklayer S4Vectors stringi stringr XVector]; }; + RNAmodR_AlkAnilineSeq = derive2 { name="RNAmodR.AlkAnilineSeq"; version="1.0.0"; sha256="01bvmc1axqrk826kp3h3l5djskc4x3bqbh9pmv9dk3lhmyn3ilas"; depends=[BiocGenerics GenomicRanges Gviz IRanges RNAmodR S4Vectors]; }; + RNAmodR_ML = derive2 { name="RNAmodR.ML"; version="1.0.0"; sha256="0g7hagnphjaswybp5k7slwy6q0k66yi72ycfnhvxxniy2ma2g4cf"; depends=[assertive BiocGenerics GenomicRanges IRanges ranger RNAmodR S4Vectors]; }; + RNAmodR_RiboMethSeq = derive2 { name="RNAmodR.RiboMethSeq"; version="1.0.0"; sha256="0pr71l2xfq4bi07y642x2c6h36730mgz2xlzdylgsmwxxw50p3j5"; depends=[BiocGenerics GenomicRanges Gviz IRanges RNAmodR S4Vectors]; }; + RNAprobR = derive2 { name="RNAprobR"; version="1.18.0"; sha256="0srv204nww6f0rzilwbpfyz1pn3272qqzjsfi4xgniv9qchxayk9"; depends=[BiocGenerics Biostrings GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr Rsamtools rtracklayer S4Vectors]; }; + RNAsense = derive2 { name="RNAsense"; version="1.0.0"; sha256="1332qqry58xih38q8a5wckbjgl70bgj3y9bz9pn2lz4hmphpil1s"; depends=[ggplot2 NBPSeq qvalue SummarizedExperiment]; }; + ROC = derive2 { name="ROC"; version="1.62.0"; sha256="1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y"; depends=[knitr]; }; + ROTS = derive2 { name="ROTS"; version="1.14.0"; sha256="08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm"; depends=[Biobase Rcpp]; }; + ROntoTools = derive2 { name="ROntoTools"; version="2.14.0"; sha256="1s2507wkkx7p3gbgp7l7n6b32w5wivxwddr5nv94p7fh4pgzp9d5"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; }; + RPA = derive2 { name="RPA"; version="1.42.0"; sha256="02v2l3ba8nahlbm80rif6gdgj2cjc9cdsjyq9r22vhmj32arj2nh"; depends=[affy BiocGenerics phyloseq]; }; + RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.8.0"; sha256="0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"; depends=[]; }; + RRHO = derive2 { name="RRHO"; version="1.26.0"; sha256="05ail8xfi6mhi3gwq7fjy7amzzs840l7x6s8g7w8bgxz91zk3xgi"; depends=[VennDiagram]; }; + RSVSim = derive2 { name="RSVSim"; version="1.26.0"; sha256="02z0d1jgqr50j5ldvvv2ndmb1wpjwqmzmrr92rxamy7hd9x96f2h"; depends=[Biostrings GenomicRanges IRanges ShortRead]; }; + RSeqAn = derive2 { name="RSeqAn"; version="1.6.0"; sha256="0x2bw6lc4x596x41403vgj67fk1c6bz4rkbrzqivn7h3mdn0c2ha"; depends=[Rcpp]; }; + RTCA = derive2 { name="RTCA"; version="1.38.0"; sha256="0zv0akxrwfdsjds9xlm93mck1vsqfmd70djhaw43k9zyvxr6vya3"; depends=[Biobase gtools RColorBrewer]; }; + RTCGA = derive2 { name="RTCGA"; version="1.16.0"; sha256="006cla1r03dzyr5slcsj4vblfbfpjn0jxkwjddiwl9smqlc5kpli"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; }; + RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.16.2"; sha256="0jyyahhgngy1qh4q72n5hyg2jvl5l4vvgvxffr209j7ng2z3j6v1"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr IRanges limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; }; + RTN = derive2 { name="RTN"; version="2.10.1"; sha256="0al89sk12k89fk3k4nnas4hhh32x772xj0fm9wy6jwq0494a378i"; depends=[data_table igraph IRanges limma minet mixtools RedeR S4Vectors snow SummarizedExperiment viper]; }; + RTNduals = derive2 { name="RTNduals"; version="1.10.0"; sha256="0m443np16hz1h031hlbchk52r3dhljc9mbkv85f27npz5391pbpa"; depends=[RTN]; }; + RTNsurvival = derive2 { name="RTNsurvival"; version="1.10.0"; sha256="1kmwxkxyrpp82i8fccqxikl6aind3gvzkfrya8cmb0rhvsp971i8"; depends=[data_table dunn_test egg ggplot2 pheatmap RColorBrewer RTN RTNduals scales survival]; }; + RTopper = derive2 { name="RTopper"; version="1.32.0"; sha256="0lzr9l3dnb1q7vs3rvwyfj6jfcagky7g31mdy6vx87m718g6zsm5"; depends=[Biobase limma multtest]; }; + RUVSeq = derive2 { name="RUVSeq"; version="1.20.0"; sha256="1ipbbzpngx988lsmwqv7vbmqm65m43xvsmipayfppkrr6jipzxrj"; depends=[Biobase EDASeq edgeR MASS]; }; + RUVcorr = derive2 { name="RUVcorr"; version="1.18.0"; sha256="15bzvc80gjxcy9bv2kgf2blcy4a1jhnp4d60i4qr60h80z0zkymb"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; }; + RUVnormalize = derive2 { name="RUVnormalize"; version="1.20.1"; sha256="18cyj7lyqzay0sllb554rcdcfyavfyx8y90q5w6k1phci4dzsrrz"; depends=[Biobase RUVnormalizeData]; }; + RVS = derive2 { name="RVS"; version="1.8.0"; sha256="0j3ya49frbad8w3wk4mm11h3ikznkhf8w3385nzrsngprq8cikpv"; depends=[gRain kinship2 snpStats]; }; + RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.10.0"; sha256="0bjlaffls74bkfq41ywbmzw7p1kgfd3s7vjbcyhsynj65cbc3h5j"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; + RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.6.0"; sha256="00vy6z74ilm1zxwiql69wyk729lfdq4q0k92x31hq4vk6rlgzzvs"; depends=[dnet igraph Matrix]; }; + RankProd = derive2 { name="RankProd"; version="3.12.0"; sha256="1sr484pbq0jfvl5mh516if0qa2w91sf7knhdjpzs08qi75h938vk"; depends=[gmp Rmpfr]; }; + RareVariantVis = derive2 { name="RareVariantVis"; version="2.14.0"; sha256="0g31n36hpl6razphgpwc3j6imww271mvm1xg4xwiqfcrzqrw6zq8"; depends=[BiocGenerics BSgenome BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores googleVis gtools IRanges phastCons100way_UCSC_hg19 S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; + Rariant = derive2 { name="Rariant"; version="1.22.0"; sha256="14imvwx7lzjdmz8i19v17cbj30216qz9a45zp81pcsn64faakbbj"; depends=[BiocGenerics dplyr exomeCopy GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges reshape2 Rsamtools S4Vectors shiny SomaticSignatures VariantAnnotation VGAM]; }; + RbcBook1 = derive2 { name="RbcBook1"; version="1.54.0"; sha256="00af0mqic5mdli63zdbv8j74zlxcsx3w51sh0i7w19fw41fix6sj"; depends=[Biobase graph rpart]; }; + Rbowtie = derive2 { name="Rbowtie"; version="1.26.0"; sha256="0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4"; depends=[]; }; + Rbowtie2 = derive2 { name="Rbowtie2"; version="1.8.0"; sha256="1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5"; depends=[]; }; + Rcade = derive2 { name="Rcade"; version="1.28.0"; sha256="0rhhvrmg94risbap6hildgczhgg1mcwcs4dc9s32l7mn54si5lgi"; depends=[baySeq GenomeInfoDb GenomicAlignments GenomicRanges IRanges plotrix rgl Rsamtools S4Vectors]; }; + RchyOptimyx = derive2 { name="RchyOptimyx"; version="2.26.0"; sha256="00p8iznilyxlyx58an01cgpw5sh0caz41zhg0g92yl2kgymj370r"; depends=[flowType graph Rgraphviz sfsmisc]; }; + RcisTarget = derive2 { name="RcisTarget"; version="1.6.0"; sha256="1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw"; depends=[AUCell BiocGenerics data_table feather GSEABase R_utils SummarizedExperiment]; }; + Rcpi = derive2 { name="Rcpi"; version="1.22.0"; sha256="16d9ydxl27yhyba0j302jdj40mi3k1jbkpw7kv38fadi1cr9s726"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; }; + Rcwl = derive2 { name="Rcwl"; version="1.2.1"; sha256="1bj15pkmfp87hvicyqdp8d4jz514krhp5s9a6px7g5fklw0wc07g"; depends=[batchtools BiocParallel codetools DiagrammeR R_utils S4Vectors shiny yaml]; }; + RcwlPipelines = derive2 { name="RcwlPipelines"; version="1.2.0"; sha256="1mlbm08m20pah8r7abzx13q8s8xnw79nb64ywvp9vcsfhl8vzp2p"; depends=[BiocFileCache dplyr jsonlite rappdirs Rcwl tximport]; }; + Rdisop = derive2 { name="Rdisop"; version="1.46.0"; sha256="0j8gmgkab3njgf4w1vymx96s8pszh5s1zjxn3g07sgj8w883z5v7"; depends=[Rcpp]; }; + ReQON = derive2 { name="ReQON"; version="1.32.0"; sha256="10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx"; depends=[rJava Rsamtools seqbias]; }; + ReactomeGSA = derive2 { name="ReactomeGSA"; version="1.0.0"; sha256="19zb9lz03pl12kcvq4wnqiy3cpyxipjjrs0s610ziy9aw3ygs49w"; depends=[ggplot2 httr jsonlite progress]; }; + ReactomePA = derive2 { name="ReactomePA"; version="1.30.0"; sha256="1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; }; + ReadqPCR = derive2 { name="ReadqPCR"; version="1.32.0"; sha256="1iafqadb49g2fwyrps2vlkvzdwg4s4aww39qxi5l06cfy8p0f3ym"; depends=[Biobase]; }; + RedeR = derive2 { name="RedeR"; version="1.34.0"; sha256="0f4k99jkbz1cclh1dzmnk1csvlfzf51nxkqgjc049fxh693vyqcn"; depends=[igraph]; }; + RefNet = derive2 { name="RefNet"; version="1.22.0"; sha256="1bf84q75nyzi5ac2ghbg523iagh972ybqdmrp01jh2sbhqysa835"; depends=[AnnotationHub BiocGenerics IRanges PSICQUIC RCurl shiny]; }; + RefPlus = derive2 { name="RefPlus"; version="1.56.0"; sha256="139bc1nixqn5mwhpwmyvix0kp4kvhxqkmq6fmfvw5h7qbhx0w93i"; depends=[affy affyPLM Biobase preprocessCore]; }; + RepViz = derive2 { name="RepViz"; version="1.2.0"; sha256="13cgj2xbid52hlwk8mdha4j2a862d2ijnhd4wnrdbnqx1fvblmy0"; depends=[biomaRt GenomicRanges IRanges Rsamtools S4Vectors]; }; + Repitools = derive2 { name="Repitools"; version="1.32.0"; sha256="0gdjr1x8aas321yaxgv93xnc9p36gy1kqi1cyp97q7q2krkfby16"; depends=[aroma_affymetrix BiocGenerics Biostrings BSgenome cluster DNAcopy edgeR GenomeInfoDb GenomicAlignments GenomicRanges gplots gsmoothr IRanges MASS Ringo Rsamtools Rsolnp rtracklayer S4Vectors]; }; + ReportingTools = derive2 { name="ReportingTools"; version="2.26.0"; sha256="0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category DESeq2 edgeR ggbio ggplot2 GOstats GSEABase hwriter IRanges knitr lattice limma PFAM_db R_utils XML]; }; + Rgin = derive2 { name="Rgin"; version="1.6.0"; sha256="13xv7v24jf1nmbgycy4nxq81w1car6k1mq5hzwygyf4hq3719g1g"; depends=[RcppEigen]; }; + Rgraphviz = derive2 { name="Rgraphviz"; version="2.30.0"; sha256="00lrkbgbb4payybckcmazsv8skysgdlglyqbl7yjb37vv3gnfc6c"; depends=[graph]; }; + Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.8.0"; sha256="17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7"; depends=[]; }; + Rhisat2 = derive2 { name="Rhisat2"; version="1.2.0"; sha256="02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49"; depends=[GenomicFeatures GenomicRanges SGSeq]; }; + Rhtslib = derive2 { name="Rhtslib"; version="1.18.1"; sha256="0gkbrmrcg55c9s5166ifljlx0v25rv4ijdyp4wf4c292xd6chy2l"; depends=[zlibbioc]; }; + RiboProfiling = derive2 { name="RiboProfiling"; version="1.16.0"; sha256="0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; }; + Ringo = derive2 { name="Ringo"; version="1.50.0"; sha256="1brr4v121h4vq0lldxmb9sqkpwskkg1qwxsnmmwszdynz6m8fdk8"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; }; + Risa = derive2 { name="Risa"; version="1.28.0"; sha256="0fqm5kbzq2561x87g19h2v178n0myswm6996kgvy5ysnjqnf6iny"; depends=[affy Biobase biocViews Rcpp xcms]; }; + Rmagpie = derive2 { name="Rmagpie"; version="1.42.0"; sha256="17gv90jwig8y7nb5zkfvc81dpz3vdzfqy32ak7chxl60kyk8rph5"; depends=[Biobase e1071 kernlab pamr]; }; + RmiR = derive2 { name="RmiR"; version="1.42.0"; sha256="1irfw3bnxas15lf7xn19i5z9ffp16h757h8jwrhxi875j9nlsxg9"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; }; + Rmmquant = derive2 { name="Rmmquant"; version="1.4.0"; sha256="0rw2gb7x67d5nd1wjsgr6jb0pps550jvx5vvmjrj9b8vmhd1lqvm"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + RnBeads = derive2 { name="RnBeads"; version="2.4.0"; sha256="1czjjvir6cvy40mi0r7pl8bn8r9qigl4p4dj4182ikmz97cmlg77"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; + RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="1.17.0"; sha256="0wbxnqhml9ga69jwcpdpawqclvgb34n0f1pvniapyqyvc1pk25l5"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; }; + Rnits = derive2 { name="Rnits"; version="1.20.0"; sha256="0j7jlf8g8snfafdjfx0kz8n4ccb8knzdc280pszb1dbdvdmrj9ar"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; }; + Roleswitch = derive2 { name="Roleswitch"; version="1.24.0"; sha256="1sqwkkakxp2wdldfrkfll0dl90l06frxda6dsajgp0qlgzbnjjyp"; depends=[Biobase biomaRt Biostrings DBI microRNA plotrix pracma reshape]; }; + RpsiXML = derive2 { name="RpsiXML"; version="2.28.0"; sha256="1zwa4k6fkv3w4ysl0ig13zkb33jpr1cjib4cqkn7gf1gi29b8ywi"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; }; + Rqc = derive2 { name="Rqc"; version="1.20.0"; sha256="1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; }; + Rsamtools = derive2 { name="Rsamtools"; version="2.2.3"; sha256="1vj43acawqqkf9yval9fzxarpsf04fmn78m2hq4f083w1k0myhyr"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges Rhtslib S4Vectors XVector zlibbioc]; }; + Rsubread = derive2 { name="Rsubread"; version="2.0.1"; sha256="0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy"; depends=[]; }; + Rtreemix = derive2 { name="Rtreemix"; version="1.48.0"; sha256="1gxyhzygqjljy8qzp3pz207x5pz071ryzvrqwfzga2jx1h6lzc3i"; depends=[Biobase graph Hmisc]; }; + S4Vectors = derive2 { name="S4Vectors"; version="0.24.3"; sha256="01f7dms4kw9ajwqlvh5s47riv748xrrs41na03byhjvn4fbdc44y"; depends=[BiocGenerics]; }; + SAGx = derive2 { name="SAGx"; version="1.60.0"; sha256="1d2hsci0vigvkg98n415cq66mx58vsyyh5mdwbkmkqfy1q0ary6p"; depends=[Biobase multtest]; }; + SAIGEgds = derive2 { name="SAIGEgds"; version="1.0.1"; sha256="1njm3zmq14ikizf7r9xp637pf8k0ybnyki2ks880cgj7zf9jyvdj"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; }; + SANTA = derive2 { name="SANTA"; version="2.24.0"; sha256="1p4f6p7ck8qhfpa0wyh4rmilar2k1b7hrwz644yhadq6wc0g6w6p"; depends=[igraph Matrix snow]; }; + SBGNview = derive2 { name="SBGNview"; version="1.0.0"; sha256="1wbqd3zi3iyh5lhy2bgsh7rqv4ab745z6cz7v9m4gv7ml0105rig"; depends=[AnnotationDbi igraph knitr pathview Rdpack rmarkdown rsvg SBGNview_data SummarizedExperiment xml2]; }; + SBMLR = derive2 { name="SBMLR"; version="1.82.0"; sha256="1nvanldh4jf4y6z3kpjv4wl4a5vkj22y62jmfkwbv2cm17xazkk5"; depends=[deSolve XML]; }; + SC3 = derive2 { name="SC3"; version="1.14.0"; sha256="1wdbcjc0qsf14v9l585g9szwwscmm1znbm5kv7js6r36vlpjgzgh"; depends=[BiocGenerics cluster doParallel doRNG e1071 foreach ggplot2 pheatmap Rcpp RcppArmadillo robustbase ROCR rrcov S4Vectors shiny SingleCellExperiment SummarizedExperiment WriteXLS]; }; + SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.28.0"; sha256="0fzl0m38cixkmcwqzxmdlpznd2s3kx1lhzcg8fw262sn93fkisqk"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; + SCANVIS = derive2 { name="SCANVIS"; version="1.0.0"; sha256="0765xn4rfc0b0svxs232n3gibh0akhwzsij9inp8af96q6qqdbvy"; depends=[IRanges plotrix RCurl rtracklayer]; }; + SCBN = derive2 { name="SCBN"; version="1.4.0"; sha256="0i424hk0hqb9b9sjc76533xcq10z41jm6d81c85jwml9gq0bmq78"; depends=[]; }; + SCnorm = derive2 { name="SCnorm"; version="1.8.2"; sha256="1dmz8dmwhyn1s0xahdcza54i3105v2fnqmhhs57wwv46xvr0c9i8"; depends=[BiocGenerics BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; }; + SDAMS = derive2 { name="SDAMS"; version="1.6.0"; sha256="0clg578nmksd0207nnd102qj9m5a64yglqazj6wcbga3vg202g8n"; depends=[qvalue SummarizedExperiment trust]; }; + SELEX = derive2 { name="SELEX"; version="1.18.0"; sha256="10w0gmvlv5kd0w2nac4rr8in2nz81ww7jr9j444awqp4zfa1rp4r"; depends=[Biostrings rJava]; }; + SEPIRA = derive2 { name="SEPIRA"; version="1.6.0"; sha256="0a4z9wnhlcp0b8b9y0075zalnd2ixnwwz96ahdb8wcnbhlpakpmq"; depends=[corpcor limma]; }; + SEtools = derive2 { name="SEtools"; version="1.0.0"; sha256="1p667nq41zm4p28afymz87j3sl9niy7lk45cid1vnhm7fsx4i9wp"; depends=[circlize ComplexHeatmap data_table pheatmap seriation SummarizedExperiment]; }; + SGSeq = derive2 { name="SGSeq"; version="1.20.0"; sha256="0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer RUnit S4Vectors SummarizedExperiment]; }; + SIAMCAT = derive2 { name="SIAMCAT"; version="1.6.0"; sha256="0y99mhrancwlr5rab4mgq8bmk7414s82sc46cbzvh1pidvk2bxxl"; depends=[beanplot corrplot glmnet gridBase gridExtra infotheo LiblineaR matrixStats mlr ParamHelpers phyloseq pROC progress PRROC RColorBrewer scales stringr]; }; + SICtools = derive2 { name="SICtools"; version="1.16.0"; sha256="11aqi06wrs2jxakkz5zn41ppzv3z8lbfb80fwm8npkh823i7lnlb"; depends=[Biostrings doParallel GenomicRanges IRanges matrixStats plyr Rsamtools stringr]; }; + SIM = derive2 { name="SIM"; version="1.56.0"; sha256="140xdixdv56a5lb11xvgc8xda6l1h11x8ajhfj5s0vy0d2vzza7g"; depends=[globaltest quantreg quantsmooth]; }; + SIMAT = derive2 { name="SIMAT"; version="1.18.0"; sha256="0v0h9vjf3pbg5gk431n907ddblyf3618aq3dqjmy617awcgakddb"; depends=[ggplot2 mzR Rcpp reshape2]; }; + SIMD = derive2 { name="SIMD"; version="1.4.0"; sha256="1dq0kdabnb5ydg3iym0xp3rmd0315sr9bi30yizvxkdbqlbvq125"; depends=[edgeR methylMnM statmod]; }; + SIMLR = derive2 { name="SIMLR"; version="1.12.0"; sha256="19qg14mawfnvq0hrfx1p2a5lzl22kdlzal67n7bjlwbyqqrwgmd1"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; }; + SISPA = derive2 { name="SISPA"; version="1.16.0"; sha256="09p8sk15s40rvfvbhpljcmpgphsl7l4l3mhv1i0rsjgx6g05xciw"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; }; + SLGI = derive2 { name="SLGI"; version="1.46.0"; sha256="0747pqwwwadk21wxzhr3088ps0hnh0k2zlry7j4i54giqhc6p03c"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice ScISI]; }; + SLqPCR = derive2 { name="SLqPCR"; version="1.52.0"; sha256="1bq59h7xb384jl10a15g21ms00gd9prwa3pak8vpnjmramkm0jzg"; depends=[]; }; + SMAD = derive2 { name="SMAD"; version="1.2.0"; sha256="10d7j1z7d34miwba0sxavj4974q33dp5xrgvarf7iaxrj24jm4vr"; depends=[dplyr magrittr matrixStats Rcpp tidyr]; }; + SMAP = derive2 { name="SMAP"; version="1.50.0"; sha256="0wi4sn82jlm9ii37k6bcjlhnra7knzncfqkf1nabf4yq9bsaymrn"; depends=[]; }; + SMITE = derive2 { name="SMITE"; version="1.14.0"; sha256="1v5381b74vgaik60ln782qfpv2jbawb99c3fwp7psnm6g7g703f6"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGG_db org_Hs_eg_db plyr reactome_db S4Vectors scales]; }; + SNAGEE = derive2 { name="SNAGEE"; version="1.26.0"; sha256="05vnwhspr29dsv67nhs09z70sdd7cpv61c86fbhpsab5i2l0sj77"; depends=[SNAGEEdata]; }; + SNPRelate = derive2 { name="SNPRelate"; version="1.20.1"; sha256="0vbs2ky9dfrmwsf81ynvvas8dkaav6h3idi6j6zrvijkrwxy2jq0"; depends=[gdsfmt]; }; + SNPchip = derive2 { name="SNPchip"; version="2.32.0"; sha256="11x6aqgzch5iycm9qi7alm6n8nsnwp6zi2lar1mggrncfpbarbf5"; depends=[Biobase foreach GenomeInfoDb GenomicRanges IRanges lattice oligoClasses S4Vectors SummarizedExperiment]; }; + SNPediaR = derive2 { name="SNPediaR"; version="1.12.0"; sha256="1g596g50sr8v4yxx5jpnbaj8rij53yv0y18n8q6dsq97lgwyav3v"; depends=[jsonlite RCurl]; }; + SNPhood = derive2 { name="SNPhood"; version="1.16.0"; sha256="1652b86x3rr4z5lj5ridwdr1j9ldqgzkcb9b0wmdv83i30bv2dkc"; depends=[BiocGenerics BiocParallel Biostrings checkmate cluster data_table DESeq2 GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges lattice RColorBrewer reshape2 Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + SPEM = derive2 { name="SPEM"; version="1.26.0"; sha256="0pap0zam2lpjfhh3xpzwrxr44rdz024c6r9q4hcdv5mxami2x3c4"; depends=[Biobase Rsolnp]; }; + SPIA = derive2 { name="SPIA"; version="2.38.0"; sha256="0h4lfd7dmfm3d4382q4r51rm2jc2wkli39cs7nck5yr34yvnqzyg"; depends=[KEGGgraph]; }; + SPLINTER = derive2 { name="SPLINTER"; version="1.12.0"; sha256="0xlb7788mv05w76nvy3z95j1y2mn6903p1c2dy8zpvqcmnjfdvp5"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 googleVis Gviz IRanges plyr S4Vectors seqLogo stringr]; }; + SPONGE = derive2 { name="SPONGE"; version="1.8.0"; sha256="06ia15gl0ks454xplkdc6784v972c86zv62m5ci09jgr2kd913nx"; depends=[Biobase data_table doRNG expm foreach glmnet gRbase igraph iterators logging MASS ppcor]; }; + SQLDataFrame = derive2 { name="SQLDataFrame"; version="1.0.0"; sha256="1hm9fbdax1261ca56zwawfyq8cz82khml3by4bd5d29qkk4g8lc9"; depends=[BiocGenerics DBI dbplyr dplyr lazyeval RSQLite S4Vectors tibble]; }; + SQUADD = derive2 { name="SQUADD"; version="1.36.0"; sha256="0lm505l0b1brijv07mxsa8yxd1lzmc1vbkih9dvs1akf1ws2ikg4"; depends=[RColorBrewer]; }; + SRAdb = derive2 { name="SRAdb"; version="1.48.2"; sha256="1cnb0chs7y3wxmmbhlgr3gp8qb1g9xqaw919slm43bvq22wn3y8f"; depends=[GEOquery graph RCurl RSQLite]; }; + SRGnet = derive2 { name="SRGnet"; version="1.12.0"; sha256="13ysx3z37fm0vfiabq7zbjq56ffcblmz8lwwsc70xy4b75a5iisy"; depends=[DMwR EBcoexpress gbm Hmisc igraph limma MASS matrixStats pvclust]; }; + SSPA = derive2 { name="SSPA"; version="2.26.0"; sha256="15qhq0n8gi5cg1y6xcp9dzm9n5dpig1j9nd1lb2zp91k6w2zf25y"; depends=[lattice limma qvalue]; }; + STAN = derive2 { name="STAN"; version="2.14.0"; sha256="0cj17903m413vwqhh7fabzcbn5qfv92b6ylpdpn91r9gac279x08"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; }; + STATegRa = derive2 { name="STATegRa"; version="1.22.0"; sha256="1rb0f490k97gj0zymyk6v0iwdn33wiwrp423d3hbi8zwd02q1ni2"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; }; + STRINGdb = derive2 { name="STRINGdb"; version="1.26.0"; sha256="1zjm4s553x9jirdjjr14l6nlzx30j1zdphacxzwiy6kcvv70k1lf"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; + STROMA4 = derive2 { name="STROMA4"; version="1.10.0"; sha256="01i8jf00sgad43i9vjkcjnj1d4ahlrb9x1md286jsi7fs287hl1n"; depends=[Biobase BiocParallel cluster matrixStats]; }; + SVAPLSseq = derive2 { name="SVAPLSseq"; version="1.12.0"; sha256="0qri2fbcwpwsgb4m7xm5z0l7wh8yggq0g4y4c89jvq64zg1qd6kf"; depends=[edgeR ggplot2 limma lmtest pls SummarizedExperiment]; }; + SWATH2stats = derive2 { name="SWATH2stats"; version="1.16.0"; sha256="04lvvh4jnxj0kapxjxcsrvwvb32w9nw3402nf5bmakba8376d1m6"; depends=[biomaRt data_table ggplot2 reshape2]; }; + SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.40.0"; sha256="08ajjfnf7vj6gwwmh1hk0wpnviv7w3afszs2d2h5cqd25n1qqjw0"; depends=[]; }; + ScISI = derive2 { name="ScISI"; version="1.58.0"; sha256="1x9900813cfv00la2ga77l4in5yzila18dxj8w0x5jd87hs0flgs"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; }; + Scale4C = derive2 { name="Scale4C"; version="1.8.0"; sha256="0bh9sj0x2gh9vri9kpy7ih3rwk3pd5b7lijxmx2g45malb9m9w8a"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; }; + Sconify = derive2 { name="Sconify"; version="1.6.0"; sha256="0hggw68zfs5ql9r5112vkr6vidq423jr83cyc1yfmrnah8rz51ah"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; }; + SemDist = derive2 { name="SemDist"; version="1.20.0"; sha256="0as7r3jgq66liflawza2ly01fm09hz8gxx8ix8f085vd4a2snaw8"; depends=[annotate AnnotationDbi GO_db]; }; + SeqArray = derive2 { name="SeqArray"; version="1.26.2"; sha256="0zqi6jla0r5ixgbiy1w6rridn5y20r49s7cf8d44wk9v1kgan9in"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; + SeqGSEA = derive2 { name="SeqGSEA"; version="1.26.0"; sha256="0kc9by4ljyh7i2sm9rlv90kcs6sy1was8lryjib3l5qfpgdlav6k"; depends=[Biobase biomaRt DESeq doParallel]; }; + SeqSQC = derive2 { name="SeqSQC"; version="1.8.1"; sha256="1558396jdrrnn7vb66x7157wxqjyr7kvl6r0z7hvhs2bfyw113iy"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; }; + SeqVarTools = derive2 { name="SeqVarTools"; version="1.24.1"; sha256="1r15l9g4n2b3mlb8j0kyi5p3rm4m6d9j792f7d84scys68zgz3xf"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix rlang S4Vectors SeqArray tidyr]; }; + SharedObject = derive2 { name="SharedObject"; version="1.0.0"; sha256="06vccj2x8wkgmc413g6gdl907ipa62kpnvzikjbmmyk0y8nhadqy"; depends=[BH BiocGenerics Rcpp xptr]; }; + ShortRead = derive2 { name="ShortRead"; version="1.44.3"; sha256="0ykyrj4g6vc67d5s46sp4659qvar2iavflzhggm79w4p50hxia4s"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; }; + SigCheck = derive2 { name="SigCheck"; version="2.18.0"; sha256="0mxc2kfqqc0nnwlr7pppr2c7hlcfx6qb03wfrkrmczhc9isfkd0s"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; }; + SigFuge = derive2 { name="SigFuge"; version="1.24.0"; sha256="125v0p2fx5djyijs0vvxxng6clc0x243d8xmz238dylbpbzskwn3"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; }; + SigsPack = derive2 { name="SigsPack"; version="1.0.0"; sha256="0r1c0rvslxnznyzib0dkkydmcprxv8hzfxlnnjdxvv2ag8wyjch4"; depends=[Biobase Biostrings BSgenome GenomeInfoDb GenomicRanges quadprog rtracklayer SummarizedExperiment VariantAnnotation]; }; + SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.24.0"; sha256="1ca8k2nic015y4lin03j49wdddy09d3js4wga4c6l2gz141s164w"; depends=[Biobase limma mclust Ringo]; }; + SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.8.0"; sha256="11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5"; depends=[BiocGenerics S4Vectors SummarizedExperiment]; }; + SingleR = derive2 { name="SingleR"; version="1.0.5"; sha256="0lkhf9r9nbp1fr1vl6nx1byknkf8vz21907sj49fbnnccfwv7l5i"; depends=[beachmat BiocNeighbors BiocParallel DelayedArray DelayedMatrixStats ExperimentHub Matrix Rcpp S4Vectors SummarizedExperiment]; }; + SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.22.0"; sha256="1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; + SpacePAC = derive2 { name="SpacePAC"; version="1.24.0"; sha256="0qzlg102v50rrgwl718qrsaml44ax571lhw5nbyj21dw017698kk"; depends=[iPAC]; }; + Spaniel = derive2 { name="Spaniel"; version="1.0.0"; sha256="0lw3dpz431bswcmdbswlj1yzbk9l1krv9k9c3zclp4rzm37jlvjq"; depends=[dplyr ggplot2 jpeg magrittr S4Vectors scater Seurat shiny SingleCellExperiment SummarizedExperiment]; }; + SparseSignatures = derive2 { name="SparseSignatures"; version="1.6.0"; sha256="0a0xkfmm44npl3g75nwkpvw3smp5q8c5mgm33rbb8ksh1ijhw7lv"; depends=[BiocGenerics Biostrings BSgenome BSgenome_Hsapiens_1000genomes_hs37d5 data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls]; }; + SpatialCPie = derive2 { name="SpatialCPie"; version="1.2.0"; sha256="1xr0lwp0wkvxw48iw3099bailq3dck52i4jmarfvxgzgjbhyf8zw"; depends=[colorspace data_table dplyr ggforce ggiraph ggplot2 ggrepel igraph lpSolve purrr readr rlang shiny shinycssloaders shinyjs shinyWidgets SummarizedExperiment tibble tidyr tidyselect zeallot]; }; + SpeCond = derive2 { name="SpeCond"; version="1.40.0"; sha256="14gw21ki7hr51mvivhs4ci0lcc7lylfsaxidpl99a5xz2kvph7k8"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; + SpectralTAD = derive2 { name="SpectralTAD"; version="1.2.0"; sha256="1sj6l5rw284zyhlmw38wpjkng23kjahljdrwd27s209ha76cryq3"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; }; + SpidermiR = derive2 { name="SpidermiR"; version="1.16.2"; sha256="19nl15gfsg1jz9qbzmkmb1bnjg2plpwg1hcprblrlmf257wb5d2j"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra MAGeCKFlute miRNAtap miRNAtap_db networkD3 org_Hs_eg_db TCGAbiolinks visNetwork]; }; + SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.26.1"; sha256="0y00pk2zbc9nvwfvrcadcz5d4db1f89baxqbczv5a7mgjn6hs9ni"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; }; + StarBioTrek = derive2 { name="StarBioTrek"; version="1.12.0"; sha256="1v8n395fzhkdqd198sc0552m1s3m0igqgvlbs1zx8mrz3cijpa4z"; depends=[AnnotationDbi e1071 ggplot2 graphite igraph MLmetrics reshape2 ROCR SpidermiR]; }; + Starr = derive2 { name="Starr"; version="1.42.0"; sha256="1ijccmkwag470k1ck2b0h35iwlbiv7pby8wzsxrxwih6a60xgwln"; depends=[affxparser affy MASS pspline Ringo zlibbioc]; }; + Streamer = derive2 { name="Streamer"; version="1.32.1"; sha256="0rsm13v2gx73pa0599fy5ddn0nyvpjjlnccs177r1dwr32p10yp9"; depends=[BiocGenerics graph RBGL]; }; + Structstrings = derive2 { name="Structstrings"; version="1.2.0"; sha256="04a82yngm5ncj8ykyya7xxilncxmkigi25qh7jw5769frzw1ll92"; depends=[assertive BiocGenerics Biostrings IRanges S4Vectors stringi stringr XVector]; }; + StructuralVariantAnnotation = derive2 { name="StructuralVariantAnnotation"; version="1.2.0"; sha256="1h9mrijs9c7qfk723p79xbz3j2npx1a5dn3sn1ag4k7znbnnqcql"; depends=[assertthat BiocGenerics Biostrings dplyr GenomicRanges rlang rtracklayer stringr VariantAnnotation]; }; + SubCellBarCode = derive2 { name="SubCellBarCode"; version="1.2.6"; sha256="1x5r5brn76ylmvd1isvkxh18iwl34knkdvbbny8pjgd4xhds7jzg"; depends=[AnnotationDbi caret e1071 ggplot2 ggrepel gridExtra networkD3 org_Hs_eg_db Rtsne scatterplot3d]; }; + SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="2.4.0"; sha256="0n9ns50fixdz1x92wd5sjyncyar48cb9c649f44hz5iqd9vjqjrh"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; }; + SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.16.1"; sha256="1z9bdk49dajafkfvv99nv6zyn6v70iyyy2jgdp5w5z8174a2bnn1"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix S4Vectors]; }; + Sushi = derive2 { name="Sushi"; version="1.24.0"; sha256="15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5"; depends=[biomaRt zoo]; }; + SwathXtend = derive2 { name="SwathXtend"; version="2.8.0"; sha256="06hv1iwzpmhaqr2f2ky4p808y52awwg4q3jy3jb04c08csqavakw"; depends=[e1071 lattice openxlsx VennDiagram]; }; + SwimR = derive2 { name="SwimR"; version="1.24.0"; sha256="0xg929r1si6l63jjcnmn4qfj4ih0rl4hrqc7fqyxxd5h9b99nlch"; depends=[gplots heatmap_plus R2HTML signal]; }; + SynMut = derive2 { name="SynMut"; version="1.2.0"; sha256="1rnv4msxpvqb9c5wnp2jwxaq9n0gzzmy330dn5akrpnhrq3zghjm"; depends=[BiocGenerics Biostrings seqinr stringr]; }; + TCC = derive2 { name="TCC"; version="1.26.0"; sha256="05l9lgw9ng1npcfd7lhy5mdjmad7zr5s90ihcvvkfpm3510bg4bi"; depends=[baySeq DESeq DESeq2 edgeR ROC]; }; + TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.14.1"; sha256="0s15ky3hnh2aj4rgfckw6wbgfmlhggs1qlisx5hb0wn7364sc6qv"; depends=[biomaRt data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma plyr purrr purrrogress R_utils RColorBrewer readr rvest S4Vectors scales selectr stringr SummarizedExperiment survival survminer sva tibble tidyr XML xml2]; }; + TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.12.0"; sha256="0jpcrz2zd2p3wdcmi2wr5iw9byg2nkhysifx3787p5qq9dbmvn15"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel maftools pathview plotly readr sesame shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; }; + TCGAutils = derive2 { name="TCGAutils"; version="1.6.2"; sha256="0dh0qwba71ss75176a500fsn3vfgpn426x92gqyk3zdal30h3030"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; + TCseq = derive2 { name="TCseq"; version="1.10.0"; sha256="0739wvq2aaja6dwajdgykzjc5phda1fdx1hhgagwxjpka5g7nx57"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; + TDARACNE = derive2 { name="TDARACNE"; version="1.36.0"; sha256="1x2q82cl8j9iwzaw7vi3s84y25rib3g14ihzyy4jfzf8hq24k0df"; depends=[Biobase GenKern Rgraphviz]; }; + TEQC = derive2 { name="TEQC"; version="4.8.0"; sha256="1wgkjfl0qg72lcrg6zrddshlbw0ankh80darg0l4sgcgzk3g0ndb"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; }; + TFARM = derive2 { name="TFARM"; version="1.8.0"; sha256="0klnxyc1wx03v33vm211a84fwihyrgh04g5hi07q7a9gf24nnix0"; depends=[arules fields GenomicRanges gplots stringr]; }; + TFBSTools = derive2 { name="TFBSTools"; version="1.24.0"; sha256="1jb6ch4ya1xsb0wxsmnc15zrg1sr2xqrim77s3ask0bppj60ziy8"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; }; + TFEA_ChIP = derive2 { name="TFEA.ChIP"; version="1.6.0"; sha256="03w16nc590gvj8wblnfbm5w1m0w6bi4kc98zidal12jiz0c2jbnd"; depends=[biomaRt dplyr GenomicFeatures GenomicRanges IRanges org_Hs_eg_db R_utils]; }; + TFHAZ = derive2 { name="TFHAZ"; version="1.8.0"; sha256="1c0g5pm03s1m73qznylbpbs89zds1v5chclv1wlcfyq7m5gzwssg"; depends=[GenomicRanges IRanges S4Vectors]; }; + TFutils = derive2 { name="TFutils"; version="1.6.0"; sha256="1kvv0cckqhjnd9h6v9lcnvckdcbdxj4yfi6rdb8jc9wh690nbnpn"; depends=[dplyr GSEABase magrittr miniUI Rsamtools shiny]; }; + TIN = derive2 { name="TIN"; version="1.18.0"; sha256="0jqxwkq19kd5cjhhlhvkczhbwgqmw8pbc6niwk2sdf2i6yjkhw4l"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; }; + TMixClust = derive2 { name="TMixClust"; version="1.8.0"; sha256="0hy6cd52xrniv3wkvwarwq94ryw7q6bmsxa6ayy1d99yjrkfq1nk"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; }; + TNBC_CMS = derive2 { name="TNBC.CMS"; version="1.2.0"; sha256="1mx190rc1k4zb5cm34f5biyk5lj69blvpv51y73vnbbqmx6w7s6s"; depends=[e1071 forestplot GGally ggplot2 ggpubr GSVA pheatmap pracma quadprog R_utils RColorBrewer SummarizedExperiment survival]; }; + TOAST = derive2 { name="TOAST"; version="1.0.0"; sha256="0pwjy0qj0zpida29r4yca2k8f8cxdfwmgrp3yh58jlvadzxsdhmm"; depends=[EpiDISH RefFreeEWAS SummarizedExperiment]; }; + TPP = derive2 { name="TPP"; version="3.14.1"; sha256="1dck4d2bif9wgppq68jdba1b77n07pfqmzqq0hk682j9vv8n3z52"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown stringr tidyr VennDiagram VGAM]; }; + TPP2D = derive2 { name="TPP2D"; version="1.2.3"; sha256="0y02cq2gffh1difrdva949i8z8ak5w43chkiclvrsr3adziwi9h3"; depends=[doParallel dplyr foreach ggplot2 MASS openxlsx RCurl stringr tidyr]; }; + TRONCO = derive2 { name="TRONCO"; version="2.18.0"; sha256="07hr0j034bwyam2i1iy8vl836h9r35hk55v37ll458yp48fm8a35"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; }; + TSCAN = derive2 { name="TSCAN"; version="1.24.0"; sha256="021p19j29cdn835xna3b5jfqik0g9ms20dif441a8zy3vn3yj6ab"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; }; + TSRchitect = derive2 { name="TSRchitect"; version="1.12.4"; sha256="0zzzfylkh3mlzg4hgscp3c7rw10bz2pin6ps1gvs5f2d6fd2534l"; depends=[AnnotationHub BiocGenerics BiocParallel dplyr GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges readxl Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + TTMap = derive2 { name="TTMap"; version="1.8.0"; sha256="10x2bfgaf37ihr5wjsgy9a858qfqbyyldcf67q0dw49hkdl2j9ln"; depends=[Biobase colorRamps rgl SummarizedExperiment]; }; + TVTB = derive2 { name="TVTB"; version="1.12.0"; sha256="0b2h499w8kcqayqsbw7waabvl821fvi0m63mh7b7wkdwkjqzpnaa"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; }; + TarSeqQC = derive2 { name="TarSeqQC"; version="1.16.0"; sha256="1w6gki9w7naygh5szdl0h49pwwagcn7kcmw1kf6al0rv5jf1prdd"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; }; + TargetScore = derive2 { name="TargetScore"; version="1.24.0"; sha256="1glk91cws0nj6jizbfh4pd63l0jdvhz653xvq9gpjbvqqclm8ki1"; depends=[Matrix pracma]; }; + TargetSearch = derive2 { name="TargetSearch"; version="1.42.1"; sha256="1yrm3fbvhf3mmsbq56bda6v4rvahyaj6bm0pdkpym1ikdd9ivfvd"; depends=[assertthat ncdf4 stringr]; }; + TimeSeriesExperiment = derive2 { name="TimeSeriesExperiment"; version="1.4.0"; sha256="0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm"; depends=[DESeq2 dplyr dynamicTreeCut edgeR ggplot2 Hmisc limma magrittr proxy S4Vectors SummarizedExperiment tibble tidyr vegan viridis]; }; + TissueEnrich = derive2 { name="TissueEnrich"; version="1.6.0"; sha256="05xvqcn5fgmakc33sjnq9ywacr7lpp1y58f3ap11zma4l46hfh8p"; depends=[dplyr ensurer ggplot2 GSEABase SummarizedExperiment tidyr]; }; + TitanCNA = derive2 { name="TitanCNA"; version="1.24.0"; sha256="1knhlmxcs5mihmb0h3zxg6c8g91fcrgadiaa0h4wgmzb88lgkndq"; depends=[BiocGenerics data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges VariantAnnotation]; }; + TnT = derive2 { name="TnT"; version="1.8.1"; sha256="1bx91hv00w8wh6nq6zwqbbj09i0yn2wfl87fhi7sgck97vnbdrhs"; depends=[Biobase data_table GenomeInfoDb GenomicRanges htmlwidgets IRanges jsonlite knitr S4Vectors]; }; + ToPASeq = derive2 { name="ToPASeq"; version="1.20.0"; sha256="0i85y3mkiicdhb4bx1ydjzapmvgm69n3cpwm4l5gr4cdfmwhzfa9"; depends=[Biobase corpcor graph graphite gRbase limma RBGL Rcpp SummarizedExperiment]; }; + TransView = derive2 { name="TransView"; version="1.30.0"; sha256="1w13wrr2r3ic1ykpn4jij8298h0w928n548kfasgdaql9jjw5gi9"; depends=[BiocGenerics GenomicRanges gplots IRanges Rhtslib S4Vectors zlibbioc]; }; + TreeSummarizedExperiment = derive2 { name="TreeSummarizedExperiment"; version="1.2.0"; sha256="04469skp4lbfapca2b02r59dyrjx68hllxanv06ky590hrdy5vd0"; depends=[ape dplyr S4Vectors SingleCellExperiment SummarizedExperiment]; }; + Trendy = derive2 { name="Trendy"; version="1.8.2"; sha256="15fhx429013xyy1qhaif650mrfnyvzsbrmpmda5cx91d93z9qp4s"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; }; + TurboNorm = derive2 { name="TurboNorm"; version="1.34.0"; sha256="12zb7j0hdvalqyfl15c17jskd3wdyg0wkb98qjvfi1kd1d45a8i1"; depends=[affy convert lattice limma marray]; }; + TxRegInfra = derive2 { name="TxRegInfra"; version="1.6.0"; sha256="0hcb79nj2r5imbh4sxswfxfxcywcm4qvm9n8vg8vpq7v4l1syafl"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; }; + TypeInfo = derive2 { name="TypeInfo"; version="1.52.0"; sha256="06kry8cd0d06c9xkjj7w69kaag9sv9b5cp7b154s130irylw98c0"; depends=[]; }; + UNDO = derive2 { name="UNDO"; version="1.28.0"; sha256="083x7q9rl5iphdqszmb32mqbm5a4pamm127ryar3yq0h2x2rwzyx"; depends=[Biobase BiocGenerics boot MASS nnls]; }; + Ularcirc = derive2 { name="Ularcirc"; version="1.4.0"; sha256="0q4k7602xr8jjvb8b2z1mqdpvdrlbg0qqh76920fpkx3sbqnbbx5"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 ggrepel gsubfn mirbase_db moments Organism_dplyr S4Vectors shiny shinydashboard shinyFiles shinyjs Sushi yaml]; }; + UniProt_ws = derive2 { name="UniProt.ws"; version="2.26.0"; sha256="08c19jrrizkflwcbyngngg19pgi560zpdyqc2f29l7s0sm82j5xb"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; }; + Uniquorn = derive2 { name="Uniquorn"; version="2.6.0"; sha256="0sz4fcxxlkbmprpd540ifb3afp6h3nlmkd2rg9zl6a2cn7pkpagn"; depends=[doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; + VCFArray = derive2 { name="VCFArray"; version="1.2.0"; sha256="060pyn32za1pr6n9r2lbav5358k1vvqi5k04f4piwb6zrs8s0d5g"; depends=[BiocGenerics DelayedArray GenomicFiles GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; + VanillaICE = derive2 { name="VanillaICE"; version="1.48.0"; sha256="1n927gbc4ha5mbs1zqgzsa0ylfs242dn5s2ya3qpk2dnpx8b42qx"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; }; + VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.32.0"; sha256="009s7rzp78s2w6iybizina42qx2w8qv3xwjbkpqphmm451maykgs"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; + VariantExperiment = derive2 { name="VariantExperiment"; version="1.0.0"; sha256="1z18b95c1k8pzfndls726qwwbsvljqgf9m2f9jaglsgkz49psxd3"; depends=[Biostrings DelayedArray DelayedDataFrame GDSArray gdsfmt GenomicRanges IRanges S4Vectors SeqArray SeqVarTools SNPRelate SummarizedExperiment]; }; + VariantFiltering = derive2 { name="VariantFiltering"; version="1.22.0"; sha256="13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores graph Gviz IRanges RBGL Rsamtools S4Vectors shiny shinyjs shinythemes shinyTree SummarizedExperiment VariantAnnotation XVector]; }; + VariantTools = derive2 { name="VariantTools"; version="1.28.0"; sha256="0aafcprsqbn1xl8jqnxfl8r2d0lmzhssqpr26lam2cprh3yk0xiv"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; + Vega = derive2 { name="Vega"; version="1.34.0"; sha256="1ispwwmjwdmrs601v84bsjd91hgaqdwfwh9l3d3vbql4qcqhy482"; depends=[]; }; + VegaMC = derive2 { name="VegaMC"; version="3.24.0"; sha256="1d7yfca6syvdrlgypsgk3dzw7abwfjwi6h6ihvpb5p1x0y9kvkkd"; depends=[Biobase biomaRt genoset]; }; + VennDetail = derive2 { name="VennDetail"; version="1.2.0"; sha256="0a1ml6blbq2skcvnf64ijh3wlg0j0ksk506nyqlf0cjcgh8c2w12"; depends=[dplyr futile_logger ggplot2 magrittr purrr tibble UpSetR VennDiagram]; }; + ViSEAGO = derive2 { name="ViSEAGO"; version="1.0.0"; sha256="029k2fmy6ngzaw2qp0q6r6jkv5kf6ywfv2f5b7jkvfx7cgj561lv"; depends=[AnnotationDbi AnnotationForge biomaRt data_table dendextend DiagrammeR DT dynamicTreeCut ggplot2 GO_db GOSemSim heatmaply htmlwidgets igraph plotly R_utils RColorBrewer scales topGO UpSetR webshot]; }; + Wrench = derive2 { name="Wrench"; version="1.4.0"; sha256="1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm"; depends=[limma locfit matrixStats]; }; + XBSeq = derive2 { name="XBSeq"; version="1.18.0"; sha256="1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; }; + XCIR = derive2 { name="XCIR"; version="1.0.0"; sha256="1dcsm9fjfpywfr3l5n5rlrpc2imkiylvfz8p6xycxrggg37pcw4s"; depends=[biomaRt data_table ggplot2 IRanges readxl S4Vectors seqminer VariantAnnotation]; }; + XDE = derive2 { name="XDE"; version="2.32.0"; sha256="12syfx7zf529n0lcdr9lxgxsyw3g4ipqc3wnp3xqwb43b0zpvnj3"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools MergeMaid mvtnorm RColorBrewer siggenes]; }; + XINA = derive2 { name="XINA"; version="1.4.0"; sha256="1aydqp18b6hvvnm47bsax3c1q826kx7ba6357f3mzc4z0w7l2djy"; depends=[alluvial Biobase ggplot2 gridExtra igraph mclust plyr STRINGdb]; }; + XVector = derive2 { name="XVector"; version="0.26.0"; sha256="0s2gg84yzl5ffkzp6n7kh0jjk1vd90z189f5hkfn18rn67cy2nv7"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; + Xeva = derive2 { name="Xeva"; version="1.2.0"; sha256="1fkyagzzrj7m4ysgwhw1zwggybw7kgj8fv4n89ki50b8bhk7dljn"; depends=[BBmisc Biobase ComplexHeatmap doParallel downloader ggplot2 nlme PharmacoGx Rmisc scales]; }; + YAPSA = derive2 { name="YAPSA"; version="1.12.0"; sha256="132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926"; depends=[circlize ComplexHeatmap corrplot dendextend GenomeInfoDb GenomicRanges GetoptLong ggplot2 gridExtra gtrellis KEGGREST lsei PMCMR reshape2 SomaticSignatures VariantAnnotation]; }; + a4 = derive2 { name="a4"; version="1.34.0"; sha256="14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; }; + a4Base = derive2 { name="a4Base"; version="1.34.1"; sha256="1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83"; depends=[a4Core a4Preproc annaffy AnnotationDbi Biobase genefilter glmnet gplots limma mpm multtest]; }; + a4Classif = derive2 { name="a4Classif"; version="1.34.0"; sha256="0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn"; depends=[a4Core a4Preproc glmnet MLInterfaces pamr ROCR varSelRF]; }; + a4Core = derive2 { name="a4Core"; version="1.34.0"; sha256="0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df"; depends=[Biobase glmnet]; }; + a4Preproc = derive2 { name="a4Preproc"; version="1.34.0"; sha256="11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd"; depends=[AnnotationDbi]; }; + a4Reporting = derive2 { name="a4Reporting"; version="1.34.0"; sha256="15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5"; depends=[annaffy xtable]; }; + aCGH = derive2 { name="aCGH"; version="1.64.0"; sha256="11r0hli1w5lppn08l6i0pb8apn001n0sicnfyc5860i2i4may5jg"; depends=[Biobase cluster multtest survival]; }; + abseqR = derive2 { name="abseqR"; version="1.4.0"; sha256="1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa"; depends=[BiocParallel BiocStyle circlize flexdashboard ggcorrplot ggdendro ggplot2 gridExtra knitr plotly plyr png RColorBrewer reshape2 rmarkdown stringr vegan VennDiagram]; }; + acde = derive2 { name="acde"; version="1.16.0"; sha256="1hdd3v1hvcwa6r1igh6mcjkhfcpagl1x9hkszvb341zvhvx5xdlb"; depends=[boot]; }; + adSplit = derive2 { name="adSplit"; version="1.56.0"; sha256="0k267sfnpr26jmqma7af8iz2ihzjflsyhds3ik3xygdxndbzf6pp"; depends=[AnnotationDbi Biobase cluster GO_db KEGG_db multtest]; }; + adaptest = derive2 { name="adaptest"; version="1.6.1"; sha256="070lszjd0qc204ahd321c1p8s1hn8ivamgqyp1682928zwvjps3z"; depends=[calibrate origami S4Vectors SummarizedExperiment tmle]; }; + adductomicsR = derive2 { name="adductomicsR"; version="1.2.0"; sha256="0hwa667f2j8bnw5zp3i32sf34kr1z6yqng0qhvw5dwvd05a9q4rf"; depends=[adductData ade4 AnnotationHub bootstrap data_table doSNOW dplyr DT ExperimentHub fastcluster foreach fpc mzR OrgMassSpecR pastecs pracma RcppEigen reshape2 rvest smoother zoo]; }; + affxparser = derive2 { name="affxparser"; version="1.58.0"; sha256="03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40"; depends=[]; }; + affy = derive2 { name="affy"; version="1.64.0"; sha256="131za66wbaz9y86gvjqcc2yd1f2ngl2b796xw726g75djhdgxgap"; depends=[affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc]; }; + affyContam = derive2 { name="affyContam"; version="1.44.0"; sha256="0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l"; depends=[affy affydata Biobase]; }; + affyILM = derive2 { name="affyILM"; version="1.38.0"; sha256="1a49pljs41rbry5ycgl2dbzks4ki41bqanrj4jpips4kkl5qx6cz"; depends=[affxparser affy Biobase gcrma]; }; + affyPLM = derive2 { name="affyPLM"; version="1.62.0"; sha256="0zxmqqa2znw1wivax7h4a66m8iyrshyjbffmi6761q5yijwpvlkc"; depends=[affy Biobase BiocGenerics gcrma preprocessCore zlibbioc]; }; + affyPara = derive2 { name="affyPara"; version="1.46.0"; sha256="0sfr5j1hk0g1rb8cy1dbn1a1ji22pyibk3bwrb79ccf2xii0rww9"; depends=[affy affyio aplpack snow vsn]; }; + affyQCReport = derive2 { name="affyQCReport"; version="1.64.0"; sha256="1z42ynlnf0fkh6n28nbn9kmvzhyc1h69snp8aqsxflqac0mkbbwb"; depends=[affy affyPLM Biobase genefilter lattice RColorBrewer simpleaffy xtable]; }; + affycomp = derive2 { name="affycomp"; version="1.62.0"; sha256="0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js"; depends=[Biobase]; }; + affycoretools = derive2 { name="affycoretools"; version="1.58.4"; sha256="1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 Glimma GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; }; + affyio = derive2 { name="affyio"; version="1.56.0"; sha256="0sbkadxdlx7qzxc8z8iv90y6j9b2f62mk3i54dijjh56x3hjy3hb"; depends=[zlibbioc]; }; + affylmGUI = derive2 { name="affylmGUI"; version="1.60.0"; sha256="09l1jklj74m77j57iqmaxdyi6qzn95hfiid2d8fbd5ssfjzysgad"; depends=[affy affyio affyPLM BiocGenerics BiocManager gcrma limma R2HTML tkrplot xtable]; }; + affypdnn = derive2 { name="affypdnn"; version="1.60.0"; sha256="0j7bbhx2kqbhf47lkzijznqrf41cyycrh6bsh3zc81kxp72fvjrq"; depends=[affy]; }; + agilp = derive2 { name="agilp"; version="3.18.0"; sha256="0wdmq4jkv82acqbvgnmmkhy0qd3y81k2p11xhn5ilc7xd40r7wxf"; depends=[]; }; + alevinQC = derive2 { name="alevinQC"; version="1.2.0"; sha256="00vls0qcihyh6xy7aazpxl7i6grgn97kj7zqf0i6sj7gsn7qv532"; depends=[cowplot dplyr DT GGally ggplot2 rjson rmarkdown shiny shinydashboard tximport]; }; + alpine = derive2 { name="alpine"; version="1.12.0"; sha256="1niwxqs4s5ywxf5qcnkzarwd3kjbikm84v0zq978w83i105qkhpf"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; }; + alsace = derive2 { name="alsace"; version="1.22.0"; sha256="1y23zh3kav7rqnbrsg7lqv5hcj08drzbizfyri0k1cygycmid6p2"; depends=[ALS ptw]; }; + altcdfenvs = derive2 { name="altcdfenvs"; version="2.48.0"; sha256="0y9q26prc3acjxqbax3b85v7j7z47ayad3nnzdyk8cqm77as03db"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; }; + amplican = derive2 { name="amplican"; version="1.8.2"; sha256="059rhvzzc6v48jj3l9yvz52m4ak30lkpi9xrl2bbmyd7clr1l80h"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; }; + anamiR = derive2 { name="anamiR"; version="1.13.0"; sha256="0sh4zvkair02kvpwkpqf9mkzkslzha52xw9gxz9h8i7r9c1lxdj2"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; }; + animalcules = derive2 { name="animalcules"; version="1.2.1"; sha256="0pwrfvylfd2k5nkx2ma5mi9wfr7sy8hmyx46jir90rnkwc2sgp00"; depends=[ape assertthat biomformat caret covr DESeq2 DMwR dplyr DT forcats ggplot2 glmnet lattice limma magrittr Matrix MultiAssayExperiment plotly plotROC reactable rentrez reshape2 S4Vectors scales shiny shinyjs SummarizedExperiment tibble tsne umap vegan XML]; }; + annaffy = derive2 { name="annaffy"; version="1.58.0"; sha256="1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16"; depends=[AnnotationDbi Biobase DBI GO_db KEGG_db]; }; + annmap = derive2 { name="annmap"; version="1.28.0"; sha256="0kw7zwf0gxprximavcjp2psaddr1b916bgas0z82xqyq9p468pgi"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; }; + annotate = derive2 { name="annotate"; version="1.64.0"; sha256="0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; }; + annotationTools = derive2 { name="annotationTools"; version="1.60.0"; sha256="1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i"; depends=[Biobase]; }; + annotatr = derive2 { name="annotatr"; version="1.12.1"; sha256="1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; }; + anota = derive2 { name="anota"; version="1.34.0"; sha256="1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m"; depends=[multtest qvalue]; }; + anota2seq = derive2 { name="anota2seq"; version="1.8.0"; sha256="1n58dmf08mm7x7hqaz0iqd9h8ds30y3wcg3b006bydl8zpzn3ijl"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; }; + antiProfiles = derive2 { name="antiProfiles"; version="1.26.0"; sha256="1341xn8c0rgg3z0zjdgl629n3aas10yzzbnm6l0kpgqpask3cbc0"; depends=[locfit matrixStats]; }; + apComplex = derive2 { name="apComplex"; version="2.52.0"; sha256="1n385w12ps40865crp8y3gixwpmdrd8i1k2x1krmgivqa25gkjbw"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; }; + apeglm = derive2 { name="apeglm"; version="1.8.0"; sha256="13i88n18ishzjdpf02af3kq5bly0zd4s6d1xxr0mxll4l93jq5j7"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; + appreci8R = derive2 { name="appreci8R"; version="1.4.0"; sha256="1bnbf6zfnidvl8ib1riya0jyqacb7d5dbp4al8aj41dz151lq378"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ESP6500SI_V2_SSA137_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools rsnps S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; }; + aroma_light = derive2 { name="aroma.light"; version="3.16.0"; sha256="0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x"; depends=[matrixStats R_methodsS3 R_oo R_utils]; }; + arrayMvout = derive2 { name="arrayMvout"; version="1.44.0"; sha256="0cyw5hckmi907k0b9msxb9r1h1inxnn91fqbs7xfd4znvbn4g0zx"; depends=[affy affyContam Biobase lumi mdqc parody simpleaffy]; }; + arrayQuality = derive2 { name="arrayQuality"; version="1.64.0"; sha256="07qllcn5rzh2mi0zss8mmngwyz5khmj5cv0qpdrpxvw327jxbrbw"; depends=[gridBase hexbin limma marray RColorBrewer]; }; + arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.42.0"; sha256="1kqshgzaijqg80grlyvsfxiprzdiy4rp91hm0i80lgrxs59k6ihx"; depends=[affy affyPLM beadarray Biobase genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG svglite vsn XML]; }; + artMS = derive2 { name="artMS"; version="1.4.3"; sha256="15dh9zbr1m0is7k6jagw631a6c88giik8svmx66524dnq1igga58"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer scales seqinr stringr tidyr UpSetR VennDiagram yaml]; }; + atSNP = derive2 { name="atSNP"; version="1.2.0"; sha256="1isrrg51ilc2jhqblwyab6a1wbymillxvmbc4d93lrq4irib4fns"; depends=[BiocFileCache BiocParallel BSgenome data_table ggplot2 motifStack rappdirs Rcpp testit]; }; + attract = derive2 { name="attract"; version="1.38.0"; sha256="04q21rkbn74gl8wkq16f06wh50lvp830ai5fmz932r03z4320f6g"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; }; + bacon = derive2 { name="bacon"; version="1.14.0"; sha256="1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86"; depends=[BiocParallel ellipse ggplot2]; }; + ballgown = derive2 { name="ballgown"; version="2.18.0"; sha256="0zki87bk6id4mb42hp3znvjkag140ivp9s1jbmlalrrxm82abqkq"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; + bamsignals = derive2 { name="bamsignals"; version="1.18.0"; sha256="0699b0pqbs0dvs91yjibcjc90lxj9mg8rcml4a6wchfr9md7n74w"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; + banocc = derive2 { name="banocc"; version="1.10.0"; sha256="19ad5yifw3a1y5f2b1dipzw2ymbqa2aakhzz4kwxgara5yi1gak0"; depends=[coda mvtnorm rstan stringr]; }; + basecallQC = derive2 { name="basecallQC"; version="1.10.0"; sha256="0nr0xspyl3h8rlv8lf5vl3j098jrdfg65p5vgl1lnwyws32nmjhn"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; }; + batchelor = derive2 { name="batchelor"; version="1.2.4"; sha256="1i9zi221xqw34saw671yikcq6c3cd05zvzy6jpb8v5nxd97gick3"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors scater SingleCellExperiment SummarizedExperiment]; }; + bayNorm = derive2 { name="bayNorm"; version="1.4.14"; sha256="04yy43n38y8x4v1112qfi9hi63qpxjds32mca81kzsh1ysrj9ii4"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Matrix Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; }; + baySeq = derive2 { name="baySeq"; version="2.20.0"; sha256="040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk"; depends=[abind edgeR GenomicRanges]; }; + bcSeq = derive2 { name="bcSeq"; version="1.8.0"; sha256="11pipxz43llvvk84zs7ich602cc91b1bvhh35m582azyzlhqgz42"; depends=[Biostrings Matrix Rcpp]; }; + beachmat = derive2 { name="beachmat"; version="2.2.1"; sha256="1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i"; depends=[BiocGenerics DelayedArray Matrix]; }; + beadarray = derive2 { name="beadarray"; version="2.36.0"; sha256="0kz9j93mrqs6i2rkp60f2f0drzj4zsagznwq7n8cacc2x1kqmm6l"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 hexbin illuminaio IRanges limma reshape2]; }; + beadarraySNP = derive2 { name="beadarraySNP"; version="1.52.0"; sha256="18kc7pnd11x37xr5168pk2jnhhxp9zb1fyvp44ghw8126khg51c8"; depends=[Biobase quantsmooth]; }; + bgafun = derive2 { name="bgafun"; version="1.48.0"; sha256="0690rqk97nvhw2jlcaaj9ill73jr02fqv60fc82qlp03bday02iq"; depends=[ade4 made4 seqinr]; }; + bgx = derive2 { name="bgx"; version="1.52.0"; sha256="0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm"; depends=[affy Biobase gcrma Rcpp]; }; + bigPint = derive2 { name="bigPint"; version="1.2.2"; sha256="1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs"; depends=[dplyr GGally ggplot2 gridExtra hexbin Hmisc htmlwidgets plotly plyr RColorBrewer reshape shiny shinycssloaders shinydashboard stringr tidyr]; }; + bigmelon = derive2 { name="bigmelon"; version="1.12.0"; sha256="0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; }; + bigmemoryExtras = derive2 { name="bigmemoryExtras"; version="1.34.0"; sha256="17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq"; depends=[bigmemory]; }; + bioCancer = derive2 { name="bioCancer"; version="1.14.02"; sha256="1p1rgnqgdaak2ccdcn7l302d47p9m44i0qz157x09c0xx8dkgzxx"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; }; + bioDist = derive2 { name="bioDist"; version="1.58.0"; sha256="0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q"; depends=[Biobase KernSmooth]; }; + bioassayR = derive2 { name="bioassayR"; version="1.24.0"; sha256="08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; + biobroom = derive2 { name="biobroom"; version="1.18.0"; sha256="1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb"; depends=[Biobase broom dplyr tidyr]; }; + biocGraph = derive2 { name="biocGraph"; version="1.48.0"; sha256="1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw"; depends=[BiocGenerics geneplotter graph Rgraphviz]; }; + biocViews = derive2 { name="biocViews"; version="1.54.0"; sha256="0yn8jys1900d31haayz0ppqk5y79mwjajwp4alz6pln3dbs70f3g"; depends=[Biobase BiocManager graph RBGL RCurl RUnit XML]; }; + biomaRt = derive2 { name="biomaRt"; version="2.42.1"; sha256="0676s8aq9xj2pdrfk28kf5j69fmssn900k4vxrp11ghwjr8z24h7"; depends=[AnnotationDbi BiocFileCache httr openssl progress rappdirs stringr XML]; }; + biomformat = derive2 { name="biomformat"; version="1.14.0"; sha256="0aa32q6sfiy8aqbds2m8gpijz0js8ch9r7wvvsnzbilqqf80zwzr"; depends=[jsonlite Matrix plyr rhdf5]; }; + biomvRCNS = derive2 { name="biomvRCNS"; version="1.26.0"; sha256="1hysm0z4kvx8wcgd3v4wkznnp70ridwr339qgg8dwns9i67wsmfc"; depends=[GenomicRanges Gviz IRanges mvtnorm]; }; + biosigner = derive2 { name="biosigner"; version="1.14.4"; sha256="0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl"; depends=[Biobase e1071 MultiDataSet randomForest ropls]; }; + biosvd = derive2 { name="biosvd"; version="2.22.0"; sha256="1irj093xiqlar4k88bqmv1jchs948hm8irmi7xi059jv2g2a5mk4"; depends=[Biobase BiocGenerics NMF]; }; + biotmle = derive2 { name="biotmle"; version="1.10.0"; sha256="17197dyl169jfk1134amw06shgah118gs4vlzqfvh5ymrvfy0inn"; depends=[assertthat BiocGenerics BiocParallel doFuture dplyr future ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tibble tmle]; }; + biovizBase = derive2 { name="biovizBase"; version="1.34.1"; sha256="04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer rlang Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + birta = derive2 { name="birta"; version="1.30.0"; sha256="1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg"; depends=[Biobase limma MASS]; }; + biscuiteer = derive2 { name="biscuiteer"; version="1.0.0"; sha256="0hgvl1rd2qc6xfsi2882y3h9bfcw6wja5vis20d6q4bvvhs9lm1l"; depends=[Biobase BiocGenerics biscuiteerData bsseq data_table DelayedMatrixStats dmrseq GenomeInfoDb GenomicRanges gtools HDF5Array Homo_sapiens impute Matrix matrixStats Mus_musculus QDNAseq qualV R_utils readr Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; + blacksheepr = derive2 { name="blacksheepr"; version="1.0.0"; sha256="0756z7qv0rdfjqpb7xbb22m70dyg2aljm0xnf034bhw5bg8irjg6"; depends=[circlize ComplexHeatmap pasilla RColorBrewer SummarizedExperiment viridis]; }; + blima = derive2 { name="blima"; version="1.20.0"; sha256="0q21hmla6xpjrf8fxjjhvkanlvkr2ry04qf0hzsy804sp3fh26lx"; depends=[beadarray Biobase BiocGenerics Rcpp]; }; + bnbc = derive2 { name="bnbc"; version="1.8.0"; sha256="0pv3vkrdkpv5w2bv6ph0w4m66d96dlybba2h832qh5dgw0dx267f"; depends=[BiocGenerics EBImage GenomeInfoDb GenomicRanges IRanges matrixStats preprocessCore Rcpp S4Vectors SummarizedExperiment sva]; }; + brainflowprobes = derive2 { name="brainflowprobes"; version="1.0.0"; sha256="1g124wm87l2xb4p5j8xcm951mqfl3v49bqdn11n3704y9zs6czpm"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 bumphunter cowplot derfinder derfinderPlot GenomicRanges GenomicState ggplot2 RColorBrewer]; }; + branchpointer = derive2 { name="branchpointer"; version="1.12.0"; sha256="14cbxm9krhwxf1s1x9brb71bsbhkg93z5gm3makh7gyy5lh1b28r"; depends=[biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg38 caret cowplot data_table gbm GenomeInfoDb GenomicRanges ggplot2 IRanges kernlab plyr rtracklayer S4Vectors stringr]; }; + breakpointR = derive2 { name="breakpointR"; version="1.4.0"; sha256="0pdn4pkb2pnp3n40gd2rbzzkrv0ss4ja5zxz96f2xxp0hv5han0d"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; }; + brendaDb = derive2 { name="brendaDb"; version="1.0.0"; sha256="0phh05kra323fi3qps6qdad3avffvwb7jc9226055qchxmx81mz8"; depends=[BiocFileCache BiocParallel crayon curl dplyr magrittr purrr rappdirs Rcpp rlang stringr tibble tidyr xml2]; }; + bridge = derive2 { name="bridge"; version="1.50.0"; sha256="0g0hdicabfzk0wak3m76y1pv2w9r7hcdaynb2pgzscvisnq5mczl"; depends=[rama]; }; + bsseq = derive2 { name="bsseq"; version="1.22.0"; sha256="12bb3a4p1yn1nwbbxy2zb68b61zmgja5j5yzd49aj3hi5k7q1dhq"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 S4Vectors scales SummarizedExperiment]; }; + bumphunter = derive2 { name="bumphunter"; version="1.28.0"; sha256="1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; + cTRAP = derive2 { name="cTRAP"; version="1.4.0"; sha256="05skca2wmr6dp1vjfbbdi1ig06g6wv03dikjzml3k5vva5pdnza4"; depends=[biomaRt cowplot data_table dplyr fgsea ggplot2 ggrepel httr limma pbapply R_utils readxl reshape2 rhdf5]; }; + caOmicsV = derive2 { name="caOmicsV"; version="1.16.0"; sha256="0jn0rpmssvrn3z9wnvjb90scbvyvcqkhavqxl4wxg3532rgv569p"; depends=[bc3net igraph]; }; + calm = derive2 { name="calm"; version="1.0.0"; sha256="1vkf2pbhgyvgg6qdglr805c91lsgh8xsqhj8j0lnnky9i379g4sy"; depends=[mgcv]; }; + canceR = derive2 { name="canceR"; version="1.20.0"; sha256="19m0wl8vr1l125g34rahaah2fr82xy1pk5qr1pbzrl45hc7zd1g8"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; + cancerclass = derive2 { name="cancerclass"; version="1.30.0"; sha256="1qqgy2nnbvsj9ks2ipkchr8havwm349gc127ds0bmlb5h0x714h4"; depends=[binom Biobase]; }; + casper = derive2 { name="casper"; version="2.20.0"; sha256="0j2h7y84mdf098kpg8czshchmyc4c7ph5d1idy9zy2was60v2hc7"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; }; + categoryCompare = derive2 { name="categoryCompare"; version="1.30.0"; sha256="1rmp14q6diviscg6bw9rjs8067vvfmhf06w8k15mpx0vx7pqb1m2"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; + cbaf = derive2 { name="cbaf"; version="1.8.1"; sha256="10r32j0phawq66v6jbldrjydm8574rs6ivmgar0f0mkwpvpnaswn"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; }; + ccfindR = derive2 { name="ccfindR"; version="1.6.0"; sha256="0p1s6dvyp9mpk8mhpayavq44rr7i6ycyq5idycv3dyhps7dypa33"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rdpack Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; + ccmap = derive2 { name="ccmap"; version="1.12.0"; sha256="1lwszqb9xh8y59vqsnp42dkkvg2ydmds3wcg55zadk5ld4ndikl4"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; }; + ccrepe = derive2 { name="ccrepe"; version="1.22.0"; sha256="0kwa8lpd9vnjq944ynd51vksnlszlcdc2yjm32d1jcy8gl15qi5c"; depends=[infotheo]; }; + celaref = derive2 { name="celaref"; version="1.4.0"; sha256="11847lq8j38ngja15wl3fmgzly2icsrgwx2vgay2jziwnghc833l"; depends=[BiocGenerics DelayedArray dplyr ggplot2 magrittr MAST Matrix readr rlang S4Vectors SummarizedExperiment tibble]; }; + celda = derive2 { name="celda"; version="1.2.4"; sha256="154jsxw89ww5h5lcgpqfyli099m7ps699iv6nz6cw82glrlk4c1h"; depends=[data_table dendextend digest doParallel enrichR foreach ggdendro ggplot2 ggrepel gridExtra gtable magrittr MAST matrixStats MCMCprecision plyr pROC RColorBrewer Rcpp RcppEigen reshape2 Rtsne S4Vectors scales stringi SummarizedExperiment uwot withr]; }; + cellGrowth = derive2 { name="cellGrowth"; version="1.30.0"; sha256="01pfl0yxn3k09viirhp6n89bvr8dylddz81pcfh9sh6r46nrbqmq"; depends=[lattice locfit]; }; + cellHTS2 = derive2 { name="cellHTS2"; version="2.50.0"; sha256="0nmqkqyrd4954kj4zx5n4xnlhmmx7zmiqx712a3dvkj3rgnnmvha"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit prada RColorBrewer splots vsn]; }; + cellTree = derive2 { name="cellTree"; version="1.16.0"; sha256="0cgbmkhjfv7zfir3qx1kq7x2b6cypxvmm12g1l99bfpbplq26whz"; depends=[gplots igraph slam topGO topicmodels xtable]; }; + cellbaseR = derive2 { name="cellbaseR"; version="1.10.0"; sha256="0i0r0a8lgaqprjsv8d3k8fcvqxwbyszi2h0lin4xl3wm3nijk0c9"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; }; + cellity = derive2 { name="cellity"; version="1.14.0"; sha256="1p04dwwi58wxrwn6jpwczys16dp9f3mr7i1dd3815wb8nvfrpps9"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; }; + cellscape = derive2 { name="cellscape"; version="1.10.0"; sha256="1fswznir81a2yaivmb6792ahi6kpfjyyd6c7zz5w5chahb9a7pa6"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; }; + cghMCR = derive2 { name="cghMCR"; version="1.44.0"; sha256="09r7kjgrm0i3nv80aq47b97vhg8fi8k6axj31kc5j73vpl022a0k"; depends=[BiocGenerics CNTools DNAcopy limma]; }; + chimera = derive2 { name="chimera"; version="1.28.0"; sha256="09ws9xkczdxyxg6rkm45glahxg8dg1z5f8m5jhr9bbfygcvxmnyz"; depends=[AnnotationDbi Biobase BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges Homo_sapiens Rsamtools TxDb_Hsapiens_UCSC_hg19_knownGene]; }; + chimeraviz = derive2 { name="chimeraviz"; version="1.12.3"; sha256="0pnnv1rdakmqq2d60qgn21zb024mhdhk14dglq7jh1g4dxfkgzib"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph gtools Gviz IRanges magick org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; }; + chipenrich = derive2 { name="chipenrich"; version="2.10.0"; sha256="1619q668ixjcb2xmx1gscwi8kppfbc445yy1c1kyvmj3qxkmy4jb"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra MASS mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; }; + chipseq = derive2 { name="chipseq"; version="1.36.0"; sha256="1ln6bn08xig3j6ryak1xfkjhvpnlm2vf1czz9hlj6f02299nbs6l"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; }; + chopsticks = derive2 { name="chopsticks"; version="1.52.0"; sha256="1v7q5n53sn3g5s3l41ixmq9hm675s9i6rm34dsffq11gyp39fpnl"; depends=[survival]; }; + chroGPS = derive2 { name="chroGPS"; version="2.4.0"; sha256="1fpf6n544q70lfm87hnvxx8288h3102hpdj5h0rsryrvgfbz2xbf"; depends=[Biobase changepoint cluster ellipse GenomicRanges ICSNP IRanges MASS vegan]; }; + chromDraw = derive2 { name="chromDraw"; version="2.16.0"; sha256="1dldh083kc4p9f1ik88amadl9bdjpnyrhcm0gakwaqwi7ymn9qxc"; depends=[GenomicRanges Rcpp]; }; + chromPlot = derive2 { name="chromPlot"; version="1.14.0"; sha256="0z5hcnlz2nd63wrrz133719x0pa51w5ns7azj6wzjamy40p3cfsm"; depends=[biomaRt GenomicRanges]; }; + chromVAR = derive2 { name="chromVAR"; version="1.8.0"; sha256="1gs351fdc715mc04jqjkjdbasgniyrav1qwbm84cqx8pji4yhdzg"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; }; + chromstaR = derive2 { name="chromstaR"; version="1.12.0"; sha256="0f9qbcrsypvcy3qkw665y5wphjdbs159kb6lgv4vbqdyjyi1n33b"; depends=[bamsignals BiocGenerics chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; }; + chromswitch = derive2 { name="chromswitch"; version="1.8.0"; sha256="1lcx14s7p6clj4r0cq4r4gfjqggvq1n7lq8zk74kb1y1c3wh0dk6"; depends=[Biobase BiocParallel cluster dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats NMF rtracklayer S4Vectors tidyr]; }; + cicero = derive2 { name="cicero"; version="1.4.4"; sha256="1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld"; depends=[assertthat Biobase BiocGenerics data_table dplyr FNN GenomicRanges ggplot2 glasso Gviz igraph IRanges Matrix monocle plyr reshape2 S4Vectors stringr tibble tidyr VGAM]; }; + circRNAprofiler = derive2 { name="circRNAprofiler"; version="1.0.0"; sha256="02kc3g6nxcjn8xvd81aqkxdx3zb9ffl1bw92d9ij68c37nnz753x"; depends=[AnnotationHub Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DESeq2 dplyr edgeR GenomeInfoDb GenomicRanges ggplot2 gwascat IRanges magrittr R_utils readr reshape2 rlang rtracklayer S4Vectors seqinr stringi stringr]; }; + cisPath = derive2 { name="cisPath"; version="1.26.0"; sha256="0p1gnxfv4dwrsbhb6mz36amkwp2h47zdspm31gg92dqjn03l6m7v"; depends=[]; }; + cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.24.0"; sha256="17bsq1fmdx9iqsmi9xk2hl8d7y8cy8ayaldvigyxlll25zq754r1"; depends=[BiocGenerics BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomeInfoDb GenomicRanges IRanges seqinr]; }; + cleaver = derive2 { name="cleaver"; version="1.24.0"; sha256="1wx5p12b502z1cfa717z1r7nylfdwrj2w0si66l32ann57plmlrr"; depends=[Biostrings IRanges S4Vectors]; }; + clippda = derive2 { name="clippda"; version="1.36.0"; sha256="1sd4wmmzqjxmrflgw57sdnhh6iy1hamls1hjr2rnf6w9kpjv2q3r"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; }; + clipper = derive2 { name="clipper"; version="1.26.0"; sha256="080vvimjqs86ibn1xiwpnzj0vhfr6nkibshv58is2lbsngcn7hbd"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; }; + cliqueMS = derive2 { name="cliqueMS"; version="1.0.2"; sha256="057x2dkr4mszsqj6v5pgrw1vy7ylim3gfyw0gm3xx099iacdhklp"; depends=[BH igraph matrixStats MSnbase qlcMatrix Rcpp RcppArmadillo xcms]; }; + clonotypeR = derive2 { name="clonotypeR"; version="1.24.0"; sha256="1sdic5s5kag6r2i4cy2yvalssy0s0bxlm42g5zk357njp7lf1qc5"; depends=[]; }; + clst = derive2 { name="clst"; version="1.34.0"; sha256="1044pjh975hk8yndbs9xf44slnz313w5rbgamc1pn7ba100zmsnh"; depends=[lattice ROC]; }; + clstutils = derive2 { name="clstutils"; version="1.34.0"; sha256="0qsx0d0wkyg31r850q6d28dnzgpjfw3ncfz2j2lnia9j4g36mn72"; depends=[ape clst lattice rjson RSQLite]; }; + clustComp = derive2 { name="clustComp"; version="1.14.0"; sha256="1i1gjm9z1ffw5ircdfc8l768jkfgxkpclmmsbgjkxvaxgbcrhyji"; depends=[sm]; }; + clusterExperiment = derive2 { name="clusterExperiment"; version="2.6.1"; sha256="1dn2a03z491qnqakbbs7kvkjaas1l406s0s6d2mm8jy0724nq94f"; depends=[ape BiocGenerics cluster DelayedArray edgeR HDF5Array howmany kernlab limma locfdr Matrix matrixStats NMF phylobase pracma RColorBrewer Rcpp RSpectra S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; + clusterProfiler = derive2 { name="clusterProfiler"; version="3.14.3"; sha256="08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg"; depends=[AnnotationDbi DOSE enrichplot ggplot2 GO_db GOSemSim magrittr plyr qvalue rvcheck tidyr]; }; + clusterSeq = derive2 { name="clusterSeq"; version="1.10.0"; sha256="0wzf2lsllz43qdymgjvk57c5x9yglwsc9pigcxnjjv8gsny7s3fd"; depends=[baySeq BiocGenerics BiocParallel]; }; + clusterStab = derive2 { name="clusterStab"; version="1.58.0"; sha256="1kxy4fnir7hgpvx90h1y18mgg7nr2jac1wj9qafz7lv0yfr4h8ab"; depends=[Biobase]; }; + cn_farms = derive2 { name="cn.farms"; version="1.34.0"; sha256="1wprimcbhrz9929x121cy434ny5qsy0s3wjgc105513v6fr7c367"; depends=[affxparser Biobase DBI DNAcopy ff lattice oligo oligoClasses preprocessCore snow]; }; + cn_mops = derive2 { name="cn.mops"; version="1.32.0"; sha256="0fbj46papqfbbgw1jcfr83xmlivbdmrqd5s0b8wgaqnp7i4y94dz"; depends=[Biobase BiocGenerics exomeCopy GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; + cnvGSA = derive2 { name="cnvGSA"; version="1.30.0"; sha256="195pqh35qxrwz2mi2m40kcnx1cbc8nakc0dh1akqlp90hfcnkc0l"; depends=[brglm doParallel foreach GenomicRanges splitstackshape]; }; + coGPS = derive2 { name="coGPS"; version="1.30.0"; sha256="09km25bmwqf3g3m63g3jk4gnwgwh4v2flarqq2fjgxp8mr703gz1"; depends=[]; }; + coMET = derive2 { name="coMET"; version="1.18.0"; sha256="1rkp63r2hcfji23np48j7r570imildll7kbika43bfn6c1bkbq83"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; }; + coRdon = derive2 { name="coRdon"; version="1.4.0"; sha256="1rnx74vqsk58v9dv3fqwyq90zg2n8dyyacd8b6hjy9qq2idgvgyi"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; }; + cobindR = derive2 { name="cobindR"; version="1.24.0"; sha256="0fxh8s03nk2lq2nn6bzbg9wg9721671hwiq1a7swndlmsllvlfsq"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust seqinr yaml]; }; + codelink = derive2 { name="codelink"; version="1.54.0"; sha256="06fprm8fpajl9i1wf23mklj60w77fgliiqz8in6y4x5aqfhms84z"; depends=[annotate Biobase BiocGenerics limma]; }; + coexnet = derive2 { name="coexnet"; version="1.8.0"; sha256="0slyg939k2kbxaynqcrhjan4l9cyacgicpmximanaqjayn1dazba"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; }; + cogena = derive2 { name="cogena"; version="1.20.0"; sha256="1wfxm1g385r0rx68yx8mir0k03r6ryx9i2w7kxk2hbvp6m4m9chd"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2]; }; + cola = derive2 { name="cola"; version="1.2.1"; sha256="0f0jwpsxkxywfy829swlyzzznsacyfqxg3zhhd1wqcl04c67w8si"; depends=[BiocGenerics brew circlize clue cluster ComplexHeatmap crayon digest eulerr GetoptLong GlobalOptions httr impute knitr markdown matrixStats mclust microbenchmark png RColorBrewer Rcpp skmeans xml2]; }; + compEpiTools = derive2 { name="compEpiTools"; version="1.20.0"; sha256="0zc7mbgr10ldirry5zkwnidjmcmncsxrijsw6a6clyk9hmvpzjkw"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; }; + compartmap = derive2 { name="compartmap"; version="1.4.0"; sha256="0f996v77qwb57bvmi3xda0niw8kbnna4jwqqj4jwj72x7j1pf6n3"; depends=[GenomicRanges gtools Homo_sapiens minfi mixOmics SummarizedExperiment]; }; + compcodeR = derive2 { name="compcodeR"; version="1.22.0"; sha256="0lkxppbpvpsh1zl5c4781g3yfy7gf36gp53wy0m43q6b4bj92ky4"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; }; + consensus = derive2 { name="consensus"; version="1.4.0"; sha256="1shp36gml63ys8lifq2h89cq92w59snmnivpgaz0nbphlqdm0w9q"; depends=[gplots matrixStats RColorBrewer]; }; + consensusDE = derive2 { name="consensusDE"; version="1.4.0"; sha256="1brq9wbd5mb4qm208xrxxykialxjnpix17k879ihrq226rpmw0m1"; depends=[airway AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings data_table dendextend DESeq2 EDASeq edgeR EnsDb_Hsapiens_v86 ensembldb GenomicAlignments GenomicFeatures limma org_Hs_eg_db pcaMethods RColorBrewer Rsamtools RUVSeq S4Vectors SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm3_ensGene]; }; + consensusOV = derive2 { name="consensusOV"; version="1.8.1"; sha256="1jvzx5anpns6q45k9xr6j4ygs981sly4ha6wcbshjgkq2mbqp6q7"; depends=[Biobase gdata genefu GSVA limma matrixStats randomForest]; }; + consensusSeekeR = derive2 { name="consensusSeekeR"; version="1.14.0"; sha256="1cva4xb72zmg5nzq20j94vqxn36pipasn1yb7l7ajb2mih1d6cqa"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges IRanges rtracklayer S4Vectors stringr]; }; + contiBAIT = derive2 { name="contiBAIT"; version="1.14.0"; sha256="0ncpqknapk9w29dsgimcr1bc8b06h09sl9pybx7r7fyprhadsyzp"; depends=[BH BiocGenerics BiocParallel clue cluster colorspace data_table diagram DNAcopy exomeCopy GenomicAlignments GenomicFiles GenomicRanges ggplot2 gplots gtools IRanges Rcpp reshape2 Rsamtools rtracklayer S4Vectors TSP]; }; + conumee = derive2 { name="conumee"; version="1.20.0"; sha256="1fh2kkhlqdb2fq9cdxjzbyn9agcr6i7icqgf7aqvgclfliz5bbbp"; depends=[DNAcopy GenomeInfoDb GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges minfi rtracklayer]; }; + convert = derive2 { name="convert"; version="1.62.0"; sha256="1i6hq3cdz8xi881hmlxlyv7y9p8d1yj1d8dch9v59bk0nfqdr982"; depends=[Biobase limma marray]; }; + copa = derive2 { name="copa"; version="1.54.0"; sha256="0wc62yxg3jhvn4l5wgr7g2vamgxz4yvk4swrc707kzgy301wa69i"; depends=[Biobase]; }; + copynumber = derive2 { name="copynumber"; version="1.26.0"; sha256="0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj"; depends=[BiocGenerics GenomicRanges IRanges S4Vectors]; }; + coseq = derive2 { name="coseq"; version="1.10.0"; sha256="0rwy92p2l9x5fv4cinw19vffn565fr5l4jz292hrqhngmpmx5s9i"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; }; + cosmiq = derive2 { name="cosmiq"; version="1.20.0"; sha256="1hgrap9jicwwidp0ri5ybn62r9h2kr9gq3vjz71531y6kpn2csdx"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; }; + countsimQC = derive2 { name="countsimQC"; version="1.4.0"; sha256="0smf4l9hc90x4ymj77lzb50zhpiv6pnj4jd17qm4ncnxligr74j4"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; }; + covEB = derive2 { name="covEB"; version="1.12.0"; sha256="1pkjhfknvrn48wmkmc5nc6y43sycbayxxfywqdz2zrzvnapm6h5l"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; }; + covRNA = derive2 { name="covRNA"; version="1.12.0"; sha256="1r51xgq9vv6cm1y67bcw44qj8cbs1adg7mk61xrpwghphwjv55gl"; depends=[ade4 Biobase genefilter]; }; + cpvSNP = derive2 { name="cpvSNP"; version="1.18.0"; sha256="0zcqy5d8zzl33wzlrddpd5l6a3p5g7yfaz6smpcxm422z1qx1777"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; }; + cqn = derive2 { name="cqn"; version="1.32.0"; sha256="1farn0hxidygy7368pf2fc83jr6sw60qq9zqrgwv7032200rhasv"; depends=[mclust nor1mix preprocessCore quantreg]; }; + crisprseekplus = derive2 { name="crisprseekplus"; version="1.12.0"; sha256="0djblb6qc18b0ql1x0fbw4wsgyn8mw16ajvr39g9x9ynb4yqr9sj"; depends=[AnnotationDbi BiocManager BSgenome CRISPRseek DT GenomicFeatures GenomicRanges GUIDEseq hash shiny shinyjs]; }; + crlmm = derive2 { name="crlmm"; version="1.44.0"; sha256="0b13ws69b7508jdl02f26afl3v20ma1xgd2qmnmwnii9ln6bygbn"; depends=[affyio beanplot Biobase BiocGenerics ellipse ff foreach illuminaio lattice limma matrixStats mvtnorm oligoClasses preprocessCore RcppEigen SNPchip VGAM]; }; + crossmeta = derive2 { name="crossmeta"; version="1.12.0"; sha256="0mm57mf8wvibg7inlq8ij0xhk75jwnw2hq9dhw2w1blwl1jpj7ns"; depends=[affxparser affy AnnotationDbi Biobase BiocGenerics BiocManager ccmap data_table DBI doParallel doRNG DT fdrtool foreach GEOquery ggplot2 limma matrixStats metaMA metap miniUI oligo plotly RColorBrewer RCurl rdrop2 reader reshape RSQLite shiny stringr sva XML]; }; + csaw = derive2 { name="csaw"; version="1.20.0"; sha256="0n4npwd1rsfbxf5p0sbv562qxwfsy1cwcczp8isq2adry2fblmp4"; depends=[AnnotationDbi BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicFeatures GenomicRanges IRanges limma Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; }; + ctc = derive2 { name="ctc"; version="1.60.0"; sha256="0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d"; depends=[amap]; }; + ctsGE = derive2 { name="ctsGE"; version="1.12.0"; sha256="10rmm2swfj2rqb8wmw7gi8g7qhq0zfd9hx11s781llrdvk9i3wg6"; depends=[ccaPP ggplot2 limma reshape2 shiny stringr]; }; + cummeRbund = derive2 { name="cummeRbund"; version="2.28.0"; sha256="1fjc3bcclm4gsvw4nq6cv3a1kbrldvrxbkyfb9306708si1n4dwk"; depends=[Biobase BiocGenerics fastcluster ggplot2 Gviz plyr reshape2 RSQLite rtracklayer S4Vectors]; }; + customProDB = derive2 { name="customProDB"; version="1.26.0"; sha256="0rqxwlpzx0rfkcwph0mhza9q0wp1xlfjn8arb6g8jdqf2whib69r"; depends=[AhoCorasickTrie AnnotationDbi biomaRt Biostrings DBI GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr RCurl Rsamtools RSQLite rtracklayer S4Vectors stringr VariantAnnotation]; }; + cycle = derive2 { name="cycle"; version="1.40.0"; sha256="0l7kx4n43n35ndp1f6f9zgxh28nz16w0y5aa3hpgid6872k4cwwk"; depends=[Biobase Mfuzz]; }; + cydar = derive2 { name="cydar"; version="1.10.0"; sha256="139yd6kz1rzqafr78agb1vhzcvwc27yzxvw745yyk9yqjg1vzzak"; depends=[Biobase BiocGenerics BiocNeighbors BiocParallel flowCore Rcpp S4Vectors shiny SingleCellExperiment SummarizedExperiment viridis]; }; + cytofast = derive2 { name="cytofast"; version="1.2.0"; sha256="0dvcbrkrdammvsdyxqbfr7q0jjrxsjiwp473dkz7d94qpaip2ga7"; depends=[flowCore FlowSOM ggplot2 ggridges RColorBrewer Rdpack reshape2]; }; + cytolib = derive2 { name="cytolib"; version="1.8.0"; sha256="1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9"; depends=[]; }; + daMA = derive2 { name="daMA"; version="1.58.0"; sha256="13yng1l24v1b652r9fry7cqnx1j70s7pm13wk2c1qnb98ykjgszc"; depends=[MASS]; }; + dada2 = derive2 { name="dada2"; version="1.14.1"; sha256="0pdqq1r2kic98zf1g75r30zwc73f524jqqlhnphk3h4d7chjzgm3"; depends=[BiocGenerics Biostrings ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; + dagLogo = derive2 { name="dagLogo"; version="1.24.0"; sha256="1ncxl636m45ilfdajygpggzab87ag978r67wy768mr31nagclvnz"; depends=[BiocGenerics biomaRt Biostrings grImport2 motifStack pheatmap UniProt_ws]; }; + dcGSA = derive2 { name="dcGSA"; version="1.14.0"; sha256="08sgbjrij0bq5jqkkc2w6f19wj16f12k5jvpqir5q835pqdh4if9"; depends=[BiocParallel Matrix]; }; + dcanr = derive2 { name="dcanr"; version="1.2.0"; sha256="0p7l6wlsmzrfhjms8nvsz0g5dvp0j2rjdb4h4mymy410s25qg8qz"; depends=[circlize doRNG foreach igraph Matrix plyr RColorBrewer reshape2 stringr]; }; + ddCt = derive2 { name="ddCt"; version="1.42.0"; sha256="0jag0wnzywpmz63jv2l3kyzka1g7rg3zrdy58l6qymsmri9jnq7v"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; }; + ddPCRclust = derive2 { name="ddPCRclust"; version="1.6.0"; sha256="0z6ccmi8lgnkacsiy6zwym0cfspsx2cdnvvn7flhwans6f21q0d5"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; + debCAM = derive2 { name="debCAM"; version="1.4.0"; sha256="0p8h445k4amvh3ks34rsh7hz7s4xriyz11b81s7n8hzhdsxbi3by"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF nnls pcaPP rJava SummarizedExperiment]; }; + debrowser = derive2 { name="debrowser"; version="1.14.2"; sha256="0bvcmhl3rd6118qag3az6i5mvf1vs5apdpm1xabd78kc3zl4m9lm"; depends=[annotate AnnotationDbi clusterProfiler colourpicker d3heatmap DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva]; }; + deco = derive2 { name="deco"; version="1.2.0"; sha256="0npbc6km3c15b3jz9dq8k0zyzpshycj0gbpca95ypjjldw5mg397"; depends=[ade4 AnnotationDbi Biobase BiocParallel BiocStyle cluster foreign gdata ggplot2 gplots gridExtra limma locfit made4 RColorBrewer reshape2 scatterplot3d sfsmisc SummarizedExperiment]; }; + decompTumor2Sig = derive2 { name="decompTumor2Sig"; version="2.2.0"; sha256="01gwcgwz8d49vs38dqrl1qr7crrx29g8f7i9p42jrs7ixqkasxda"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg19 data_table GenomicFeatures GenomicRanges ggplot2 ggseqlogo gridExtra Matrix plyr quadprog S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation vcfR]; }; + decontam = derive2 { name="decontam"; version="1.6.0"; sha256="1fcqiyc56wnr0cg7ianvwfrz0niz56ppi0rhzjcv89c36ldp3jhs"; depends=[ggplot2 reshape2]; }; + deepSNV = derive2 { name="deepSNV"; version="1.32.0"; sha256="0kanxnb3xhhxki2b447lkcivh1jc3zgjbnam3m4dkp5nbb4yag49"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; }; + deltaCaptureC = derive2 { name="deltaCaptureC"; version="1.0.0"; sha256="1wk0yikab50ax5fagfyq8g37lc7wpg49h3w6mmsmgf5g6h3yncjc"; depends=[DESeq2 GenomicRanges ggplot2 IRanges SummarizedExperiment]; }; + deltaGseg = derive2 { name="deltaGseg"; version="1.26.0"; sha256="0mgjvhyp52hf1ybidgj4chxnjgw94a23k5kz4smivvy5azqa5h19"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; }; + derfinder = derive2 { name="derfinder"; version="1.20.0"; sha256="0hpq439j7gkvgb6iyylb48m0i3s13mpxrqmljzzzfbnpb29ndmgh"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; + derfinderHelper = derive2 { name="derfinderHelper"; version="1.20.0"; sha256="0mh20vig4nl6qf7733f5l0bhp6d5gy1vd6fdkcvlzmnmg6zmqaj1"; depends=[IRanges Matrix S4Vectors]; }; + derfinderPlot = derive2 { name="derfinderPlot"; version="1.20.0"; sha256="0bbz3zqbv6gr4mdx0lf3636rhajgrd224ydg84jfxcw1invr8fj1"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer reshape2 S4Vectors scales]; }; + destiny = derive2 { name="destiny"; version="3.0.1"; sha256="1hzg53p1cz21bvnfyyz40bpvjhg89zi3rahlqf0c4w85iwc1i4vi"; depends=[Biobase BiocGenerics ggplot_multistats ggplot2 ggthemes irlba knn_covertree Matrix pcaMethods proxy Rcpp RcppEigen RcppHNSW RSpectra scales scatterplot3d SingleCellExperiment smoother SummarizedExperiment tidyr tidyselect VIM]; }; + dexus = derive2 { name="dexus"; version="1.26.0"; sha256="02xg39jfijzf2r7riz9dc5ybf51l3c38mh66gzvliqkp1hj1l9vq"; depends=[BiocGenerics]; }; + diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.68.0"; sha256="1prr0dkk6lalipai19m3857yjgs7gzikahyx5f19l7pra369mbfq"; depends=[minpack_lm]; }; + diffHic = derive2 { name="diffHic"; version="1.18.0"; sha256="18abr5mzzrag8jnlp29fk2r6sgp2lpyxl4qi0zwmijgmffgcm8si"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; }; + diffcoexp = derive2 { name="diffcoexp"; version="1.6.0"; sha256="01cin5szziv46cqhral7skb7p9y75dlbp23yybv1g3ysji3c6mqh"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; }; + diffcyt = derive2 { name="diffcyt"; version="1.6.4"; sha256="1fqd556zvnkvnz1qjqxrq6q313da8lf0crqmn0sg43idg9jd3926"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; }; + diffloop = derive2 { name="diffloop"; version="1.14.0"; sha256="08aysn0hyldrlmvkz6ay463b89nxil7acdgnqrz1msbbccadsv8b"; depends=[Biobase biomaRt data_table dplyr edgeR foreach GenomeInfoDb GenomicRanges ggplot2 IRanges limma locfit matrixStats pbapply plyr readr reshape2 rtracklayer S4Vectors statmod Sushi]; }; + diffuStats = derive2 { name="diffuStats"; version="1.6.0"; sha256="15gy6z8ldl69i75405fcsg1myndxfbdw3s6mign0nv5p8mnyx59a"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; }; + diggit = derive2 { name="diggit"; version="1.18.0"; sha256="0spp8pifibda5i0hfsd9sbhdyp6xmcqn1wwfqz2bww1yrzrl2hii"; depends=[Biobase ks viper]; }; + discordant = derive2 { name="discordant"; version="1.10.0"; sha256="06crhc8fw32fnwh1f17plj7f5z85c215ayn1fqca4vii13m7b589"; depends=[Biobase biwt gtools MASS]; }; + divergence = derive2 { name="divergence"; version="1.2.0"; sha256="14agb6r0y90vm3jdqv7zkbvgv07nw74r8fjbk25s0fl8ipx0scmm"; depends=[SummarizedExperiment]; }; + dks = derive2 { name="dks"; version="1.32.0"; sha256="16lr86003skyg5n7dgbqll8c1k824ggpjz3wb5k719gw2rmf678i"; depends=[cubature]; }; + dmrseq = derive2 { name="dmrseq"; version="1.6.0"; sha256="01k36v3j7869ni39v0ns5x38g0zc7i6zvzfz3c85qsdlan3kb2sr"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; + doppelgangR = derive2 { name="doppelgangR"; version="1.14.0"; sha256="0qcy9hx7hwq057yqi6697hvsxk65dwqh48f4hv4d48qnsx7h5d8d"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; }; + doseR = derive2 { name="doseR"; version="1.2.0"; sha256="0r8cfb9r52gh4rs6hwaici7a28alwwgr3z112a2ph2f75bcbravl"; depends=[digest edgeR lme4 matrixStats mclust RUnit S4Vectors SummarizedExperiment]; }; + drawProteins = derive2 { name="drawProteins"; version="1.6.0"; sha256="1zqbzqdi1hvkmwcrmdqbpnljvahnqn6b20sm2qyni0yynk036yrl"; depends=[dplyr ggplot2 httr readr stringr tidyr]; }; + dualKS = derive2 { name="dualKS"; version="1.46.0"; sha256="1skddvf6ac3fa2dzg8zv0vmqfx6zpli9arph4yny8xal46s7qr4z"; depends=[affy Biobase]; }; + dupRadar = derive2 { name="dupRadar"; version="1.16.0"; sha256="0raqy48hcibpas7fysx7bd0sl746jkssi9bn5vgqpii8mdk8nv79"; depends=[Rsubread]; }; + dyebias = derive2 { name="dyebias"; version="1.46.0"; sha256="0j9699nan23mf3s9yiidvnlypgcwzz4w7kv3qbksphydycrm6jz8"; depends=[Biobase marray]; }; + easyRNASeq = derive2 { name="easyRNASeq"; version="2.22.2"; sha256="1a78rq2lrchm11f4psyyvg9fz8gv0zkfwd1bb10fid78q80g30hf"; depends=[Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD rappdirs Rsamtools S4Vectors ShortRead SummarizedExperiment]; }; + ecolitk = derive2 { name="ecolitk"; version="1.58.0"; sha256="1jh36g8i556n5p8gyz23y1i1n0cj58539m76j0qbzj83jld9x34f"; depends=[Biobase]; }; + edge = derive2 { name="edge"; version="2.18.0"; sha256="178f1nvnaq51z95aizdbf5abxkdzia6s741931w1pq6x1bz9nb60"; depends=[Biobase jackstraw MASS qvalue snm sva]; }; + edgeR = derive2 { name="edgeR"; version="3.28.1"; sha256="07dv99kl7jfa62nzcq705r56gcpb1hq7p4px48j71y2ddi1rqmr6"; depends=[limma locfit Rcpp]; }; + eegc = derive2 { name="eegc"; version="1.12.0"; sha256="0cy1xzjblc0y4ly5syh3q2vh4i5zp5zgq8s2ln4yslw4j2f33dgv"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; }; + eiR = derive2 { name="eiR"; version="1.26.0"; sha256="0pngb5vns9iad4qda1960jissh6k2rigszsj1lslqav6dff1q5sp"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; }; + eisa = derive2 { name="eisa"; version="1.38.0"; sha256="0pdilgdhr1k74xljq9nhzn5w20kjqx9wrqxpsmdb4xgikk5dw2ff"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; }; + enrichTF = derive2 { name="enrichTF"; version="1.2.3"; sha256="01pwzp1381ibq42q3259fc4y8yrpyazv7mfcn8sz2x66d6g26qf1"; depends=[BiocGenerics BSgenome clusterProfiler GenomeInfoDb GenomicRanges ggplot2 ggpubr heatmap3 IRanges JASPAR2018 magrittr motifmatchr pipeFrame R_utils rmarkdown rtracklayer S4Vectors TFBSTools]; }; + enrichplot = derive2 { name="enrichplot"; version="1.6.1"; sha256="0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x"; depends=[AnnotationDbi cowplot DOSE europepmc ggplot2 ggplotify ggraph ggridges GOSemSim gridExtra igraph purrr RColorBrewer reshape2]; }; + ensemblVEP = derive2 { name="ensemblVEP"; version="1.28.0"; sha256="0bfp4zsc33xz5k05izc2cs46f1vqc5jvzxf7qq59y5173r03ziai"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; + ensembldb = derive2 { name="ensembldb"; version="2.10.2"; sha256="02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; + epiNEM = derive2 { name="epiNEM"; version="1.10.0"; sha256="0frmj3r6qcvkyxk17dyx4ma16r46svx76ck1zck4xvgq4zf7xm4j"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; }; + epigenomix = derive2 { name="epigenomix"; version="1.26.0"; sha256="1rf8xjc4n88wdqk6w9kldp6qynw5r50vh763k6g2wijcrf8ihzxq"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; }; + epihet = derive2 { name="epihet"; version="1.2.0"; sha256="1c9jrv9j9jl6i44rjhl0kcs5n2nrb27ji2sj9jaizpgn44abxzhq"; depends=[data_table doParallel EntropyExplorer foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; }; + epivizr = derive2 { name="epivizr"; version="2.16.0"; sha256="1q99yfnrch7kg7qg8l1sw7vr2cnixpphrjq2930m97cl22szydal"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; }; + epivizrChart = derive2 { name="epivizrChart"; version="1.8.0"; sha256="071111z61x9l5gd4x6a3bavv7njr0nxanbiwiss5c3kr6yqrns6b"; depends=[BiocGenerics epivizrData epivizrServer htmltools rjson]; }; + epivizrData = derive2 { name="epivizrData"; version="1.14.0"; sha256="0jqs4knxjywxfkzj4vz0zf5jwwvvyabv48inrigzm01r5dpkv3r2"; depends=[Biobase ensembldb epivizrServer GenomeInfoDb GenomicFeatures GenomicRanges IRanges OrganismDbi S4Vectors SummarizedExperiment]; }; + epivizrServer = derive2 { name="epivizrServer"; version="1.14.0"; sha256="1dc3bffwkvlqrsbb04mkclinyvv5j862jrnl2r16dac1jiky8313"; depends=[httpuv mime R6 rjson]; }; + epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.14.0"; sha256="1zm9yr2hahq59kx71h21qglz028k0rlmxfrqywsh0zxswmisrbr4"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; }; + erccdashboard = derive2 { name="erccdashboard"; version="1.20.0"; sha256="0gxcf79i5rw7gnv8y6n0c9l6jqvill3jjqv2i6h1lj4agpaclalg"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; }; + erma = derive2 { name="erma"; version="1.2.0"; sha256="085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel GenomeInfoDb GenomicFiles GenomicRanges ggplot2 Homo_sapiens IRanges rtracklayer S4Vectors shiny SummarizedExperiment]; }; + esATAC = derive2 { name="esATAC"; version="1.8.0"; sha256="0pjgb3ix0bvdkpddqbb6z2cvmhm3zms8f8ww9cgs58cx7s3wdc3g"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; }; + esetVis = derive2 { name="esetVis"; version="1.12.0"; sha256="0i0fi7vbhvyi4hlflczf5csnspwwhm45dnlvr51gd34y1bg15q7d"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; }; + eudysbiome = derive2 { name="eudysbiome"; version="1.16.0"; sha256="0p6fpf8z60il597fq7n9kawm4ysxrcdhrpmjcc44d1m46xihi4dc"; depends=[Biostrings plyr R_utils Rsamtools]; }; + evaluomeR = derive2 { name="evaluomeR"; version="1.2.41"; sha256="1z9a0alk7paqk0yix9780nz0sfqwbr75725fwrwnhgxk247rc29q"; depends=[cluster corrplot fpc ggdendro ggplot2 matrixStats MultiAssayExperiment plotrix Rdpack reshape2 SummarizedExperiment]; }; + exomeCopy = derive2 { name="exomeCopy"; version="1.32.0"; sha256="0qfwp68ivcwaxcbjyb77bcyp6bmsmlcszjqqnfvqxiyhx6dl5v6r"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; }; + explorase = derive2 { name="explorase"; version="1.50.0"; sha256="1gk7c7h90g5lxg6n6dqz718fd60y05ckdxx66fr3x4r1bh67a9fk"; depends=[limma rggobi RGtk2]; }; + fCCAC = derive2 { name="fCCAC"; version="1.12.0"; sha256="138cip14cnmjdh3d1fqar9rk2n2vgfvp1mfbzs2wafsbj19avgws"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; + fCI = derive2 { name="fCI"; version="1.16.0"; sha256="1wj704pliljncch9xhy4hmqp62yzwrsxrxdzjj7l533m3laavv1n"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; + fabia = derive2 { name="fabia"; version="2.32.0"; sha256="1nqcb1w93xpljp8avyxbdk6pbjikfrvbzbvdsax235shx0273cvg"; depends=[Biobase]; }; + factDesign = derive2 { name="factDesign"; version="1.62.0"; sha256="0gsn6npfkn5ya8kvw80k5lv0xl7y73a270f1gq3vq0426m547sb4"; depends=[Biobase]; }; + farms = derive2 { name="farms"; version="1.38.0"; sha256="1c2vvinzph3v7vjzcfn62jslxrcif6aq2iw0yg8fc4qxc3ajsvya"; depends=[affy Biobase MASS]; }; + fastLiquidAssociation = derive2 { name="fastLiquidAssociation"; version="1.22.0"; sha256="0k0f8ifyhc5jd4hbx1xi6cffkv1i785rcqlpmlfr59f3jiwf4p9j"; depends=[doParallel Hmisc impute LiquidAssociation preprocessCore WGCNA]; }; + fastseg = derive2 { name="fastseg"; version="1.32.0"; sha256="1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors]; }; + fcScan = derive2 { name="fcScan"; version="1.0.0"; sha256="0cj9gs1880y6wcqg4c2291jy94d72294ypqmkn7541fszdcmyqdp"; depends=[GenomicRanges IRanges plyr rtracklayer SummarizedExperiment VariantAnnotation]; }; + fcoex = derive2 { name="fcoex"; version="1.0.0"; sha256="1mzx6pkaf69n8pqasy5cqim9hlnns8jpwb776zff70db2crmf9zy"; depends=[clusterProfiler data_table dplyr FCBF ggplot2 ggrepel igraph intergraph network pathwayPCA progress scales SingleCellExperiment sna stringr]; }; + fdrame = derive2 { name="fdrame"; version="1.58.0"; sha256="1qw2zl6fycpm4l8vrj844k6s2nsh33lwm832lcxlzc45zjw40jcp"; depends=[]; }; + ffpe = derive2 { name="ffpe"; version="1.30.0"; sha256="0rzvan5cx93ncg24ciz2656h51mh5kq9x7n2ycrpj949snk0kl57"; depends=[affy Biobase BiocGenerics lumi methylumi sfsmisc TTR]; }; + fgsea = derive2 { name="fgsea"; version="1.12.0"; sha256="0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1"; depends=[BH BiocParallel data_table fastmatch ggplot2 gridExtra Matrix Rcpp]; }; + fishpond = derive2 { name="fishpond"; version="1.2.0"; sha256="0qdgy5n6zxkpd5aqinjl3b00isavp4vpij83vgi3gbxqnfp583kl"; depends=[abind gtools matrixStats qvalue Rcpp S4Vectors SummarizedExperiment svMisc]; }; + flagme = derive2 { name="flagme"; version="1.42.0"; sha256="0h706f0yn9nxc77bb2zpnanhb9s2c6i1yiy5985bp7wqsilx88nk"; depends=[CAMERA gcspikelite gplots MASS SparseM xcms]; }; + flowAI = derive2 { name="flowAI"; version="1.16.0"; sha256="14il02kz8m17gvby7n91clp792awgbpb68ny06q2mhzpp9rm6cnj"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; }; + flowBeads = derive2 { name="flowBeads"; version="1.24.0"; sha256="0g48b71rks6gsxxi50hlyvb7zl3rz2193fqrb7h46bxbpcf7w5sw"; depends=[Biobase flowCore knitr rrcov xtable]; }; + flowBin = derive2 { name="flowBin"; version="1.22.0"; sha256="0j3imi0svy05rmfsgiin81pmxvb8g9vfb7g8ybrlaj8qcp15ari7"; depends=[BiocGenerics class flowCore flowFP limma snow]; }; + flowCHIC = derive2 { name="flowCHIC"; version="1.20.0"; sha256="0c90b3p78p2y4100r634nihmfvpd15mxl5kn10d2csyjjzvjd53v"; depends=[EBImage flowCore ggplot2 hexbin vegan]; }; + flowCL = derive2 { name="flowCL"; version="1.24.0"; sha256="1wgv2x6k9pqmhs0y5njx6n2wb3zyj0rdgsj171mlwp43v6i4djn2"; depends=[graph Rgraphviz SPARQL]; }; + flowClean = derive2 { name="flowClean"; version="1.24.0"; sha256="1xc0qqijmnb3nh1dzqr5gziikgn8wyqz2v6hz2jhjkkrg9hr9r5p"; depends=[bit changepoint flowCore sfsmisc]; }; + flowClust = derive2 { name="flowClust"; version="3.24.0"; sha256="0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s"; depends=[Biobase BiocGenerics clue corpcor ellipse flowCore flowViz graph mnormt]; }; + flowCore = derive2 { name="flowCore"; version="1.52.1"; sha256="08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2"; depends=[BH Biobase BiocGenerics cytolib matrixStats Rcpp]; }; + flowCyBar = derive2 { name="flowCyBar"; version="1.22.0"; sha256="16zf0vvvpzbrb22yhgdjbpj97m69m2fz63hgflxcg6n7l271p6kx"; depends=[gplots vegan]; }; + flowDensity = derive2 { name="flowDensity"; version="1.20.0"; sha256="1yj25mlhj0fz2jfdmzsa3kkgscja527nkqp1x19hianwg0ap2x9h"; depends=[car flowCore flowViz flowWorkspace gplots RFOC rgeos sp]; }; + flowFP = derive2 { name="flowFP"; version="1.44.0"; sha256="0hddklcr2px6xchdr5lr787vwazr7609wfhcanwpk5jiic83y0s6"; depends=[Biobase BiocGenerics flowCore flowViz]; }; + flowFit = derive2 { name="flowFit"; version="1.24.0"; sha256="0ny8jsfizqbnjdkgr93gkhca96lj588lz2s9ciajvqsisb88b647"; depends=[flowCore flowViz gplots kza minpack_lm]; }; + flowMap = derive2 { name="flowMap"; version="1.24.0"; sha256="1hc1ckfx234p7ng9v19l0zxpss70nkrwnyrf3sdjphmpz5ksvpxr"; depends=[abind ade4 doParallel Matrix reshape2 scales]; }; + flowMatch = derive2 { name="flowMatch"; version="1.22.0"; sha256="0yn8g3mx5s8wqbdgqf1fil6r8byvg44pa46w6hs61vl4q3zl0flj"; depends=[Biobase flowCore Rcpp]; }; + flowMeans = derive2 { name="flowMeans"; version="1.46.0"; sha256="1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h"; depends=[Biobase feature flowCore rrcov]; }; + flowMerge = derive2 { name="flowMerge"; version="2.34.0"; sha256="068wibdpkzm4kapsg2ysbad6lqwd7inc9vmyzkwr1ikymmyac9iw"; depends=[feature flowClust flowCore foreach graph Rgraphviz rrcov snow]; }; + flowPeaks = derive2 { name="flowPeaks"; version="1.32.0"; sha256="0ylgfrsmwjm09wqbq3lzr891nc4s43kjj9sndpzbvrlqfr2cya1z"; depends=[]; }; + flowPloidy = derive2 { name="flowPloidy"; version="1.12.0"; sha256="191dqis8jnvb41wb2hw73zi4y2abk20asw5r72zsp1491a1rybda"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; }; + flowPlots = derive2 { name="flowPlots"; version="1.34.0"; sha256="0fpdsl9k86q30f14s2sc77fadrcl2lfhcsmrykq8z6xy9f6r063s"; depends=[]; }; + flowSpecs = derive2 { name="flowSpecs"; version="1.0.2"; sha256="1i0z2a590k6r3v62xjh0092lvz2082091bd3qschls5m1dyz5m20"; depends=[BiocGenerics BiocParallel flowCore ggplot2 reshape2 zoo]; }; + flowSpy = derive2 { name="flowSpy"; version="1.0.4"; sha256="0q8rid59xxmrc85d7kc5r4z08q8y6ll31zhpd6ln4391xr56hkg8"; depends=[Biobase BiocNeighbors cluster destiny flowCore FlowSOM flowUtils ggplot2 gmodels igraph limma Matrix matrixStats mclust pheatmap prettydoc RANN Rcpp Rtsne scatterpie scatterplot3d stringr sva umap]; }; + flowStats = derive2 { name="flowStats"; version="3.44.0"; sha256="0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"; depends=[Biobase BiocGenerics cluster fda flowCore flowViz flowWorkspace KernSmooth ks lattice MASS ncdfFlow RColorBrewer rrcov]; }; + flowTime = derive2 { name="flowTime"; version="1.10.0"; sha256="1dy9mgai8h6w2pfy51ak2nb16zx0y4j3qbyh7vbhhlrlis1xrz45"; depends=[flowCore plyr]; }; + flowTrans = derive2 { name="flowTrans"; version="1.38.0"; sha256="1dlwn6rgw8shvbifc6z5cjnhwz1z8vq6y4n62m47h1byiri2ds5w"; depends=[flowClust flowCore flowViz]; }; + flowType = derive2 { name="flowType"; version="2.24.0"; sha256="165m8c47dcg1y6v8cpmssir6jhich0gdb52b01b5lf3zl7ysr97n"; depends=[BH Biobase flowClust flowCore flowMeans flowMerge Rcpp rrcov sfsmisc]; }; + flowUtils = derive2 { name="flowUtils"; version="1.50.0"; sha256="1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81"; depends=[Biobase corpcor flowCore graph RUnit XML]; }; + flowVS = derive2 { name="flowVS"; version="1.18.0"; sha256="17g6dnbyqy5m7d7g8klniqaxnmicpy5f80qn2z4kv2b5pvds659p"; depends=[flowCore flowStats flowViz]; }; + flowViz = derive2 { name="flowViz"; version="1.50.0"; sha256="0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; }; + flowWorkspace = derive2 { name="flowWorkspace"; version="3.34.1"; sha256="1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"; depends=[BH Biobase BiocGenerics cytolib data_table digest dplyr flowCore flowViz graph gridExtra lattice latticeExtra matrixStats ncdfFlow RBGL RColorBrewer Rcpp RcppParallel Rgraphviz RProtoBufLib scales stringr]; }; + flowcatchR = derive2 { name="flowcatchR"; version="1.20.0"; sha256="0js2rzabq35ayj9w6v1zlicml90rpk75gbnzk4n679jxbwv5ar23"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; + fmcsR = derive2 { name="fmcsR"; version="1.28.0"; sha256="1jksxf9kzik0bd1dx50vpn5cvc9h570rdx33a1fq6i09f63z6ka1"; depends=[BiocGenerics ChemmineR RUnit]; }; + focalCall = derive2 { name="focalCall"; version="1.20.0"; sha256="0q622ibmliyvd50y6svfqam7f4ydrmqajacmf249jfjlsm7kd3a2"; depends=[CGHcall]; }; + frma = derive2 { name="frma"; version="1.38.0"; sha256="1kzi0v803a1n0jzs5yv1rk17p88vk62aq6lhqbsdgdr55fjclmgr"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; }; + frmaTools = derive2 { name="frmaTools"; version="1.38.0"; sha256="0n7ds1gw2vmq67wkxw749ppj5yy4bs4m39xsjvai6lqzcpdr1xfd"; depends=[affy Biobase DBI preprocessCore]; }; + funtooNorm = derive2 { name="funtooNorm"; version="1.10.0"; sha256="1532ig7zk8l67xnw5392vnlpwhkdnqgbij9qq6r5draw2fjw3y8k"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; }; + gCMAP = derive2 { name="gCMAP"; version="1.30.0"; sha256="1sgwrwzc3w6v1k890rh1khdsgz8lqqq689xr94k1vxvgqgdvcj2b"; depends=[annotate AnnotationDbi bigmemory bigmemoryExtras Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; }; + gCMAPWeb = derive2 { name="gCMAPWeb"; version="1.26.0"; sha256="1pdf40p4ww7yzm0hh49j5541i1r6y32jjz02ld3k5j0i13s0afxg"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; }; + gCrisprTools = derive2 { name="gCrisprTools"; version="1.14.0"; sha256="11frml3hhnffikimwpasrmn7nadal80azfjap4zgi441wixickgm"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; }; + gQTLBase = derive2 { name="gQTLBase"; version="1.18.0"; sha256="1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x"; depends=[BatchJobs BBmisc BiocGenerics bit doParallel ff ffbase foreach GenomicFiles GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; }; + gQTLstats = derive2 { name="gQTLstats"; version="1.18.0"; sha256="1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f"; depends=[AnnotationDbi BatchJobs BBmisc beeswarm Biobase BiocGenerics doParallel dplyr erma ffbase foreach GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges ggbeeswarm ggplot2 gQTLBase HardyWeinberg Homo_sapiens IRanges limma mgcv plotly reshape2 S4Vectors shiny snpStats SummarizedExperiment VariantAnnotation]; }; + gaga = derive2 { name="gaga"; version="2.32.0"; sha256="0ffiz855lz73wr9kf3bwfqwpfvxj0ib7bzlabg049l3r4x7vjm3m"; depends=[Biobase coda EBarrays mgcv]; }; + gage = derive2 { name="gage"; version="2.36.0"; sha256="1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6"; depends=[AnnotationDbi graph KEGGREST]; }; + gaggle = derive2 { name="gaggle"; version="1.54.0"; sha256="19wzcx57cracwx9x7xlfqwlv9fi4ncfngqpzc7y6swhpi8kymxfa"; depends=[graph rJava RUnit]; }; + gaia = derive2 { name="gaia"; version="2.30.0"; sha256="19s74c9nvcb8h45b1b6dmhqzyfz4zzx5jwszgyw74z5il9bhlgy7"; depends=[]; }; + garfield = derive2 { name="garfield"; version="1.14.0"; sha256="1gm8448ww7siwk6gxklgj964wiv2lxpp6rfv7agd2hg8k73j2pkl"; depends=[]; }; + gcapc = derive2 { name="gcapc"; version="1.10.0"; sha256="1aws5n2xa0bgqsrq4dv2pa94ifb451ycvlc17ykydsnx6c1flarf"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; }; + gcatest = derive2 { name="gcatest"; version="1.16.0"; sha256="1ys39mdqk0v5rvcl6m027dxbi7v3c8ggabmw8a2la4581ashkl1n"; depends=[lfa]; }; + gcrma = derive2 { name="gcrma"; version="2.58.0"; sha256="0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; }; + gdsfmt = derive2 { name="gdsfmt"; version="1.22.0"; sha256="0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9"; depends=[]; }; + geNetClassifier = derive2 { name="geNetClassifier"; version="1.26.0"; sha256="14hw0gla8jfldv3l7q75v7zchgnkbqxird9mf0xiv0p77vvs6xk2"; depends=[Biobase e1071 EBarrays minet]; }; + geecc = derive2 { name="geecc"; version="1.20.0"; sha256="1hj4rh5gdk253yswqkhz0y95wa5ybd6rgbgjnwz9apvhvmm6gxdm"; depends=[gplots hypergea MASS Rcpp]; }; + gemini = derive2 { name="gemini"; version="1.0.0"; sha256="0vin6h3f3cgjy531lj41p4j3zhv2yfissg3lgfwlynlf51ymjnvb"; depends=[dplyr ggplot2 magrittr mixtools pbmcapply scales]; }; + genArise = derive2 { name="genArise"; version="1.62.0"; sha256="0hzaxjfjg2xyr8gmgk4vwy9cxrvwnsiqbh4jx9qwd1bjfaminzfx"; depends=[locfit tkrplot xtable]; }; + genbankr = derive2 { name="genbankr"; version="1.14.0"; sha256="1sb8irk1ii18q4n1zmsk4vqndq7fgnim07qspdlg2fabwpbz2k6y"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; }; + geneAttribution = derive2 { name="geneAttribution"; version="1.12.0"; sha256="12v89vb92zl2vkpa4vn4n17srr5cf5f9vdksaw2fpq7xi654crrc"; depends=[BiocGenerics GenomeInfoDb GenomicFeatures GenomicRanges IRanges org_Hs_eg_db rtracklayer]; }; + geneClassifiers = derive2 { name="geneClassifiers"; version="1.10.0"; sha256="0ql4ryv5m2l8b4hkdy6ipbhkwskclwfq2953gc0255c84mqrhi19"; depends=[Biobase BiocGenerics]; }; + geneRecommender = derive2 { name="geneRecommender"; version="1.58.0"; sha256="1gwipi1nj1azw0hlc2b9w896grwvh0447f8jxw2g2z23vdq4fbq5"; depends=[Biobase]; }; + geneRxCluster = derive2 { name="geneRxCluster"; version="1.22.0"; sha256="119bfq1z7ly71nm26l2rzwj8w8b02szwhbll622pl3w7kqm5l1kw"; depends=[GenomicRanges IRanges]; }; + geneXtendeR = derive2 { name="geneXtendeR"; version="1.12.0"; sha256="0rkglc7393bhxgzjyafybr9z6frrskv2mkigy1imr04lx8px50dg"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; }; + genefilter = derive2 { name="genefilter"; version="1.68.0"; sha256="1xjr02qhldspjwd6y374wgik18fgywb6408wsz471i8b4ik98ckc"; depends=[annotate AnnotationDbi Biobase BiocGenerics survival]; }; + genefu = derive2 { name="genefu"; version="2.18.1"; sha256="09dyy98k2d8sld7gn7sms0avp8hxqsj55xl7qjfbxdw53636kvkw"; depends=[AIMS amap biomaRt iC10 impute limma mclust survcomp]; }; + geneplast = derive2 { name="geneplast"; version="1.12.2"; sha256="17y65g501g9gh18n13829znzkzsi787v86ph3wrnxjwcpsa7ryqh"; depends=[ape data_table igraph snow]; }; + geneplotter = derive2 { name="geneplotter"; version="1.64.0"; sha256="1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; }; + genoCN = derive2 { name="genoCN"; version="1.38.0"; sha256="0rj9hvaah8x9wcm044wcs5yk7gzphpvwvabpb2wjhmykq8a8bjd6"; depends=[]; }; + genomation = derive2 { name="genomation"; version="1.18.0"; sha256="1sba928h23b67gr3i4yj1bg655g24l3bcgsf5gvymzrv5idrss1l"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer RUnit S4Vectors seqPattern]; }; + genomeIntervals = derive2 { name="genomeIntervals"; version="1.42.0"; sha256="1mqhlvjslig1rhdcypi4f6cqwxy5wn1lzmsslg56q7qd3ks7wck7"; depends=[BiocGenerics GenomeInfoDb GenomicRanges intervals IRanges S4Vectors]; }; + genomes = derive2 { name="genomes"; version="3.16.0"; sha256="1rn1pgrgc8vgs32miag8yby2i05l1v4har372fjj374aailhszgc"; depends=[curl readr]; }; + genoset = derive2 { name="genoset"; version="1.42.0"; sha256="1x46qfc3p42r6m03vv70a81lsvybjah1b5aa5p4dslff22xbcxmr"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; + genotypeeval = derive2 { name="genotypeeval"; version="1.18.0"; sha256="1xd9ys2myb1dqd65x3zkf1fwivi5ylpli3p26z23bj5lgsiyr2by"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; }; + genphen = derive2 { name="genphen"; version="1.14.0"; sha256="1vm52rray6xnir5vhjb63c99f4dv6dy58xa4fr4rsw0ycj4vm785"; depends=[Biostrings doParallel e1071 foreach ranger Rcpp rPref rstan]; }; + gep2pep = derive2 { name="gep2pep"; version="1.6.0"; sha256="1zqizigfhdy1369pcilwcp9jzch9vz7pr34b03jy41af62a86lpv"; depends=[Biobase digest foreach GSEABase iterators repo rhdf5 XML]; }; + gespeR = derive2 { name="gespeR"; version="1.18.0"; sha256="1k83d6z39llwjk86cxk47rz3lggdpwix00iapb0q06whg0dhh8di"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; }; + ggbio = derive2 { name="ggbio"; version="1.34.0"; sha256="13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 rlang Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + ggcyto = derive2 { name="ggcyto"; version="1.14.1"; sha256="16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer rlang scales]; }; + ggtree = derive2 { name="ggtree"; version="2.0.2"; sha256="1lmcw518n6h3rlyl1hsyydfb0k9q7fw0cq551pfx1q9hhi2krb76"; depends=[ape dplyr ggplot2 magrittr purrr rlang rvcheck tidyr tidytree treeio]; }; + girafe = derive2 { name="girafe"; version="1.38.0"; sha256="1yh161yskh00qgkhw7jdp8w18ylciwgmaqywfpm3l0lpbsyhig0y"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; + glmSparseNet = derive2 { name="glmSparseNet"; version="1.4.0"; sha256="1kv9wznag126dsrm8yf04132rzl14q70hhvkgpnc5msammxjclp6"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet loose_rock Matrix MultiAssayExperiment readr reshape2 rlang sparsebn sparsebnUtils STRINGdb stringr SummarizedExperiment survminer]; }; + globalSeq = derive2 { name="globalSeq"; version="1.14.0"; sha256="137bwb1p676yhf2d5x4mnk7xzzap6dxgr9c4y0xw4hrkj2687i4g"; depends=[]; }; + globaltest = derive2 { name="globaltest"; version="5.40.0"; sha256="0265j3vj26d76l63k1y8ligsn9626zg66by5dbc6bw27hwsgrxli"; depends=[annotate AnnotationDbi Biobase survival]; }; + gmapR = derive2 { name="gmapR"; version="1.28.0"; sha256="087pl171cfmvpdgfa10sl0i19n6y4mzr1c1cbgg0ky77fv8jmc2k"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; + goProfiles = derive2 { name="goProfiles"; version="1.48.0"; sha256="0l5fkw35j2m26i9wq6s42nr68chpffr0nq88axkl5qqm0kcjh3ry"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; }; + goSTAG = derive2 { name="goSTAG"; version="1.10.0"; sha256="1kcm1zbckgvr6z29d1m35c00m95v84yap2d2arlqb8lvgk5yk0df"; depends=[AnnotationDbi biomaRt GO_db memoise]; }; + goTools = derive2 { name="goTools"; version="1.60.0"; sha256="1fink5xfvhzbdnk224h71n51265s5yqzqcarpz71cim3zwjbnfqh"; depends=[AnnotationDbi GO_db]; }; + goseq = derive2 { name="goseq"; version="1.38.0"; sha256="11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; }; + gpart = derive2 { name="gpart"; version="1.4.0"; sha256="01l0hy83jxbscljzl4vvfi1xa8aixbjpzx3g0pbqwpclwxkqndcq"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + gpls = derive2 { name="gpls"; version="1.58.0"; sha256="1x0p9xi4i3rqmjni1d3f732iba9d8kkzwiai66ny7y4wnfrgs3vp"; depends=[]; }; + gprege = derive2 { name="gprege"; version="1.30.0"; sha256="0qqzkrk8hj7bd6za7nlb7c1i6wg9b1nq6mmsh5hj1wcxc9mfg2l6"; depends=[gptk]; }; + gramm4R = derive2 { name="gramm4R"; version="1.0.0"; sha256="0jf0l44r4avfk58cxd66bhbl6l67fi8svx7i9qd70dygk33jgcdn"; depends=[basicTrendline DelayedArray DMwR investr minerva phyloseq psych SummarizedExperiment]; }; + graper = derive2 { name="graper"; version="1.2.0"; sha256="1y0nm1jhz3p11622xkz1qh3yql7vzlalm663y2qv8kscwbb37x9m"; depends=[BH cowplot ggplot2 Matrix matrixStats Rcpp RcppArmadillo]; }; + graph = derive2 { name="graph"; version="1.64.0"; sha256="1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc"; depends=[BiocGenerics]; }; + graphite = derive2 { name="graphite"; version="1.32.0"; sha256="1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd"; depends=[AnnotationDbi checkmate graph httr rappdirs]; }; + groHMM = derive2 { name="groHMM"; version="1.20.0"; sha256="0ywr8f6bfhg2ia3n4rmsxr4v1xqmlyhkwh0rvkgh3yqgnbvihndg"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; }; + gscreend = derive2 { name="gscreend"; version="1.0.0"; sha256="1p5kkqq5hbsphgcigx0wbzylmvkgjka85jdmc5j6n727clj9xsfw"; depends=[BiocParallel fGarch nloptr SummarizedExperiment]; }; + gsean = derive2 { name="gsean"; version="1.6.0"; sha256="1lcb3ig2ggc6bv89ipiy0j62gr4gml4skvi1maqpdf362s4b2vga"; depends=[fgsea PPInfer]; }; + gtrellis = derive2 { name="gtrellis"; version="1.18.0"; sha256="0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z"; depends=[circlize GenomicRanges GetoptLong IRanges]; }; + gwascat = derive2 { name="gwascat"; version="2.18.0"; sha256="038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges Homo_sapiens IRanges Rsamtools rtracklayer S4Vectors]; }; + gwasurvivr = derive2 { name="gwasurvivr"; version="1.4.0"; sha256="05fzpdxlxp5gs1sh5wmshmycbbl26m1jqhmqx9jhygkxvxhchq0z"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; }; + h5vc = derive2 { name="h5vc"; version="2.20.0"; sha256="1dbqi1syjs94fww4yn8y8i8v3chklv29n9zhfpm163xxpl6jvyca"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rhtslib Rsamtools S4Vectors]; }; + hapFabia = derive2 { name="hapFabia"; version="1.28.0"; sha256="01m96ms65rqvr9dq2iy6cbj119zmirkayn42aqzc5jprn0fr8lk8"; depends=[Biobase fabia]; }; + heatmaps = derive2 { name="heatmaps"; version="1.10.0"; sha256="0gpar3a0kn2baf5gb66bvf21lbda6ywa7b8p03hbnab85k2r8hg5"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; }; + hiAnnotator = derive2 { name="hiAnnotator"; version="1.20.0"; sha256="1sz8wgqk23vbjw29x0f2dv3qsd1yj7651x174z6142svspmd52wh"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; }; + hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.22.0"; sha256="1qwbd53n5j7cfb4bjfwmsiwf8vll4iadmaxaw72s5b74bxaik409"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl sonicLength]; }; + hicrep = derive2 { name="hicrep"; version="1.10.0"; sha256="08mfih5nkp3kinvqp8w6jxi9k7n62i675wgg59av741vpszzr56s"; depends=[]; }; + hierGWAS = derive2 { name="hierGWAS"; version="1.16.0"; sha256="0kljcsnbzsp7zg80gxbd2j1r664ijgyn008v7rq28v8w2ar4430g"; depends=[fastcluster fmsb glmnet]; }; + hierinf = derive2 { name="hierinf"; version="1.4.0"; sha256="0zzw5kpfjyqw5qfq3mda7wwr0nhk9vxn93sgf0m9rkiqnl36kp7f"; depends=[fmsb glmnet]; }; + hipathia = derive2 { name="hipathia"; version="2.2.1"; sha256="1gs91r8152n25z4wcqk65a5jx8bdqblspaxc5y40b95gnlyz6m3h"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; }; + hmdbQuery = derive2 { name="hmdbQuery"; version="1.6.1"; sha256="114mi89wc8s10mgagsrg52cbbvndw21qvfmax2nih22r53g1phjn"; depends=[S4Vectors XML]; }; + hopach = derive2 { name="hopach"; version="2.46.0"; sha256="085k66hv3jdrpas2nfa7ymva1gwbq1laaxis8qg6qn5srjsl7bir"; depends=[Biobase BiocGenerics cluster]; }; + hpar = derive2 { name="hpar"; version="1.28.0"; sha256="1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m"; depends=[]; }; + hypeR = derive2 { name="hypeR"; version="1.2.0"; sha256="0zrpx25casvdny16zzn0b6ldkr6brdx9cr68ski0jrwai88qgg8r"; depends=[dplyr DT ggforce ggplot2 gh igraph kableExtra magrittr msigdbr openxlsx purrr R6 rlang rmarkdown scales visNetwork]; }; + hyperdraw = derive2 { name="hyperdraw"; version="1.38.0"; sha256="0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj"; depends=[graph hypergraph Rgraphviz]; }; + hypergraph = derive2 { name="hypergraph"; version="1.58.0"; sha256="1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m"; depends=[graph]; }; + iASeq = derive2 { name="iASeq"; version="1.30.0"; sha256="0p0xb5c4ll6cxh6z0vxwss59xc36xsm9nkbpgdagqrfjqym0iakm"; depends=[]; }; + iBBiG = derive2 { name="iBBiG"; version="1.30.0"; sha256="1sb51mlb2aayb14z3ki3qgzkmzqsqn70k0akcwkxm3411fawlmip"; depends=[ade4 biclust xtable]; }; + iBMQ = derive2 { name="iBMQ"; version="1.26.0"; sha256="1i5diz2p2xzxbdxjn18zsh8qpfw27ydf9wnyq0c8h759q5yxn2x5"; depends=[Biobase ggplot2]; }; + iCARE = derive2 { name="iCARE"; version="1.14.0"; sha256="1v3phjn551xr9rxq8ck2zql0mj0p2jbizbghfnc8zmzirs7kh4ya"; depends=[gtools Hmisc plotrix]; }; + iCNV = derive2 { name="iCNV"; version="1.6.0"; sha256="185kp6smgpz9gd484vhx2k88rrwiszjckacvjjddrcvgwjzl1qvy"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; + iCOBRA = derive2 { name="iCOBRA"; version="1.14.0"; sha256="1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz"; depends=[dplyr DT ggplot2 limma reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; + iCheck = derive2 { name="iCheck"; version="1.16.0"; sha256="0r35k27d1l0zg0gmyfy4dd3kqvwjhbqk7a3wcrasqnpqy1xw44kn"; depends=[affy Biobase GeneSelectMMD gplots limma lmtest lumi MASS preprocessCore randomForest rgl scatterplot3d]; }; + iChip = derive2 { name="iChip"; version="1.40.0"; sha256="161n54q7z7vzgz8bwwbd1b97pqsicjhg8kk4gmhicza1rw081zh9"; depends=[limma]; }; + iClusterPlus = derive2 { name="iClusterPlus"; version="1.22.0"; sha256="1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37"; depends=[]; }; + iGC = derive2 { name="iGC"; version="1.16.0"; sha256="1ff58ik1sqjr8w4az6xk9jjga4k0wni2w4jyrvyn89v9zkmfvyq3"; depends=[data_table plyr]; }; + iPAC = derive2 { name="iPAC"; version="1.30.0"; sha256="0pw60ybraw5g9rfrw3hn3q2zdlddk8cgsv2snibkgrldp4rzfbr0"; depends=[Biostrings gdata multtest scatterplot3d]; }; + iSEE = derive2 { name="iSEE"; version="1.6.1"; sha256="0sg72r78qn7w1vni8pwyn0njwhib0yfd92vfvqq5pwqx403ys3b3"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; }; + iSeq = derive2 { name="iSeq"; version="1.38.0"; sha256="1cmj5247f8wfgcp5qksv3ss8h98rsk70v1hsw0rfm36wz2qf2713"; depends=[]; }; + iasva = derive2 { name="iasva"; version="1.4.0"; sha256="0fqywk3g9gdcpxix4g1b3b3gfy1z30y87ib7r6lw93qi3ylj5bvg"; depends=[BiocParallel cluster irlba SummarizedExperiment]; }; + ibh = derive2 { name="ibh"; version="1.34.0"; sha256="1kxpmyaq7f5d4hb3llxgbh32zdj7d5azkrdnfaikdpjhmmqsv81v"; depends=[simpIntLists]; }; + icetea = derive2 { name="icetea"; version="1.4.0"; sha256="1xpfpb97n64f0pv5nnbini77bbcrmf35fmcz6snl5d3k2d7gj05n"; depends=[BiocGenerics BiocParallel Biostrings csaw DESeq2 edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; + ideal = derive2 { name="ideal"; version="1.10.0"; sha256="0iskqbdl9xifya47m4pg8aqm8ssrpip11i7713xy0b033bk641ij"; depends=[AnnotationDbi base64enc BiocParallel d3heatmap DESeq2 dplyr DT GenomicRanges ggplot2 ggrepel GO_db goseq GOstats gplots IHW IRanges knitr limma pcaExplorer pheatmap rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; + idiogram = derive2 { name="idiogram"; version="1.62.0"; sha256="08ahl8lifr2q3xlkrlsx39hmhy3nkn2yqqhal144aszg1v1w316j"; depends=[annotate Biobase plotrix]; }; + idr2d = derive2 { name="idr2d"; version="1.0.4"; sha256="0mp91i4dm2ilrl4f6w46pggjd2agy8a5mql82vgn1a7x56b6qwmw"; depends=[dplyr futile_logger GenomeInfoDb GenomicRanges ggplot2 idr IRanges magrittr reticulate scales stringr]; }; + igvR = derive2 { name="igvR"; version="1.6.1"; sha256="0brzlb4nivwg6j4wc4s31fhm5z99f1d9fpr275fqhfp7fqvwksyk"; depends=[BiocGenerics BrowserViz GenomicAlignments GenomicRanges httpuv MotifDb randomcoloR rtracklayer seqLogo VariantAnnotation]; }; + illuminaio = derive2 { name="illuminaio"; version="0.28.0"; sha256="1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh"; depends=[base64]; }; + imageHTS = derive2 { name="imageHTS"; version="1.36.0"; sha256="1p8419zjkmxjmkfmj2a3xffaxp1bdxqz6hsm3x7h2w5xd29g3jqb"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; }; + immunoClust = derive2 { name="immunoClust"; version="1.18.1"; sha256="14lbxlqg0h4fn3vx7j1qr2mbdfrkka6icbawzj0a6nlds8la7jzb"; depends=[flowCore lattice]; }; + impute = derive2 { name="impute"; version="1.60.0"; sha256="0igz1phjd1j9bg9z4kyy7j8v9bxi9sdwz4df26r51i2vavlbrf4q"; depends=[]; }; + infercnv = derive2 { name="infercnv"; version="1.2.1"; sha256="0aqcxmjkrxw7lyqvlpqdvzh690bjydbqqx8xxvmzh8w1y9gsr492"; depends=[ape argparse BiocGenerics caTools coda coin digest doParallel dplyr edgeR fastcluster fitdistrplus foreach futile_logger future ggplot2 gplots gridExtra HiddenMarkov Matrix RColorBrewer reshape rjags SingleCellExperiment SummarizedExperiment tidyr]; }; + intansv = derive2 { name="intansv"; version="1.26.0"; sha256="1fpvcy46gili5j6vgclfiz101405gkwpvbpkxn2fhbdqs08n2gnx"; depends=[BiocGenerics GenomicRanges ggbio IRanges plyr]; }; + interactiveDisplay = derive2 { name="interactiveDisplay"; version="1.24.0"; sha256="0y2q0l686zfj3yvyiwvbp2qm775ha6v7d85hvpxfs8g39vhqn2qn"; depends=[AnnotationDbi BiocGenerics Category ggplot2 gridSVG interactiveDisplayBase plyr RColorBrewer reshape2 shiny XML]; }; + interactiveDisplayBase = derive2 { name="interactiveDisplayBase"; version="1.24.0"; sha256="0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n"; depends=[BiocGenerics shiny]; }; + inveRsion = derive2 { name="inveRsion"; version="1.34.0"; sha256="02zrgg6xg6x56h42nppqvvi0s54rhbv6qvgcmjgbizhq1l1dkx9k"; depends=[haplo_stats]; }; + ipdDb = derive2 { name="ipdDb"; version="1.4.0"; sha256="069q37c46mavggbm3gyvr9f3d6ckfz5yv1gadhw2alms4585xg0q"; depends=[AnnotationDbi AnnotationHub assertthat Biostrings DBI GenomicRanges IRanges RSQLite]; }; + isobar = derive2 { name="isobar"; version="1.32.0"; sha256="1cc8780kqzxl38j6vlh3dfrwjws5whlgsx5x2qqml006sb63wync"; depends=[Biobase biomaRt distr ggplot2 plyr]; }; + isomiRs = derive2 { name="isomiRs"; version="1.14.0"; sha256="0d1y5nnp3v57gl7n3r3p9k0zipci1vxp3zrz6cbc8624ff97nk8x"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics broom cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; }; + iterClust = derive2 { name="iterClust"; version="1.8.0"; sha256="0qalm8s4nmy75rqdrg20kr5zfvhncmwk2q167m8619iq4zgjwdbq"; depends=[Biobase cluster]; }; + iterativeBMA = derive2 { name="iterativeBMA"; version="1.44.0"; sha256="1nmb1yf2k3h0xqdlklqgpix2xcqsy4qb92xajmbfx80p7iga4rcr"; depends=[Biobase BMA leaps]; }; + iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.44.0"; sha256="1byb09b53l81n12vzfvjw9lk7fv8a6c7b6kzgv88ihpc3qj28vba"; depends=[BMA leaps survival]; }; + iteremoval = derive2 { name="iteremoval"; version="1.6.0"; sha256="178h5a2hdh63rahbq4w86xgxwkk9vsa5srin76qpfbiy40yiwawq"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; }; + ivygapSE = derive2 { name="ivygapSE"; version="1.8.0"; sha256="0wazpa0nbnw0cpin4v4m6v91czg0083bwd10as0g89slsvgqkh0c"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; }; + joda = derive2 { name="joda"; version="1.34.0"; sha256="0n6bcx29rnsc75zwgaj1wq0jg5pi40fcx9qrslabv827a7w77qad"; depends=[bgmm RBGL]; }; + karyoploteR = derive2 { name="karyoploteR"; version="1.12.4"; sha256="03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v"; depends=[AnnotationDbi bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; + kebabs = derive2 { name="kebabs"; version="1.20.0"; sha256="14a6bk0zqki8fhz47i2gkr0sgvd1dpi0bgxv5cyzph5ah62kjjxg"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; + keggorthology = derive2 { name="keggorthology"; version="2.38.0"; sha256="0g6s4fh48zvfvxg96x0k8163d9hpbpxcsmnijj5q4gv1v1bn6rhk"; depends=[AnnotationDbi DBI graph hgu95av2_db]; }; + kimod = derive2 { name="kimod"; version="1.14.0"; sha256="0sx68f74kc086q9np7559s0spawfn2adjx9cnpa1a0qca97z9xdq"; depends=[Biobase cluster]; }; + kissDE = derive2 { name="kissDE"; version="1.6.0"; sha256="179a416w3h6ssqsni32av0sqgz66hlv6akz7h4v9rp16ihfxxqvf"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; }; + lapmix = derive2 { name="lapmix"; version="1.52.0"; sha256="1bd88mflk9djkq6n921hl9frxrlqxinsjyc798v3wym88y0s80yp"; depends=[Biobase]; }; + ldblock = derive2 { name="ldblock"; version="1.16.0"; sha256="0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x"; depends=[BiocGenerics EnsDb_Hsapiens_v75 ensembldb GenomeInfoDb GenomicFiles httr Matrix Rsamtools snpStats VariantAnnotation]; }; + les = derive2 { name="les"; version="1.36.0"; sha256="12ykbc8nxagldz20rqwx58ixxkjx3w92mr78fmpnk61hl2980qbz"; depends=[boot fdrtool gplots RColorBrewer]; }; + levi = derive2 { name="levi"; version="1.4.0"; sha256="0d49wdbwdwgpvh4y2bw27b91x4hba426lxjsm1gfs030dxnbgz15"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 shiny shinydashboard shinyjs testthat xml2]; }; + lfa = derive2 { name="lfa"; version="1.16.0"; sha256="0cyb8gqxv2kx341z0xgmf0cipbhc0rwpk8a4pjy0qv7448swgw74"; depends=[corpcor]; }; + limma = derive2 { name="limma"; version="3.42.2"; sha256="1nd01r7rd7jb5qz84vbgfnyrmgm9wiq7fsdji68537kjgvrzmm9z"; depends=[]; }; + limmaGUI = derive2 { name="limmaGUI"; version="1.62.0"; sha256="1b3wxyl16mn5kp1v3wx5mrf8z03qh8pmy1k1nf9bcg2r21y5sqr9"; depends=[limma R2HTML tkrplot xtable]; }; + lionessR = derive2 { name="lionessR"; version="1.0.0"; sha256="1q64dmd0w9xlxcdizpjq8lfkfbr0vmqizrhc54rmlv35avk56z8f"; depends=[S4Vectors SummarizedExperiment]; }; + lipidr = derive2 { name="lipidr"; version="2.0.0"; sha256="1d87k9qg74rkqj299zil7aa8818b2m0a94711p0b84nsy2xlihgc"; depends=[data_table dplyr fgsea forcats ggplot2 limma magrittr rlang ropls S4Vectors SummarizedExperiment tidyr]; }; + lmdme = derive2 { name="lmdme"; version="1.28.0"; sha256="103p63srpc6nx5axmxi3rawxkfak7wvssbjkm8dwbm072c1spjk6"; depends=[limma pls stemHypoxia]; }; + loci2path = derive2 { name="loci2path"; version="1.6.0"; sha256="0r8znxqx8m8n6j70lv2fx271rvm0d2iyysnry2iczj3pfqg0qzy0"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; + logicFS = derive2 { name="logicFS"; version="2.6.0"; sha256="0a507w1n3h8b0lj2k3wci0li6j3z27wkfxswcfnj21gl8sd3fy7f"; depends=[LogicReg mcbiopi survival]; }; + logitT = derive2 { name="logitT"; version="1.44.0"; sha256="1pk2shrg5dkzhgh3l4ml2xkpfib52lcqcl0rqmic9slggmsidb9q"; depends=[affy]; }; + lol = derive2 { name="lol"; version="1.34.0"; sha256="0x03dnn12h61n19iy6cd3nrsqlsqwg56a5jwrhcc41rqr30fwil4"; depends=[Matrix penalized]; }; + lpNet = derive2 { name="lpNet"; version="2.18.0"; sha256="05d8shryk6p99lfpand58pvrsdw7afwx4lp9wpyikivnkbadp3s0"; depends=[lpSolve nem]; }; + lpsymphony = derive2 { name="lpsymphony"; version="1.14.0"; sha256="0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv"; depends=[]; }; + lumi = derive2 { name="lumi"; version="2.38.0"; sha256="0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm"; depends=[affy annotate AnnotationDbi Biobase DBI GenomicFeatures GenomicRanges KernSmooth lattice MASS methylumi mgcv nleqslv preprocessCore RSQLite]; }; + mAPKL = derive2 { name="mAPKL"; version="1.16.0"; sha256="1dskvrwsjs1d12bpwil9mmx2xcnrf9hzpd45v6jg71vsc547a5xr"; depends=[AnnotationDbi apcluster Biobase clusterSim e1071 igraph limma multtest parmigene reactome_db]; }; + mBPCR = derive2 { name="mBPCR"; version="1.40.0"; sha256="12iq2lr2gp9xh0kr2ipba5201bp47k5saja0fz577i77ww6v22lj"; depends=[Biobase oligoClasses SNPchip]; }; + mCSEA = derive2 { name="mCSEA"; version="1.6.0"; sha256="179pf50b0f1lh955rkzigrsrwnflhg1ny61vfp3yfbx133ljgrbk"; depends=[biomaRt fgsea GenomicFeatures GenomicRanges ggplot2 Gviz Homo_sapiens IRanges limma mCSEAdata S4Vectors SummarizedExperiment]; }; + maCorrPlot = derive2 { name="maCorrPlot"; version="1.56.0"; sha256="0n4svscf1gigaqzh1cpmpdsnw2krz3qn1ja9vaz6gpmkxqxyblrn"; depends=[lattice]; }; + maPredictDSC = derive2 { name="maPredictDSC"; version="1.24.0"; sha256="1zsp1n99rhbhkdnrdphnnpwwl1560anxsjmc7icdmhg2ddfg9cpw"; depends=[affy AnnotationDbi caret class e1071 gcrma hgu133plus2_db limma LungCancerACvsSCCGEO MASS ROC ROCR]; }; + maSigPro = derive2 { name="maSigPro"; version="1.58.0"; sha256="1nk8lq6496xhlpafhhri8an7cmz8z1islmadpw11zrgim9vyq7hf"; depends=[Biobase MASS mclust venn]; }; + maanova = derive2 { name="maanova"; version="1.56.0"; sha256="1n6rx45252l7ya0hjsz5hdpna5kz3dqrlbc3lh1h2qx3bkl0myds"; depends=[Biobase]; }; + macat = derive2 { name="macat"; version="1.60.0"; sha256="0whl4l69i99q97v9mqa7n4kfpf560v57ggvw83wvcyqjarnhsqxx"; depends=[annotate Biobase]; }; + made4 = derive2 { name="made4"; version="1.60.0"; sha256="14zxx8g3r42rv2gix8im8kvm56irbivwqwdz347r1aj99r9m2k58"; depends=[ade4 gplots RColorBrewer scatterplot3d]; }; + maftools = derive2 { name="maftools"; version="2.2.10"; sha256="025yiy286qc1g39m1926ldb0lbfsc6c3dns7kc6b04m4v9ibd03d"; depends=[data_table RColorBrewer survival wordcloud]; }; + maigesPack = derive2 { name="maigesPack"; version="1.50.0"; sha256="10vn06v64lq4dnq89czl9szqd4395vzawaj0nfz0vzwm339g1sdh"; depends=[convert graph limma marray]; }; + makecdfenv = derive2 { name="makecdfenv"; version="1.62.0"; sha256="0bgcsic5anyb8fz25cgknq2z5jc0s1s01a8mf5vf2ks51q73wk93"; depends=[affy affyio Biobase zlibbioc]; }; + manta = derive2 { name="manta"; version="1.32.0"; sha256="19m3a5kbzgg6bfzw0avlzc4awby36ijl346i6xrzmaswwj0s2x21"; depends=[caroline edgeR Hmisc]; }; + mapscape = derive2 { name="mapscape"; version="1.10.0"; sha256="1f2znc70v648pmrcdsfdyvgpha1c7dbrp2pmmr0453qskjaripvw"; depends=[base64enc htmlwidgets jsonlite stringr]; }; + marray = derive2 { name="marray"; version="1.64.0"; sha256="1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl"; depends=[limma]; }; + martini = derive2 { name="martini"; version="1.6.0"; sha256="0j0fj6s84j3295ysmp17f72j04g21nsd5jxv3vy20n6dnl2zbfac"; depends=[igraph Matrix Rcpp RcppEigen Rgin S4Vectors snpStats]; }; + maser = derive2 { name="maser"; version="1.4.0"; sha256="0fvd517qwbqaxvl4yp858z8ygy71yzx4av524sjk291xq8vfw5vy"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; + maskBAD = derive2 { name="maskBAD"; version="1.30.0"; sha256="0g5ivyb351xxl6ydzsckhvirns339m9ssj0w406lnpl2myr35d5m"; depends=[affy gcrma]; }; + massiR = derive2 { name="massiR"; version="1.22.0"; sha256="1zjrgqij5w6x9cc9pw01klwrphvbrxwc2760h27nm5x00kr3ag4i"; depends=[Biobase cluster diptest gplots]; }; + matchBox = derive2 { name="matchBox"; version="1.28.0"; sha256="1hsk5d8kcyl0sf1sm9fnfpqwy42ax2dr2zv73hzhqa1vgc276k1q"; depends=[]; }; + matter = derive2 { name="matter"; version="1.12.0"; sha256="0fj8fis97p1n1x2cg749rkd8zgsx5fh05qr3d0knjbrr4iyal6lb"; depends=[biglm BiocGenerics BiocParallel digest irlba ProtGenerics]; }; + mbkmeans = derive2 { name="mbkmeans"; version="1.2.0"; sha256="0a48imb0idsm27pmh2kliwfk9rrg46dngaw0fn1h4hyjc03sll9h"; depends=[beachmat benchmarkme ClusterR DelayedArray Matrix Rcpp RcppArmadillo Rhdf5lib SingleCellExperiment SummarizedExperiment]; }; + mcaGUI = derive2 { name="mcaGUI"; version="1.34.0"; sha256="1nch781pcsmbr4lbbkjcn3grjm4469mxy63zk2cmjg5x31jgjs99"; depends=[bpca foreign gWidgets gWidgetsRGtk2 lattice MASS OTUbase proto vegan]; }; + mdgsa = derive2 { name="mdgsa"; version="1.18.0"; sha256="0c5xza1mvgpi9cdl33s5iyal23az2jrkds01jh19asac71gjcqj4"; depends=[AnnotationDbi cluster DBI GO_db KEGG_db Matrix]; }; + mdp = derive2 { name="mdp"; version="1.6.0"; sha256="0n999nxdmrym40wqvbybzlp11zpcsyq2d80d1195r7smsdqvlx3w"; depends=[ggplot2 gridExtra]; }; + mdqc = derive2 { name="mdqc"; version="1.48.0"; sha256="0lbk71qaqxiba0g9103s5pz33y2pzbq13ypjigx3vgxz6m8a55gr"; depends=[cluster MASS]; }; + meshes = derive2 { name="meshes"; version="1.12.0"; sha256="1s2gm9k117mwjd65xh5vr0bv0a0l2zsv1czcx2grfni8nk7fy8j0"; depends=[AnnotationDbi DOSE enrichplot GOSemSim MeSH_db rvcheck]; }; + meshr = derive2 { name="meshr"; version="1.22.0"; sha256="1d86ilhladx8qs6kgvj7p5a7ik49fl9sisccgl79yax8znwlkjmj"; depends=[BiocGenerics Category cummeRbund fdrtool MeSH_Aca_eg_db MeSH_AOR_db MeSH_Bsu_168_eg_db MeSH_db MeSH_Hsa_eg_db MeSH_PCR_db MeSH_Syn_eg_db MeSHDbi org_Hs_eg_db RSQLite S4Vectors]; }; + messina = derive2 { name="messina"; version="1.22.0"; sha256="1vygzmfw1zp34pazrn181q8xsil2i7dnfwcpqh99vcn4laayvj4f"; depends=[foreach ggplot2 plyr Rcpp survival]; }; + metaArray = derive2 { name="metaArray"; version="1.64.0"; sha256="133rghxihyvrqk9d3b1182gsai7m2p25nhxn1jp4a64b9kb71xwx"; depends=[Biobase MergeMaid]; }; + metaCCA = derive2 { name="metaCCA"; version="1.14.0"; sha256="1qiifrs8x6vw83d2cvy9rxr43rmkgflz7plziaf77ljmlmrnz7a9"; depends=[]; }; + metaMS = derive2 { name="metaMS"; version="1.22.0"; sha256="0ci8lwmk15fky3x2x195nqxkpb1f0azwki44i27hjclbyb8ncs8r"; depends=[BiocGenerics CAMERA Matrix robustbase xcms]; }; + metaSeq = derive2 { name="metaSeq"; version="1.26.0"; sha256="0w75fmmppgv48k4j8jjvhwpbqpk6cxj07j0q2j75pp37jskpw24w"; depends=[NOISeq Rcpp snow]; }; + metabomxtr = derive2 { name="metabomxtr"; version="1.20.0"; sha256="1vwad5q2bkgsvr9pm53fqr1vhqwgaahibm97xz57rik5f987x3kz"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; }; + metagene = derive2 { name="metagene"; version="2.18.0"; sha256="1fz4zq18cpylgzaiazf5c4xhmmmd9p3v00x9k8q017sb1jfhhar2"; depends=[BiocParallel data_table DBChIP EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; }; + metagene2 = derive2 { name="metagene2"; version="1.2.1"; sha256="11ix77hv0q8k3b3ski5ji6pwm4qc50b6hwnqw43xsrralj8w89kr"; depends=[BiocParallel data_table DBChIP dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges magrittr purrr R6 Rsamtools rtracklayer]; }; + metagenomeFeatures = derive2 { name="metagenomeFeatures"; version="2.6.0"; sha256="1vlx4j566vdzq1q6lwh8j2njsijiz8zixbzc3i928ja6gdwsfn36"; depends=[ape Biobase Biostrings dbplyr DECIPHER dplyr lattice lazyeval magrittr RSQLite S4Vectors stringr]; }; + metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.28.2"; sha256="0nrnzmlkn3v5l30fg5x0apjq69hhjhh41f217q17dk5v4v78701y"; depends=[Biobase foreach glmnet gplots IHW limma Matrix matrixStats RColorBrewer Wrench]; }; + metahdep = derive2 { name="metahdep"; version="1.44.0"; sha256="0dpvjv1bji8086j7w0l5ylfls4y4sfwjaalkk2ixhhlqpmd1zah7"; depends=[]; }; + metaseqR = derive2 { name="metaseqR"; version="1.26.0"; sha256="07pjhg0cn6xchnci651k1jr89fygkxrwjv1ngfm1g3rvc0azp5ln"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; }; + metavizr = derive2 { name="metavizr"; version="1.10.0"; sha256="0xv5w133a7cnn35ym8i9b3jm1c3i741yvkblvrb20736yg05wjmz"; depends=[Biobase data_table digest epivizr epivizrData epivizrServer epivizrStandalone GenomeInfoDb httr metagenomeSeq phyloseq vegan]; }; + methInheritSim = derive2 { name="methInheritSim"; version="1.8.0"; sha256="1mrnd6d40ygzyf5si7vqm5ypm1989q3a3lvzhkxg4pzja6vd7m3q"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges methylKit msm S4Vectors]; }; + methVisual = derive2 { name="methVisual"; version="1.38.0"; sha256="0jk1jvhylcci8mkyy90hd7m44xm2wzgzp6rvprik6v61prk5d5zd"; depends=[Biostrings ca gridBase gsubfn IRanges plotrix sqldf]; }; + methimpute = derive2 { name="methimpute"; version="1.8.0"; sha256="05rr9di0g296v2wvs8kry36xnhdllkbzd4vp7iync1f5b6csh52p"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; }; + methrix = derive2 { name="methrix"; version="1.0.05"; sha256="1b91bizp7a1mqkkapbhrxgrsnpjxw5598m212p95nzr739296k32"; depends=[BSgenome data_table DelayedArray DelayedMatrixStats ggplot2 HDF5Array matrixStats rjson SummarizedExperiment]; }; + methyAnalysis = derive2 { name="methyAnalysis"; version="1.28.0"; sha256="11k444c5kj8bpqav52bx738gaq81maj8mmiyb7dn5rwpfxjjpfpz"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges genoset Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; }; + methylCC = derive2 { name="methylCC"; version="1.0.0"; sha256="00rm9rh04bhwn92cczysgfckm6v5km0m3ipw0hngw837wnrxzja4"; depends=[Biobase bsseq bumphunter dplyr FlowSorted_Blood_450k genefilter GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IRanges magrittr minfi plyranges quadprog S4Vectors]; }; + methylGSA = derive2 { name="methylGSA"; version="1.4.9"; sha256="0wfb7c9f6hy9s9bp9gcl5c1843xlmgp885iijk49shl3q5qrym6x"; depends=[AnnotationDbi BiocParallel clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b4_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg shiny stringr]; }; + methylInheritance = derive2 { name="methylInheritance"; version="1.10.0"; sha256="03h5gmz6pqqa3jfa2rx2wc9xc6lgim1879jy4v4dyciz05vzrmga"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; }; + methylKit = derive2 { name="methylKit"; version="1.12.0"; sha256="0klwc0sbmrxj1lxbz16pl39rxjm0pi57gjw547hlgnac1p9fspzy"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust mgcv qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; }; + methylMnM = derive2 { name="methylMnM"; version="1.24.0"; sha256="031k2jx0wm2gmfh794aa0yjlnap9dapw64a9l4v4a55yd9hbql9q"; depends=[edgeR statmod]; }; + methylPipe = derive2 { name="methylPipe"; version="1.20.0"; sha256="0g36fylp7j56n5m377cpnhhjk8lqhiyx3z1vr4hbgvn86adza2ra"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; }; + methylumi = derive2 { name="methylumi"; version="2.32.0"; sha256="0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; }; + methyvim = derive2 { name="methyvim"; version="1.8.0"; sha256="13m1xkmgm5h3x1avfhrclszcwb507i0g4h4ns6zviqr3n1ksmxkj"; depends=[BiocGenerics BiocParallel bumphunter cluster doFuture dplyr future GenomeInfoDb ggplot2 ggsci gridExtra gtools IRanges limma minfi S4Vectors SummarizedExperiment superheat tmle]; }; + mfa = derive2 { name="mfa"; version="1.8.0"; sha256="08fm767hmic2qhwg3s8lmj2j325l31czj141z6fmpj6hb8l72dl5"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; }; + mgsa = derive2 { name="mgsa"; version="1.34.0"; sha256="0jg47jzbk83rkdjwag9ysn8fj88c7f969jwaivjsh0nily835zal"; depends=[gplots]; }; + miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.10.0"; sha256="04bmrybcb8p2v31815w3dykyqg4vxzsl6h1xsk9cjf5v1a2z35bs"; depends=[]; }; + miRLAB = derive2 { name="miRLAB"; version="1.16.0"; sha256="073h8c3680852vzvvymfggarwjz3m9vyy05l1mji6wnj7j85qisn"; depends=[Category ctc dplyr energy entropy glmnet GOstats gplots heatmap_plus Hmisc httr impute InvariantCausalPrediction limma org_Hs_eg_db pcalg RCurl Roleswitch stringr SummarizedExperiment TCGAbiolinks]; }; + miRNAmeConverter = derive2 { name="miRNAmeConverter"; version="1.14.0"; sha256="1idqw575gjzr4hlbcxphx6h5h80v3zclm89m05qvqrk6gcy9slnw"; depends=[AnnotationDbi DBI miRBaseVersions_db reshape2]; }; + miRNApath = derive2 { name="miRNApath"; version="1.46.0"; sha256="16qjp0a1mrnp3gqcbp0rzb298k5sphpz4ri6whs3ikgkmdy0bn6s"; depends=[]; }; + miRNAtap = derive2 { name="miRNAtap"; version="1.20.0"; sha256="1kgywyj39cvng8mc9s0cmi7aqnfb7zmjl9a2nxvfy99zyqq7jbrb"; depends=[AnnotationDbi DBI plyr RSQLite sqldf stringr]; }; + miRSM = derive2 { name="miRSM"; version="1.4.1"; sha256="1sy0kj0sisady6hby814ggffc4izk8sp3hn45ifd7sfg4h1vkqy5"; depends=[BiBitR BicARE biclust Biobase dbscan dynamicTreeCut energy fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MatrixCorrelation MCL mclust miRspongeR NMF org_Hs_eg_db PMA ppclust Rcpp rqubic runibic s4vd SOMbrero subspace SummarizedExperiment WGCNA]; }; + miRcomp = derive2 { name="miRcomp"; version="1.16.0"; sha256="05riz927pvhyc1krvrnn5brbrj2k3dffs9rg8lzbgl7kaa85mvxc"; depends=[Biobase KernSmooth miRcompData]; }; + miRmine = derive2 { name="miRmine"; version="1.8.0"; sha256="1p4978miafirs5rk134vl1iyl08cizdj2rd2fp05kywhay9lay51"; depends=[SummarizedExperiment]; }; + miRspongeR = derive2 { name="miRspongeR"; version="1.12.0"; sha256="0hna616pp029ldlbprlcb3rfxn1xj2ngfvv7vg9yil85alayzyf5"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL org_Hs_eg_db Rcpp ReactomePA survival varhandle]; }; + microRNA = derive2 { name="microRNA"; version="1.44.0"; sha256="0jf16ghbyfg15hc0ggck1ixsqa9vlnvr839z9qh37cw3drkcn5id"; depends=[Biostrings]; }; + microbiome = derive2 { name="microbiome"; version="1.8.0"; sha256="118yp0xy8hkdp4sb3da9yy95z6zkh3v6i91z35xyhrvi0rwwmvn1"; depends=[dplyr ggplot2 phyloseq reshape2 Rtsne scales tidyr vegan]; }; + microbiomeDASim = derive2 { name="microbiomeDASim"; version="1.0.0"; sha256="0vmvjdgd520gkaq82nc4mjx9sgfzdmrg5g7asj2r7x8g3fdn18ar"; depends=[ggplot2 MASS Matrix mvtnorm pbapply tmvtnorm]; }; + mimager = derive2 { name="mimager"; version="1.10.0"; sha256="01zylwqcl7z147h81xp115zv9nglp1s26nf3bk6lqivlz8bw1ylw"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; }; + minet = derive2 { name="minet"; version="3.44.1"; sha256="1ag9pj8mdr0dvi33jrhwx8vm03i5f0lcbs7lpndambkk6spj5pxk"; depends=[infotheo]; }; + minfi = derive2 { name="minfi"; version="1.32.0"; sha256="177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; }; + mirIntegrator = derive2 { name="mirIntegrator"; version="1.16.0"; sha256="0v5y7bh4p8x71pnwds31pwv5agdh6y0agrgilg7pr52gdi55gnv5"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; }; + missMethyl = derive2 { name="missMethyl"; version="1.20.4"; sha256="1qsdqrmvkdx66yx223nm6px07hx53wvmh13qdb6729dph8485c6j"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; }; + missRows = derive2 { name="missRows"; version="1.6.0"; sha256="13j65247xyf3ixnmz8zn5ndlf8xfpbfh2cxxb57v334kq639k8lx"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; }; + mitoODE = derive2 { name="mitoODE"; version="1.24.0"; sha256="18ikad7q651yqq8hl4ygh2jq4fdmsihvn9fnnlz93nvzkshl6ajf"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; }; + mixOmics = derive2 { name="mixOmics"; version="6.10.9"; sha256="0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; }; + mlm4omics = derive2 { name="mlm4omics"; version="1.3.0"; sha256="14wpxidl2g2zfphxa5j2f7w5vjbqrxzzjdlnjv5mcf67fia1n7nj"; depends=[BH ggplot2 MASS Matrix Rcpp RcppEigen rstan rstantools StanHeaders]; }; + mnem = derive2 { name="mnem"; version="1.2.0"; sha256="0q8f0gicr92m8jj9asl59plgw2pdpril7g3sz69x3dmi1sagfd5q"; depends=[cluster data_table epiNEM flexclust graph lattice Linnorm matrixStats naturalsort nem Rcpp RcppEigen Rgraphviz snowfall tsne]; }; + mogsa = derive2 { name="mogsa"; version="1.20.0"; sha256="0yyic7qz4pnlyp96xl8gm20rhv5snyhmzm4sjl3hxgkx5br3sjd7"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; }; + monocle = derive2 { name="monocle"; version="2.14.0"; sha256="18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; }; + mosaics = derive2 { name="mosaics"; version="2.24.0"; sha256="0zgi32bkakh0ysazfqh4w740cm8hjwzpdjdyw8dfip8m8r47s0lx"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; }; + motifRG = derive2 { name="motifRG"; version="1.30.0"; sha256="0s6wdr036lra9x93r9k8wvicbkgzypjh3jp46h92yacw8d829k0d"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 IRanges seqLogo XVector]; }; + motifStack = derive2 { name="motifStack"; version="1.30.0"; sha256="00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg"; depends=[ade4 Biostrings ggplot2 grImport2 htmlwidgets MotIV scales XML]; }; + motifbreakR = derive2 { name="motifbreakR"; version="2.0.0"; sha256="190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr SummarizedExperiment TFMPvalue VariantAnnotation]; }; + motifcounter = derive2 { name="motifcounter"; version="1.10.0"; sha256="05knhki6w7yxrhf3gkh4wqj9yi11q60fd0c0qrxkplbhgd656r7z"; depends=[Biostrings]; }; + motifmatchr = derive2 { name="motifmatchr"; version="1.8.0"; sha256="1yvgaggx61rbrrspln2qf85lxqj1wg979mv1ya5xvjcv2qyw6s4z"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; }; + mpra = derive2 { name="mpra"; version="1.8.0"; sha256="1wflgcc9ns9mliz8f4xwvqkfx9qikb0am8skgp2wi96isyz4n0qc"; depends=[BiocGenerics limma S4Vectors scales statmod SummarizedExperiment]; }; + msPurity = derive2 { name="msPurity"; version="1.12.2"; sha256="1wg6mn9sz7ashxzn2zq7224p20a2wsz1614n60drfbjfflb7xpxz"; depends=[DBI dbplyr doSNOW dplyr fastcluster foreach ggplot2 jsonlite magrittr mzR plyr Rcpp reshape2 RSQLite stringr uuid]; }; + msa = derive2 { name="msa"; version="1.18.0"; sha256="0nd7kw6z4rkpsi3xwr7a3xivislgndj2xrad9rbppdz5a44yrjs4"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; }; + msgbsR = derive2 { name="msgbsR"; version="1.10.0"; sha256="1kjjhbyfjz6mx181slfcf4wb30d4qvyhvv26nhrxwkqdf83h0vn5"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; }; + msmsEDA = derive2 { name="msmsEDA"; version="1.24.0"; sha256="1g7j18i0qddasaqnmiw2qcswz8vm60acqqk628yh175kiczdlj0b"; depends=[gplots MASS MSnbase RColorBrewer]; }; + msmsTests = derive2 { name="msmsTests"; version="1.24.0"; sha256="1wn8nps8rd0fva48485pszlcs7hlvyid07lwr04hxjm9dm3m87gj"; depends=[edgeR msmsEDA MSnbase qvalue]; }; + multiClust = derive2 { name="multiClust"; version="1.16.0"; sha256="1c77c7mwvn7cb69r2frflafvqq1rd24k1xs99dj4axvg41yb69nn"; depends=[amap cluster ctc dendextend mclust survival]; }; + multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.4.0"; sha256="0sfx8m6p5rfvkzdhm15nzl6bajinx1gmgrglz95jbxljv8izqlzr"; depends=[BiocParallel BLMA data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare metap pbapply pheatmap qqman]; }; + multiMiR = derive2 { name="multiMiR"; version="1.8.0"; sha256="0f6ms2bzr58zjmhnv4zazxqmi1s42j5vf3qkfcgp80zb7vhfmd45"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; + multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.10.0"; sha256="0q1vcv8d9dwkibwgg3x304fr8qg1wljlbgwdb4zkgqlg2lcg288y"; depends=[doParallel foreach SummarizedExperiment]; }; + multiscan = derive2 { name="multiscan"; version="1.46.0"; sha256="0kf2byzpxdlcy74imh39zmn6w0gr3kk6qnaxv9qllpf60h4br4g4"; depends=[Biobase]; }; + multtest = derive2 { name="multtest"; version="2.42.0"; sha256="0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari"; depends=[Biobase BiocGenerics MASS survival]; }; + muscat = derive2 { name="muscat"; version="1.0.1"; sha256="105ra0by7iqp3m5az6r111g7q490if22nl1a9g5ccgg96wjf5mpf"; depends=[BiocParallel blme ComplexHeatmap data_table DESeq2 doParallel dplyr edgeR ggplot2 glmmTMB limma lme4 lmerTest magrittr Matrix matrixStats progress purrr reshape2 S4Vectors scales scater sctransform SingleCellExperiment SummarizedExperiment tibble variancePartition viridis]; }; + muscle = derive2 { name="muscle"; version="3.28.0"; sha256="0rv3sh46fh4z6nvwf781418s6bjhibvib2x5z3mz965k61j8f4zh"; depends=[Biostrings]; }; + mygene = derive2 { name="mygene"; version="1.22.0"; sha256="1xc272zh23z5ajglbmlaj376b8ackh36nqyfjcym44xi6p5bw2mk"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; }; + myvariant = derive2 { name="myvariant"; version="1.16.0"; sha256="17a20ipyhq7s829jqgzrc09c9jmc1rqi77hfpjbv8hj9wfcqpsan"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; }; + mzID = derive2 { name="mzID"; version="1.24.0"; sha256="1glcv096bn6pxlw89dlij1nzpwnjvrbxysvw2gm6qgm7rhxlaxrw"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; }; + mzR = derive2 { name="mzR"; version="2.20.0"; sha256="1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13"; depends=[Biobase BiocGenerics ncdf4 ProtGenerics Rcpp Rhdf5lib zlibbioc]; }; + nanotatoR = derive2 { name="nanotatoR"; version="1.2.0"; sha256="0754dnkwm89fy9i47kyfg0mmfn817n427l0jvgqbla17346xfdj3"; depends=[AnnotationDbi hash httr knitr openxlsx org_Hs_eg_db rentrez rtracklayer stringr testthat]; }; + ncGTW = derive2 { name="ncGTW"; version="1.0.0"; sha256="17sqc59ykgyylpnci2pv9xpny6fnl59mwid0d7lq0iwcvnvfqc9a"; depends=[BiocParallel Rcpp xcms]; }; + ncdfFlow = derive2 { name="ncdfFlow"; version="2.32.0"; sha256="06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i"; depends=[BH Biobase BiocGenerics flowCore Rcpp RcppArmadillo Rhdf5lib zlibbioc]; }; + ndexr = derive2 { name="ndexr"; version="1.8.0"; sha256="0hkkmizvdf89ilmsdf39g0dniwcgrw5fzy9g5161gz6vm8lb0kk1"; depends=[httr igraph jsonlite plyr tidyr]; }; + nem = derive2 { name="nem"; version="2.60.0"; sha256="11q1pf0qf7zsb14klz8inb7a4vbnq317v9kiqgaazb524xv49gf5"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; }; + netReg = derive2 { name="netReg"; version="1.10.0"; sha256="0pfl1g3plr2lv11a4x1vcczkdk1cha9g321q94lz5g8131sicc1q"; depends=[Rcpp RcppArmadillo]; }; + netSmooth = derive2 { name="netSmooth"; version="1.6.0"; sha256="06xssnln3j956gw94jirb3xmqvy1kx2bzls4hahz4410wa88130y"; depends=[cluster clusterExperiment data_table DelayedArray entropy HDF5Array Matrix scater SingleCellExperiment SummarizedExperiment]; }; + netbenchmark = derive2 { name="netbenchmark"; version="1.18.0"; sha256="1v23as3sk1qs7wvr9r5ck412ljfh0w7r0zwzggr4iph4f7sbg90d"; depends=[c3net corpcor fdrtool GeneNet GENIE3 grndata Matrix minet pracma Rcpp]; }; + netbiov = derive2 { name="netbiov"; version="1.20.0"; sha256="1w9ypgf9vr0sqvm9ahjmw97xnsfy5aps7svxvpdnj35hm0h32vdw"; depends=[igraph]; }; + netboost = derive2 { name="netboost"; version="1.2.2"; sha256="016pvgssgyablly2zym0a2m24a8z0a0sljg0krkf9znxyx3s34xy"; depends=[colorspace dynamicTreeCut impute R_utils Rcpp RcppParallel WGCNA]; }; + nethet = derive2 { name="nethet"; version="1.18.0"; sha256="0vblp9w3lyg9cdmgr7pacain7j3hwn3bblpkjy1bk0z0b37s39g5"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; }; + netprioR = derive2 { name="netprioR"; version="1.12.0"; sha256="01syisi6wyva4l5ysin7dk9yh4yadisp952v3nwb1jjkasnay7wr"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; }; + netresponse = derive2 { name="netresponse"; version="1.46.0"; sha256="0fkskjsrb36mig8jpv2vmzasmy4j9378hc81ihjkc732aa207ahv"; depends=[dmt ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz]; }; + networkBMA = derive2 { name="networkBMA"; version="2.26.0"; sha256="0lblgfm3hj4mc018cxhqk5k2a2rifrs43rb68w7vb2xx300k0mw7"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; }; + ngsReports = derive2 { name="ngsReports"; version="1.2.0"; sha256="1kqydrjkra3sihds8cd4r7w4zzbdi6w8p3ir79g0nhk4bcai2mbv"; depends=[BiocGenerics Biostrings checkmate dplyr FactoMineR ggdendro ggplot2 kableExtra lubridate pander plotly readr reshape2 rmarkdown Rsamtools scales ShortRead stringr tibble tidyr tidyselect truncnorm viridisLite XVector zoo]; }; + nnNorm = derive2 { name="nnNorm"; version="2.50.0"; sha256="18zdvbpahqqvqzamhx4v4z3dinhxmsp7p37lzx7ps3j6287h43ll"; depends=[marray nnet]; }; + nondetects = derive2 { name="nondetects"; version="2.16.0"; sha256="1vyyjca4if446fsnjgv1cl3089fc7h1942l856xj6qwix87anshs"; depends=[arm Biobase HTqPCR limma mvtnorm]; }; + normalize450K = derive2 { name="normalize450K"; version="1.14.0"; sha256="1apld57pniq94qrq8sllg5krq67lh8y6asy5chshb7pakr4zps1s"; depends=[Biobase illuminaio quadprog]; }; + normr = derive2 { name="normr"; version="1.12.0"; sha256="1bi4kf2l3wp13mnf00c072l6anfswz2zcw7irb6nb337yl82i72s"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; }; + npGSEA = derive2 { name="npGSEA"; version="1.22.0"; sha256="1llygxq61lk2b9nk6cb829n3ggj5s1xvzi6bgb9bydlscvacgys9"; depends=[Biobase BiocGenerics GSEABase]; }; + nuCpos = derive2 { name="nuCpos"; version="1.4.0"; sha256="0d7bw60c3ch1rs6nsliq2rwcs7kfqcvads6fcs9hz4lg2wpf6ak6"; depends=[]; }; + nucleR = derive2 { name="nucleR"; version="2.18.4"; sha256="1rbvkfbn2zsxmyz223n56kkgywn36m80mpj38jn9gllfsciby76y"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; }; + nucleoSim = derive2 { name="nucleoSim"; version="1.14.0"; sha256="1jkv8kxy72ssh81sr14qghdn2dsaghvcn5wdmjhvzgwyq8xzr87q"; depends=[IRanges S4Vectors]; }; + occugene = derive2 { name="occugene"; version="1.46.0"; sha256="0g5hyqqzci486kmnlphr63whqn8xw7p9npqwfl20lnqi727ypz2l"; depends=[]; }; + odseq = derive2 { name="odseq"; version="1.14.0"; sha256="0lxl1hzjcjynxz2wkb25r47v7k9bw2zlr4xzz2iqn1y539gxnv73"; depends=[kebabs mclust msa]; }; + oligo = derive2 { name="oligo"; version="1.50.0"; sha256="01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; }; + oligoClasses = derive2 { name="oligoClasses"; version="1.48.0"; sha256="02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf"; depends=[affyio Biobase BiocGenerics BiocManager Biostrings DBI ff foreach GenomicRanges IRanges RSQLite S4Vectors SummarizedExperiment]; }; + omicRexposome = derive2 { name="omicRexposome"; version="1.8.0"; sha256="0xjsl9sm35d9rxn2dbd5bmikac4jdcpih6b81izcd8m4yklqa2ns"; depends=[Biobase ggplot2 ggrepel gridExtra isva limma MultiDataSet omicade4 PMA rexposome SmartSVA stringr SummarizedExperiment sva]; }; + omicade4 = derive2 { name="omicade4"; version="1.26.0"; sha256="1c0kfns2c4lfjq20f11ff8zzrvm8gzjpsylrrgrh4v77kk23rsp9"; depends=[ade4 made4]; }; + omicplotR = derive2 { name="omicplotR"; version="1.6.1"; sha256="0br13a908zy68vd9gs75ddsiczv2qf6ijksacfnp4y7wzdv1r6wv"; depends=[ALDEx2 compositions DT jsonlite knitr matrixStats rmarkdown shiny vegan zCompositions]; }; + omicsPrint = derive2 { name="omicsPrint"; version="1.6.0"; sha256="12mi0hmmg8srkb7p9bkqlxjxpdm4jhpirbk44zhgvwsax75sj02a"; depends=[MASS matrixStats MultiAssayExperiment RaggedExperiment SummarizedExperiment]; }; + oncomix = derive2 { name="oncomix"; version="1.8.0"; sha256="181sayzb6rp0mp80gnmc39mgxi2qwyanj19kfhbvn1b80ahx009s"; depends=[ggplot2 ggrepel mclust RColorBrewer SummarizedExperiment]; }; + oneSENSE = derive2 { name="oneSENSE"; version="1.8.0"; sha256="15wi2xaj03p11knk4ixn2xnj06nnnxysr4ay663xrr2s40163wfh"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; }; + onlineFDR = derive2 { name="onlineFDR"; version="1.4.0"; sha256="0ym44nmz0357d5wpmkrb526fc7wylp1x3and8nfm8cx5pcmms8m4"; depends=[]; }; + ontoProc = derive2 { name="ontoProc"; version="1.8.1"; sha256="0hwayxivl6xkbklza8qn6kiyxn2ykqvh5ixm75m7vphsrql8kd42"; depends=[AnnotationDbi Biobase dplyr graph magrittr ontologyIndex ontologyPlot Rgraphviz S4Vectors shiny]; }; + openCyto = derive2 { name="openCyto"; version="1.24.0"; sha256="0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"; depends=[Biobase BiocGenerics clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; }; + openPrimeR = derive2 { name="openPrimeR"; version="1.8.0"; sha256="0xc5l1pkvzjx089ci60gmakc63yvh9jy5dm6qnyx9xn1p84b8q18"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr tinytex uniqtag XML]; }; + openPrimeRui = derive2 { name="openPrimeRui"; version="1.8.0"; sha256="1453zwcccm189kymdsyk43apy0absk98zsa8732vbz0g4wipl1jz"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; }; + oposSOM = derive2 { name="oposSOM"; version="2.4.0"; sha256="0pcwxr474az7ckxzvq2gw4pbcvd5jrl441hi8zf2d83iyaj4ym27"; depends=[ape Biobase biomaRt fastICA fdrtool igraph pixmap Rcpp RcppParallel scatterplot3d tsne]; }; + oppar = derive2 { name="oppar"; version="1.14.0"; sha256="0jmxvi2j654xqsvy7kdf20rj728gfspp5lvfnhglca73iy10alhk"; depends=[Biobase GSEABase GSVA]; }; + oppti = derive2 { name="oppti"; version="1.0.0"; sha256="147iikac07i7xb9y3qisc7nl3c674v6pdvv8yksxi4nd8g2yj96j"; depends=[devtools ggplot2 knitr limma pheatmap RColorBrewer reshape]; }; + pRoloc = derive2 { name="pRoloc"; version="1.26.0"; sha256="0k4cbx486vpxs88ljq51h1p2z3x4lll37h9isi08cajkpfbnxzdg"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class coda dendextend e1071 FNN ggplot2 gtools hexbin kernlab knitr LaplacesDemon lattice MASS mclust mixtools MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; }; + pRolocGUI = derive2 { name="pRolocGUI"; version="1.20.0"; sha256="1f15wl5r71rclb8d5m3w5l1vvcrgky04q45jjmhd9076clkwdvyi"; depends=[Biobase dplyr DT ggplot2 MSnbase pRoloc scales shiny]; }; + paircompviz = derive2 { name="paircompviz"; version="1.24.0"; sha256="1ygrcpy39661dll83fs8hfb1akyzk2mnnr6lh9yyizn848sbpnga"; depends=[Rgraphviz]; }; + pandaR = derive2 { name="pandaR"; version="1.18.0"; sha256="1immn3vgqzxahh5m3sb0lkyszqnf7vgdqkfi0jxkb49ck7p7mn7d"; depends=[Biobase BiocGenerics ggplot2 hexbin igraph matrixStats plyr reshape RUnit]; }; + panelcn_mops = derive2 { name="panelcn.mops"; version="1.8.0"; sha256="1xi893chr0v7r2v3f57i61xzmvvx56xzil4q4yrvbpj24hg57nm9"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; + panp = derive2 { name="panp"; version="1.56.0"; sha256="07xa5smdjwzyz547lr4h4fl01frjfla4386gslwrxc8y5p7k96vv"; depends=[affy Biobase]; }; + parglms = derive2 { name="parglms"; version="1.18.0"; sha256="1i82sjb5g6fhn6pysg25l2ac47798y3134mbry1vr34vc2r87sq7"; depends=[BatchJobs BiocGenerics doParallel foreach]; }; + parody = derive2 { name="parody"; version="1.44.0"; sha256="1zb0ysp31b1j40j452dsjq0kkwi1prvz3ms0dm8qwgpysd2piwfi"; depends=[]; }; + pathRender = derive2 { name="pathRender"; version="1.54.0"; sha256="07vl6bq0d2dpkin1q5ghz644fbvz6gpi7ry1lmq44dw1z2fap3q6"; depends=[AnnotationDbi cMAP graph RColorBrewer Rgraphviz]; }; + pathVar = derive2 { name="pathVar"; version="1.16.0"; sha256="14ngfscsa5pxs55chs51d252z909v3yjm0ra0q0zsfziwan2w6fn"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; }; + pathifier = derive2 { name="pathifier"; version="1.24.0"; sha256="1yp0b749ji3rh0dbag0zpw97al7ckbqx023fih72z2hhddpayr3v"; depends=[princurve R_oo]; }; + pathprint = derive2 { name="pathprint"; version="1.16.0"; sha256="1kff31wiyx0mqlqlkamy4q0g1s6ww6j5hjj9z8xncsfp58gll4yp"; depends=[]; }; + pathview = derive2 { name="pathview"; version="1.26.0"; sha256="1df54hf8ihdh80clpxk5mzdvz5jwvlhx4whrp7pg9wm3rg1n2a4s"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; + pathwayPCA = derive2 { name="pathwayPCA"; version="1.2.0"; sha256="1scm2vq2vwj7d0dn1g8976r6aya121jl51591gpa7hqzyfndc4js"; depends=[lars survival]; }; + paxtoolsr = derive2 { name="paxtoolsr"; version="1.20.0"; sha256="1fwbkanm28vi4lssgxcxy12xsadspp2lgs9ilf2v45l0cj85gq4l"; depends=[httr igraph jsonlite plyr R_utils readr rJava rjson XML]; }; + pcaExplorer = derive2 { name="pcaExplorer"; version="2.12.0"; sha256="1s7nw7iw4i5gy5cwagvby8810jk1b8a616jf8j6f6yrl460kkmig"; depends=[AnnotationDbi base64enc biomaRt d3heatmap DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats IRanges knitr limma NMF pheatmap plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; + pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.30.0"; sha256="0cj7aqi8pdm5xqgx0v2g8nwjl944kgnpywjdvqbj2pc1i9wi87c2"; depends=[AnnotationDbi Biostrings ellipse]; }; + pcaMethods = derive2 { name="pcaMethods"; version="1.78.0"; sha256="1wir67kfjm0m9gf0ki8qmvh45n4gx2k0wfl9pd1hp4g62fbrj1pj"; depends=[Biobase BiocGenerics MASS Rcpp]; }; + pcot2 = derive2 { name="pcot2"; version="1.54.0"; sha256="056zpd8r870sn9ar9ckm6xhw760bgpsyk8xqplf8g2vf3wssbsg4"; depends=[amap Biobase]; }; + pcxn = derive2 { name="pcxn"; version="2.8.0"; sha256="1rq6g0rdfm0nglyfp30yczqrwfsaakyx17dpm13yf1rhdj070jhi"; depends=[pcxnData pheatmap]; }; + pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.50.0"; sha256="18zk2n40kn472p3k05kzwqfv4k8ia12pvn76hipkbavzbq4sr86j"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; + peakPantheR = derive2 { name="peakPantheR"; version="1.0.0"; sha256="00qq596ggl9bgxpkl091s95k4fxi0qff5n74f3c0qi40vs2ln80b"; depends=[doParallel foreach ggplot2 gridExtra minpack_lm MSnbase mzR scales stringr XML]; }; + pepStat = derive2 { name="pepStat"; version="1.20.0"; sha256="179kaw9js96i3gsx5msqg4s20zfb6q5iva2cqgw0dnv0dzrvrzxg"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; }; + pepXMLTab = derive2 { name="pepXMLTab"; version="1.20.0"; sha256="08mbcvlfg9rx9z37q8ral9vi97r9fxcpajd8axnqd3rgzzdbihif"; depends=[XML]; }; + perturbatr = derive2 { name="perturbatr"; version="1.6.0"; sha256="1rmcqyh3773p1fmq9yshzkyd5nf309nkcpsy2y09i5in0xjhap2q"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; }; + pgca = derive2 { name="pgca"; version="1.10.0"; sha256="041476hq4c6vn7rpmwf3jsis3i9ql001rhl3cvyl9v1xl08qyyzy"; depends=[]; }; + phantasus = derive2 { name="phantasus"; version="1.6.0"; sha256="0av1an61zcg7w79sygwynb9lfxyls52ps7c1vcnf99xlwww8vs5g"; depends=[AnnotationDbi assertthat Biobase ccaPP fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix Matrix_utils opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; }; + phemd = derive2 { name="phemd"; version="1.1.1"; sha256="0vplb6x91p51idb7xpvvcpb2zbn29r0cign2vdhl5vrqi2162kk4"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle pheatmap pracma RANN RColorBrewer Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; }; + phenoTest = derive2 { name="phenoTest"; version="1.34.0"; sha256="0ri3z95bl9bn5rgxysy2q0b3zk5j3sv2nggmdn58abz8hk1rjr7s"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach HTSanalyzeR limma mgcv SNPchip survival xtable]; }; + phenopath = derive2 { name="phenopath"; version="1.10.0"; sha256="0x3ibb3pxkhi5y6zyfi68m2csy36946nwq1gmm5bxygbphpwcdcb"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; }; + philr = derive2 { name="philr"; version="1.12.0"; sha256="0l1krm78ywmphvlif3k3wxh2ymlgdkjxww23vj2ggpz5dkhdk83d"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; + phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.10.0"; sha256="11r7hm2lbbx51qsw4v0sxkczy22x4qmsyw34admnvqbyshza9hzv"; depends=[matrixStats plyr]; }; + phyloseq = derive2 { name="phyloseq"; version="1.30.0"; sha256="07b7g3dx7mpp2jjys3r9l7fwlabjdk8vbgv33zhrlip2vix95s9w"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; }; + piano = derive2 { name="piano"; version="2.2.0"; sha256="1f1nlibsnkgnklalw2fbgjm6dzbbni1l0cp25zh073dklhkigzd3"; depends=[Biobase BiocGenerics DT fgsea gplots htmlwidgets igraph marray relations scales shiny shinydashboard shinyjs visNetwork]; }; + pickgene = derive2 { name="pickgene"; version="1.58.0"; sha256="07mw40qg7x4zzjrh7mxr5za234biddqh6xsxa8z2lbzkkcwcrk61"; depends=[MASS]; }; + pint = derive2 { name="pint"; version="1.36.0"; sha256="0dr74z7wbygjzxy6hsc88zms98s1kf0jn36s3w35xb2jki1pmq4g"; depends=[dmt Matrix mvtnorm]; }; + pipeFrame = derive2 { name="pipeFrame"; version="1.2.2"; sha256="0cdqc61cawa7ar9yvspnahmswdb57b0gh2syaj3mxk5lm9c5mwyy"; depends=[Biostrings BSgenome digest GenomeInfoDb magrittr visNetwork]; }; + pkgDepTools = derive2 { name="pkgDepTools"; version="1.52.0"; sha256="11jh69yvzsm1jacj63c0pgw26gmbgbpmnkmgyc12r8drcsxyhji2"; depends=[graph RBGL]; }; + plethy = derive2 { name="plethy"; version="1.24.0"; sha256="1rqh20ymri7806rq9m6nn2ca30jzrx7a8sbggxsp54hmha0k6ill"; depends=[Biobase BiocGenerics DBI ggplot2 IRanges plyr RColorBrewer reshape2 RSQLite S4Vectors Streamer]; }; + plgem = derive2 { name="plgem"; version="1.58.0"; sha256="0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v"; depends=[Biobase MASS]; }; + plier = derive2 { name="plier"; version="1.56.0"; sha256="18jqnmv1zwig6md430adgin9hsg67vxlmnmvjlfcx3i81hymx33n"; depends=[affy Biobase]; }; + plotGrouper = derive2 { name="plotGrouper"; version="1.4.0"; sha256="0a34ijxxfa4648xcm4c9jxncsaj5qh2l035cjfv7xzd9wk02aprm"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; }; + plrs = derive2 { name="plrs"; version="1.26.0"; sha256="0gcv9ld5jhi9abanw0layy5c03fvg83xww3bjar9w83bq1hysd2c"; depends=[Biobase BiocGenerics CGHbase ic_infer marray quadprog Rcsdp]; }; + plw = derive2 { name="plw"; version="1.46.0"; sha256="040vhc75dprnnazjryrzndvxi4i33yfd97k3pmr3mk7h21x68wpf"; depends=[affy MASS]; }; + plyranges = derive2 { name="plyranges"; version="1.6.10"; sha256="1bmwjzc0y98xd8rf3lwgh9vf456cssw4nd6yvxm47dpnbshmkm0n"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyselect]; }; + pmm = derive2 { name="pmm"; version="1.18.0"; sha256="1fy90inxiqyr8szxamz33rkd5hh2qi9bmkb8z6jgip8pwj8vs0zb"; depends=[lme4]; }; + podkat = derive2 { name="podkat"; version="1.18.0"; sha256="0qfcl6gyv063q8bk2w44ga5234yi3m2bhhcabdwsq8gq2kxiwn6n"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rhtslib Rsamtools]; }; + pogos = derive2 { name="pogos"; version="1.6.0"; sha256="0mwcwcr5pz2s4x0jgsyynm1fqmnys78z0zq6l8ngdi51xj2216qn"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; }; + polyester = derive2 { name="polyester"; version="1.22.0"; sha256="1jrq9qlr1jswz20xfnipzawva7mn2czwpn2q4nabv1mhhmlf0mwm"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; }; + powerTCR = derive2 { name="powerTCR"; version="1.6.0"; sha256="0g6sy7b6igb9q1yfsfbk0g47k7zwk7bqx0gckmf5jbnc3sp4kyn6"; depends=[cubature doParallel evmix foreach magrittr purrr tcR truncdist vegan VGAM]; }; + ppiStats = derive2 { name="ppiStats"; version="1.52.0"; sha256="0a9lds7j5qdcmmwy9qdb364gqrfc0gb78la693l9mkml4rnz4j8q"; depends=[Biobase Category graph lattice ppiData RColorBrewer ScISI]; }; + pqsfinder = derive2 { name="pqsfinder"; version="2.2.0"; sha256="1y2wlzw7wi5kbmvmf1imzy0car65g4irvaiz4x601wvxxyzqy74s"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; + prada = derive2 { name="prada"; version="1.62.0"; sha256="1c614ciqkqj95xzvr8z5lkvdw6xiw795fnqk900ly8g2kkfkg1kz"; depends=[Biobase BiocGenerics MASS RColorBrewer rrcov]; }; + pram = derive2 { name="pram"; version="1.2.0"; sha256="0hdzjqx4d8mgf1vwp6a5gmjncgvr64mgv4lf8q98v9rk1rrnbzwa"; depends=[BiocGenerics BiocParallel data_table GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; + prebs = derive2 { name="prebs"; version="1.26.0"; sha256="0fqg3adgzjizzqx03r0h43ic6v8fs953v1h942h9hiw6r1q5hnxg"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; + predictionet = derive2 { name="predictionet"; version="1.32.0"; sha256="0m6lrcd0bckk0wic8pnqi4sc83jk9l65dgyfd62hg42wx9292wxv"; depends=[catnet igraph MASS penalized RBGL]; }; + preprocessCore = derive2 { name="preprocessCore"; version="1.48.0"; sha256="0zrb9hx60vppkg0priczdb301nhq5f0dj8lkc8rcc4xrqqr915qm"; depends=[]; }; + primirTSS = derive2 { name="primirTSS"; version="1.4.0"; sha256="08hwq0yn5lnccdvj67cpqa12na4fx25gpk8vcvymi0icqpx9ga5p"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg38 dplyr GenomicRanges GenomicScores Gviz IRanges JASPAR2018 phastCons100way_UCSC_hg38 purrr R_utils rtracklayer S4Vectors shiny stringr TFBSTools tibble tidyr]; }; + proBAMr = derive2 { name="proBAMr"; version="1.20.0"; sha256="06aifq4lbq2fvwgshnr3jazqqh000rapypd2cl4sqf267nfyqrvi"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; }; + proBatch = derive2 { name="proBatch"; version="1.2.0"; sha256="1hlcs4faqx8z9f72fdy9hfnk2c2jv4rnb8zvv2j6gj027pwy8jgl"; depends=[Biobase corrplot data_table dplyr ggfortify ggplot2 lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales sva tibble tidyr viridis wesanderson WGCNA]; }; + proDA = derive2 { name="proDA"; version="1.0.0"; sha256="1l6baxhiybxzddhk1dks46hmrich6bw2nyzsbid3byh5rkf6msxc"; depends=[BiocGenerics extraDistr S4Vectors SummarizedExperiment]; }; + proFIA = derive2 { name="proFIA"; version="1.12.0"; sha256="1p0kgapd5fmgaz537chj8ymyxp9vg8wdfc5vf8l09f0xjfm2cahm"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; }; + procoil = derive2 { name="procoil"; version="2.14.0"; sha256="1pmv2z2pvj996yc8d8988bfzqf4qqk5ap5grh21fsfjvhiry87hx"; depends=[Biostrings kebabs S4Vectors]; }; + profileScoreDist = derive2 { name="profileScoreDist"; version="1.14.0"; sha256="01nqbx5szvfl7pkpfx8kqfvp3pr3g5lkscr2mxd3fm0z2lmzc6g6"; depends=[BiocGenerics Rcpp]; }; + profileplyr = derive2 { name="profileplyr"; version="1.2.0"; sha256="0f9rc8shz5pxlga8wbgsj3d8lfhyckvlpm9l9hi8imr0zkkrhsrn"; depends=[BiocGenerics BiocParallel ChIPseeker circlize ComplexHeatmap dplyr EnrichedHeatmap GenomeInfoDb GenomicFeatures GenomicRanges IRanges magrittr org_Hs_eg_db org_Mm_eg_db pheatmap R_utils rGREAT rjson rtracklayer S4Vectors soGGi SummarizedExperiment tidyr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + progeny = derive2 { name="progeny"; version="1.8.0"; sha256="0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq"; depends=[Biobase]; }; + projectR = derive2 { name="projectR"; version="1.2.0"; sha256="15jkninksmy92f1rw9mi9c4cdlqcc0cwpqrq46zrgpbcfsfbqc9r"; depends=[cluster CoGAPS limma NMF ROCR]; }; + proteinProfiles = derive2 { name="proteinProfiles"; version="1.26.0"; sha256="0qcl4270prwa5cgg9c3i4nlbw5kz7qi6cc1yizjdvk4wmbxcr736"; depends=[]; }; + proteoQC = derive2 { name="proteoQC"; version="1.21.0"; sha256="0jkadb255qgjy131w1zkmznxwj1hpx95v8qhq3cc27krgdv6nnd3"; depends=[dplyr ggplot2 MSnbase Nozzle_R1 plotly plyr reshape2 rmarkdown rpx rTANDEM seqinr tidyr VennDiagram XML]; }; + psichomics = derive2 { name="psichomics"; version="1.12.1"; sha256="12l8lap1zgdn1qr75x9msjymys67aab7jy79dazjs061zqk2mac4"; depends=[AnnotationDbi AnnotationHub BiocFileCache cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools org_Hs_eg_db pairsD3 plyr R_utils Rcpp recount reshape2 shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; }; + psygenet2r = derive2 { name="psygenet2r"; version="1.18.0"; sha256="1ivybrwm1a3clnwkby10300707sy33llyka989id7s1p3l5amjgv"; depends=[BgeeDB Biobase BiocManager biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; + pulsedSilac = derive2 { name="pulsedSilac"; version="1.0.1"; sha256="1xjmqjx2z0cyijqnky68xcckk0rzbfsgwzizymby4lygwqkf0k6c"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment taRifx UpSetR]; }; + puma = derive2 { name="puma"; version="3.28.0"; sha256="1fhv9dbfzwlhpg8k3hm7iml81fqcq6c33dx5ya3a94hvzmyavxay"; depends=[affy affyio Biobase mclust oligo oligoClasses]; }; + pvac = derive2 { name="pvac"; version="1.34.0"; sha256="04vn3dm3ld46xz7q14svc5wcj5i23dr6dvwx1iyyhs984ya4d1ym"; depends=[affy Biobase]; }; + pvca = derive2 { name="pvca"; version="1.26.0"; sha256="1n7fv8ia96zdfpm9ca5ibmps3i4b4rmp7bghk4d6rzfjsid9xvl8"; depends=[Biobase lme4 Matrix vsn]; }; + pwOmics = derive2 { name="pwOmics"; version="1.18.0"; sha256="0nds20c0z4jj6x53mpvr3h3nqlmgsb9lq5dw2afwla1cfxp2lsyk"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; }; + pwrEWAS = derive2 { name="pwrEWAS"; version="1.0.0"; sha256="0xm9b9nv3iy27gb4nvg17pk92dgg7ifihrsc8sjbds21nnqxyc87"; depends=[abind BiocManager CpGassoc doParallel doSNOW foreach genefilter ggplot2 limma pwrEWAS_data shiny shinyBS shinyWidgets truncnorm]; }; + qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.4.0"; sha256="0rjks6gknwbyqngbi37c4gfi4kniwsyl1jarc5wyfiy7d0vsbzqg"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr GenomicRanges ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer statmod stringr tibble tidyr]; }; + qckitfastq = derive2 { name="qckitfastq"; version="1.2.0"; sha256="1h6yvyn8c099p1wx67skx4rhrr562z4gbd4y3f4mrjnicwb9vi9q"; depends=[data_table dplyr ggplot2 magrittr Rcpp reshape2 rlang RSeqAn seqTools zlibbioc]; }; + qcmetrics = derive2 { name="qcmetrics"; version="1.24.0"; sha256="0l1kx9ndfryvbxx1b2i5rkqznv6f5iwanbhdiy5zjpg92ij86qhc"; depends=[Biobase knitr Nozzle_R1 pander S4Vectors xtable]; }; + qpcrNorm = derive2 { name="qpcrNorm"; version="1.44.0"; sha256="0zxz39c3ki8x1dgk7pji1xrk4nbax3b9mqwwm41ql3xgmbv4p36v"; depends=[affy Biobase limma]; }; + qpgraph = derive2 { name="qpgraph"; version="2.20.0"; sha256="1s8gcvw3bgavdnvazxxc3kp874ypiyk5xdjpj2hfkm4ahcfqq490"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; + qrqc = derive2 { name="qrqc"; version="1.40.0"; sha256="095nig1qj31hl07ix909lxq1pgypfzb8qizizvj1px41dcd7l9hr"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rhtslib testthat xtable]; }; + qsea = derive2 { name="qsea"; version="1.12.0"; sha256="14375h5pljdfc0y74zaz2phjn8zn2im1rjln2794d812yh2a4hk6"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; }; + qsmooth = derive2 { name="qsmooth"; version="1.2.0"; sha256="05mir3p0yf1sn40p4s1q3s971igfg581if0w4cqg83rvg6m8ygi8"; depends=[SummarizedExperiment sva]; }; + quantro = derive2 { name="quantro"; version="1.20.0"; sha256="09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m"; depends=[Biobase doParallel foreach ggplot2 iterators minfi RColorBrewer]; }; + quantsmooth = derive2 { name="quantsmooth"; version="1.52.0"; sha256="12x0aavwaglf9c2w3s0j128q2hjj3mx98xl4ss803msm6zi54k4c"; depends=[quantreg]; }; + qusage = derive2 { name="qusage"; version="2.20.0"; sha256="0ffk6bwd6c9lkya9hzhjv8cn6sqg4kzclgxrf9985wiifarn6d64"; depends=[Biobase emmeans limma nlme]; }; + qvalue = derive2 { name="qvalue"; version="2.18.0"; sha256="0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j"; depends=[ggplot2 reshape2]; }; + r3Cseq = derive2 { name="r3Cseq"; version="1.32.0"; sha256="0bdhfn9j7n6q3ml3vxp89xqb142v4j5lrmriif523lx8dfin4nnd"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges IRanges qvalue RColorBrewer Rsamtools rtracklayer sqldf VGAM]; }; + rBiopaxParser = derive2 { name="rBiopaxParser"; version="2.26.0"; sha256="0dr160pnq4ypvq20mxd4q8q1gzdgdh3gkqd6pma6zqf6nfp863hj"; depends=[data_table XML]; }; + rCGH = derive2 { name="rCGH"; version="1.16.0"; sha256="0wxrzb6vj83kan5flj92ajpldzkb5mdr0w62xz2n4wqc1ln37brv"; depends=[aCGH affy AnnotationDbi DNAcopy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges lattice limma mclust org_Hs_eg_db plyr shiny TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + rDGIdb = derive2 { name="rDGIdb"; version="1.12.0"; sha256="1z6gkm7qr7sijaxx02lbwbl1avcz5xcigbscvk9lq6haq6s9mvxj"; depends=[httr jsonlite]; }; + rGADEM = derive2 { name="rGADEM"; version="2.34.1"; sha256="12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h"; depends=[Biostrings BSgenome GenomicRanges IRanges seqLogo]; }; + rGREAT = derive2 { name="rGREAT"; version="1.18.0"; sha256="0ffc2a409amsnf82vfgdp17sgqg1rmlj598p9bgb9k6hrrbw464b"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; }; + rRDP = derive2 { name="rRDP"; version="1.20.0"; sha256="04zpnsss602ix8vhhwbymip3z7rqi88vxa1gq8754m58djcy92fh"; depends=[Biostrings]; }; + rScudo = derive2 { name="rScudo"; version="1.2.0"; sha256="0xn608lan6c2as7mc0pc90c45b63q14y5cbrriv23vj7bcgr8fwp"; depends=[Biobase BiocGenerics igraph S4Vectors stringr SummarizedExperiment]; }; + rTANDEM = derive2 { name="rTANDEM"; version="1.26.0"; sha256="0m260a0b05k1mx4r4hh7y7gzw9647b64f7564vzk3vznq248n43p"; depends=[data_table Rcpp XML]; }; + rTRM = derive2 { name="rTRM"; version="1.24.0"; sha256="1g2ifckx1jqnizfn9xd55xxjn772xz8vfx10bspg3wplp2w00qah"; depends=[AnnotationDbi DBI igraph RSQLite]; }; + rTRMui = derive2 { name="rTRMui"; version="1.24.0"; sha256="03i21djhcdm8c4wmf83cblxrb2f035jff3vgxi31abcfbf2advvi"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; }; + rWikiPathways = derive2 { name="rWikiPathways"; version="1.6.1"; sha256="17zy066j7ga5k4s22fxqibzssi43hsd879zvlsd0gz45np4l0l3v"; depends=[caTools httr rjson XML]; }; + rain = derive2 { name="rain"; version="1.20.0"; sha256="17z5dkvv7p568ga0m5rcjp0f5bxzrm14hf93z36l71r09d2p58f7"; depends=[gmp multtest]; }; + rama = derive2 { name="rama"; version="1.60.0"; sha256="0vyl2yz1j0ah78wqapvzfk9cr1fsphdpcql6jma66iyjzbqqqvk3"; depends=[]; }; + ramwas = derive2 { name="ramwas"; version="1.10.5"; sha256="0ly1yccf4qgxkcdgm2pjr8fnz969v9ms74jzy08zji0242vh6rky"; depends=[BiocGenerics biomaRt Biostrings digest filematrix GenomicAlignments glmnet KernSmooth Rsamtools]; }; + randPack = derive2 { name="randPack"; version="1.32.0"; sha256="04dvvsqgj6rw02a949v0gy8a5as56ay1wadvhph9c80g0xkac0pp"; depends=[Biobase]; }; + rbsurv = derive2 { name="rbsurv"; version="2.44.0"; sha256="1ia4bkg3c67h858qcx079kfx9ry8nj96w5ycnyahk19y7sqdz3k8"; depends=[Biobase survival]; }; + rcellminer = derive2 { name="rcellminer"; version="2.8.0"; sha256="0nfrkrk523idf16i2qa588ak494ffiw9aqh2zha661wwf4pv991h"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; }; + readat = derive2 { name="readat"; version="1.11.0"; sha256="1x649yqwcqwqy0r991h98pkrw6a17jswicj039jcxxz35qlxbxyk"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx reshape2 stringi SummarizedExperiment testthat tidyr]; }; + reb = derive2 { name="reb"; version="1.64.0"; sha256="0w45c6bs2r3s77bm21ziqc9brs4cwag515m0ggqi835f0dszwa6s"; depends=[Biobase idiogram]; }; + recount = derive2 { name="recount"; version="1.12.1"; sha256="0w1ia3qcvj6r4mjz6nqqm51iy7sp7ybjycyc736brgcxpfa85cxs"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; }; + recoup = derive2 { name="recoup"; version="1.14.0"; sha256="16x027v5knylbv9p724sp5k7p37y01n0l1n5458zfhf5dvdic4zy"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; }; + regionReport = derive2 { name="regionReport"; version="1.20.0"; sha256="0g1phm4crgg4jijqfnl4vhla5hi0awqsvf9s3amg8rbia4lpzaxb"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; }; + regioneR = derive2 { name="regioneR"; version="1.18.1"; sha256="0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; + regsplice = derive2 { name="regsplice"; version="1.12.6"; sha256="06znb21lwx9y6a9yfbs29yagsww6d43avc7r90n46ifwrhxzmvn4"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; }; + restfulSE = derive2 { name="restfulSE"; version="1.8.0"; sha256="1dhxw93xya0x612zjhgz7szpcmzh677whvg076g9a597v02ggz2l"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; }; + rexposome = derive2 { name="rexposome"; version="1.8.0"; sha256="13d0fr9m8v84c40mh55mzsl6las1k6fq8i1f0fh2ay3r6amarj4i"; depends=[Biobase circlize corrplot FactoMineR ggplot2 ggrepel glmnet gplots gridExtra gtools Hmisc imputeLCMD lme4 lsr mice pryr reshape2 S4Vectors scales scatterplot3d stringr]; }; + rfPred = derive2 { name="rfPred"; version="1.24.0"; sha256="0vbx7avsn20jk0pccrh9ymg4ihs1lwf1s22rbimz98zzxsvnjr1b"; depends=[data_table GenomicRanges IRanges Rsamtools]; }; + rgsepd = derive2 { name="rgsepd"; version="1.18.0"; sha256="0s2bi5g2nh431sjcll8gpxvj5cnylr103fdj0s125a8j30g6218i"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots hash org_Hs_eg_db SummarizedExperiment]; }; + rhdf5 = derive2 { name="rhdf5"; version="2.30.1"; sha256="18pv74jj4wr1981r92ss10qkgf5g1b09dsbz3im3j70a4l5l0df0"; depends=[Rhdf5lib]; }; + rhdf5client = derive2 { name="rhdf5client"; version="1.8.0"; sha256="00b62nsmipmx55xl6xcfay9ip123ml6s84r84m9wbwszivq7j891"; depends=[DelayedArray httr R6 rjson S4Vectors]; }; + riboSeqR = derive2 { name="riboSeqR"; version="1.20.0"; sha256="1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; }; + rmelting = derive2 { name="rmelting"; version="1.2.0"; sha256="1im1i8mrpz774ynbik4zvx24bn41f64lk83hhrlr5x50k297q6r3"; depends=[Rdpack rJava]; }; + rnaSeqMap = derive2 { name="rnaSeqMap"; version="2.44.0"; sha256="1a76ys3qhkvcsfiap48n02msy10nzdmpj2mn9z8wjlq6xlbyciiw"; depends=[Biobase DBI DESeq edgeR GenomicAlignments GenomicRanges IRanges Rsamtools]; }; + rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.16.0"; sha256="1bvahrcplr3plvqy2j64shcyc6pq05q8m6pp40al7wlgj4h2ka40"; depends=[RColorBrewer]; }; + roar = derive2 { name="roar"; version="1.22.0"; sha256="1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; }; + rols = derive2 { name="rols"; version="2.14.0"; sha256="14a0dh00j5xis6h805rvbm5inck903zvknzmjazc38vrf8l7mj0m"; depends=[Biobase BiocGenerics httr jsonlite progress]; }; + ropls = derive2 { name="ropls"; version="1.18.8"; sha256="033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a"; depends=[Biobase MultiDataSet]; }; + rpx = derive2 { name="rpx"; version="1.22.0"; sha256="1pmhmaziv7rg3m2r4l1bb643wyr47gmd52bs0hwrhrk398wjdq9z"; depends=[RCurl xml2]; }; + rqt = derive2 { name="rqt"; version="1.12.0"; sha256="1p5anp2if7v43pfjm17xbs7cnw6cnifzyv2vg7vr3c5d3yvymjw2"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; + rqubic = derive2 { name="rqubic"; version="1.32.0"; sha256="0pqzfgdwv6zq8p0wvyqrdcsvz7ll06nqq1n4v10nys4fm323kml4"; depends=[biclust Biobase BiocGenerics]; }; + rsbml = derive2 { name="rsbml"; version="2.44.0"; sha256="1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa"; depends=[BiocGenerics graph]; }; + rtracklayer = derive2 { name="rtracklayer"; version="1.46.0"; sha256="0lp9xsm8kqrgpwgwj7qaqcv1z6qynbz084grlpwp94zsp2ppf0n6"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; }; + runibic = derive2 { name="runibic"; version="1.8.0"; sha256="1m6xr10wn9k55xi23h6n7sk38m1p0hkip2f6f1pyl17gcx4b0lm2"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; + sRACIPE = derive2 { name="sRACIPE"; version="1.2.0"; sha256="0irr4cxvyg0185j0mwnq6sfvygjrljqn27syw24yfwngs86mijf4"; depends=[BiocGenerics ggplot2 gplots gridExtra htmlwidgets MASS RColorBrewer Rcpp reshape2 S4Vectors shiny shinyBS shinyjs SummarizedExperiment umap visNetwork]; }; + sRAP = derive2 { name="sRAP"; version="1.26.0"; sha256="05sjq25jz6mnfax37fh5yx6nri00ax1bhfy6wxri0hszsxvw367f"; depends=[gplots pls qvalue ROCR WriteXLS]; }; + sSeq = derive2 { name="sSeq"; version="1.24.0"; sha256="0a4hn0spva8am4rdg1syfv8pvsfb3rhwagvn8kbvfgdm9b5mzihk"; depends=[caTools RColorBrewer]; }; + safe = derive2 { name="safe"; version="3.26.0"; sha256="004vh97vdnjmwkfgris4sxkbmw8fla6snlmawkvmakc4cx1pgcb4"; depends=[AnnotationDbi Biobase SparseM]; }; + sagenhaft = derive2 { name="sagenhaft"; version="1.56.0"; sha256="0py7ddy35v4la8kpj8gaacj76b1fd5asq8wn41zjz1dyg9rxw1rj"; depends=[SparseM]; }; + samExploreR = derive2 { name="samExploreR"; version="1.10.0"; sha256="0434q03pm171da6nhbqi2lz8cg4vg1xglk0vacl6is7yyqh4adbc"; depends=[edgeR ggplot2 RNAseqData_HNRNPC_bam_chr14 Rsubread]; }; + sampleClassifier = derive2 { name="sampleClassifier"; version="1.10.0"; sha256="1dcy0ckn1v88i4inrp7yyc0qalgaka0gs097ggisj3hh4l2ghvpx"; depends=[annotate e1071 ggplot2 MGFM MGFR]; }; + sangerseqR = derive2 { name="sangerseqR"; version="1.22.0"; sha256="0vx8rsrwvvnhjyg9pkki74y50g6zg5xbn6g1swgmpjih6049111p"; depends=[Biostrings shiny]; }; + sapFinder = derive2 { name="sapFinder"; version="1.24.0"; sha256="13ygpq51wn6mrl1s2d2fz79d8bbbn363595g0p6im58m2hsp7mpd"; depends=[pheatmap Rcpp rTANDEM]; }; + savR = derive2 { name="savR"; version="1.24.0"; sha256="1lsnqjl6qxbj0wai05qb2wrxrhxq5iarv2livmvwiwv70iigqygf"; depends=[ggplot2 gridExtra reshape2 scales XML]; }; + scAlign = derive2 { name="scAlign"; version="1.2.0"; sha256="0mgdgpa3829wm8mqyx43bq2r84cziiz3sfffmr1284gnnbdi1irv"; depends=[FNN ggplot2 irlba PMA purrr Rtsne Seurat SingleCellExperiment tensorflow]; }; + scBFA = derive2 { name="scBFA"; version="1.0.0"; sha256="03hvj6pj6pa69073z9n227b9nqdkfz04q40y2pniidzgwha208fa"; depends=[copula DESeq2 ggplot2 MASS Seurat SingleCellExperiment SummarizedExperiment zinbwave]; }; + scDD = derive2 { name="scDD"; version="1.10.0"; sha256="0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4"; depends=[arm BiocParallel EBSeq fields ggplot2 mclust outliers S4Vectors scran SingleCellExperiment SummarizedExperiment]; }; + scDblFinder = derive2 { name="scDblFinder"; version="1.1.8"; sha256="0gmjvz6rpndv8r9n2ds4rn6hfmrj6mmmzbf1pyvvffidcjz2p8hz"; depends=[BiocNeighbors BiocParallel data_table DelayedArray dplyr ggplot2 igraph Matrix matrixStats randomForest scater scran SingleCellExperiment SummarizedExperiment]; }; + scFeatureFilter = derive2 { name="scFeatureFilter"; version="1.6.0"; sha256="1066y6mskhv4b6r105lp7yibhx9fh69dyl6nkvmdfhqfy3jgky27"; depends=[dplyr ggplot2 magrittr rlang tibble]; }; + scGPS = derive2 { name="scGPS"; version="1.0.0"; sha256="1xxyb1s8c0dk7pypp00jy9ljypi7ijjhgf2hzz1s6a2ahvdpz0jl"; depends=[caret DESeq dplyr dynamicTreeCut fastcluster ggplot2 glmnet locfit Rcpp RcppArmadillo RcppParallel SingleCellExperiment SummarizedExperiment]; }; + scMerge = derive2 { name="scMerge"; version="1.2.0"; sha256="1wn3plqsj77pffy8wgxh9hm9wzxljgvsfw0sr8hwkfb2kxn0cp22"; depends=[BiocParallel BiocSingular cluster DelayedArray DelayedMatrixStats distr igraph M3Drop pdist proxy Rcpp RcppEigen ruv S4Vectors SingleCellExperiment SummarizedExperiment testthat]; }; + scPCA = derive2 { name="scPCA"; version="1.0.0"; sha256="1yalszwzwj4ipksy0d8xc6792bfxkrnl2gifq0q99j3l3y2gi0l3"; depends=[assertthat BiocParallel cluster dplyr elasticnet kernlab origami purrr Rdpack stringr tibble]; }; + scPipe = derive2 { name="scPipe"; version="1.8.0"; sha256="0wxrgmh6nrsql94bly8ps40pw21x7pzlsld0657q9kidbaili5rr"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase rtracklayer S4Vectors scales SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; }; + scRecover = derive2 { name="scRecover"; version="1.2.0"; sha256="1284h5h5prc7b1yxwxwvhp4r655p24fzg1n3d8qac4nacm4nc9ll"; depends=[bbmle BiocParallel doParallel foreach gamlss kernlab MASS Matrix penalized preseqR pscl Rmagic rsvd SAVER]; }; + scTGIF = derive2 { name="scTGIF"; version="1.0.0"; sha256="1n2hbmmqjz6n4vzmbkdpmxcf6vydfq1hxswafdbgg8ax8lgdqzsa"; depends=[Biobase BiocStyle GSEABase knitr msigdbr nnTensor plotly RColorBrewer Rcpp rmarkdown S4Vectors scales SingleCellExperiment SummarizedExperiment tagcloud]; }; + scTensor = derive2 { name="scTensor"; version="1.2.1"; sha256="0difmdfj0pmp43ymh08wa76py7nq0hdhc85pv2rfw0z3smw7kfj2"; depends=[abind AnnotationDbi AnnotationHub BiocManager BiocStyle Category checkmate crayon DOSE GOstats heatmaply igraph knitr MeSHDbi meshr nnTensor outliers plotly plotrix reactome_db ReactomePA rmarkdown RSQLite rTensor S4Vectors SingleCellExperiment SummarizedExperiment tagcloud visNetwork]; }; + scater = derive2 { name="scater"; version="1.14.6"; sha256="0sxd1s8wdlj9926bagq4crjrk1nnmh3j3bhgrw160zfgc3y8pzck"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats ggbeeswarm ggplot2 Matrix Rcpp S4Vectors SingleCellExperiment SummarizedExperiment viridis]; }; + scde = derive2 { name="scde"; version="2.14.0"; sha256="0g0hh8s09makjgyf9vfx2hv45c1vx3fp9df45zh3nqxqp2ncyc6a"; depends=[BiocParallel Cairo edgeR extRemes flexmix MASS mgcv nnet pcaMethods quantreg RColorBrewer Rcpp RcppArmadillo rjson RMTstat Rook]; }; + scds = derive2 { name="scds"; version="1.2.0"; sha256="00p3qf67wyh1ibkb9qwbsbkrxkdny5s9amcpssspcaphzj58vm4v"; depends=[dplyr Matrix pROC S4Vectors SingleCellExperiment SummarizedExperiment xgboost]; }; + scfind = derive2 { name="scfind"; version="1.8.0"; sha256="185mxjzr4r173djjxpx8wy0b3x5laa7mw04ly3izhzgrdnm13ydr"; depends=[bit dplyr hash Rcpp reshape2 SingleCellExperiment SummarizedExperiment]; }; + schex = derive2 { name="schex"; version="1.0.55"; sha256="08f7q8231lxhi4pw9p3408sqa7yzz5jm5fy7hzvm8ylkydalxvw1"; depends=[cluster dplyr entropy ggplot2 hexbin Seurat SingleCellExperiment]; }; + scmap = derive2 { name="scmap"; version="1.8.0"; sha256="0jsd0fzsnf8ixssd8n3a5wcfjrjqyizbxwh27rasyy6paini375d"; depends=[Biobase BiocGenerics dplyr e1071 ggplot2 googleVis matrixStats proxy randomForest Rcpp RcppArmadillo reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; }; + scmeth = derive2 { name="scmeth"; version="1.6.0"; sha256="0qig5jyw2pv1qdf9ghl8fa46f1y8xarsq673d18jfdnpndg2ma3h"; depends=[AnnotationHub annotatr Biostrings BSgenome bsseq DelayedArray DT GenomeInfoDb GenomicRanges HDF5Array knitr reshape2 rmarkdown SummarizedExperiment]; }; + scone = derive2 { name="scone"; version="1.10.0"; sha256="1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; }; + scoreInvHap = derive2 { name="scoreInvHap"; version="1.8.0"; sha256="1wxg79qla1vax6kng70wv50alzy85kkzfsdhr14pgzzf5rhjm47r"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; }; + scran = derive2 { name="scran"; version="1.14.6"; sha256="1y8wlgk5zbv7c7gcp0ahfpbh9lifab7y3zwf0093fzaw7vr1y6cr"; depends=[beachmat BH BiocGenerics BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats dqrng edgeR igraph limma Matrix Rcpp S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; }; + scruff = derive2 { name="scruff"; version="1.4.2"; sha256="1wcw2af6pas5x4j8widnvgk8y41bg80pmn2dxfrijq1ipvfw8lj1"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr Rsamtools rtracklayer S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; }; + scsR = derive2 { name="scsR"; version="1.22.0"; sha256="1rp24r88br8d3k47a7nx7ffm8xr76aihbl8ar24275scjmw24g04"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; }; + segmentSeq = derive2 { name="segmentSeq"; version="2.20.0"; sha256="079jzm0q69mw15c3i6pcgr9zxlkw7kwshk48qpavsg666v5nhjm7"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; }; + semisup = derive2 { name="semisup"; version="1.10.0"; sha256="07qwjf5gifbpy4xaf7216xgawyy9b3k4cs2260bis7h3slmrjzs2"; depends=[VGAM]; }; + seq2pathway = derive2 { name="seq2pathway"; version="1.18.0"; sha256="01kgn4cxiy51bmzc5kvc5g8k1gk45wzlhs3cvl0b7wknz8ggyzgk"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; }; + seqCAT = derive2 { name="seqCAT"; version="1.8.1"; sha256="1pqm0dslwwa04qy185k10br879lnis6d7qbg03d62dql71hqjggv"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges rlang rtracklayer S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; + seqCNA = derive2 { name="seqCNA"; version="1.32.0"; sha256="170s5j4qsmvmnimsbdf04436xi8jcy4hd0ivqymzadcwn34l3nx5"; depends=[adehabitatLT doSNOW GLAD seqCNA_annot]; }; + seqLogo = derive2 { name="seqLogo"; version="1.52.0"; sha256="0s94aahp8ma1crmp83dz65ifjwrx6wqi3q6005lmbp8yk2x1rkj4"; depends=[]; }; + seqPattern = derive2 { name="seqPattern"; version="1.18.0"; sha256="1gxrq6s2hiyac69idh5r1nbr1s69n0hg4ap2skm4g6857av9pwqf"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; }; + seqTools = derive2 { name="seqTools"; version="1.20.0"; sha256="04d1n2rl4d64vczclc32nslw9q50ji15nl9ndnjm0brx5qfym447"; depends=[zlibbioc]; }; + seqbias = derive2 { name="seqbias"; version="1.34.0"; sha256="19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq"; depends=[Biostrings GenomicRanges Rhtslib]; }; + seqcombo = derive2 { name="seqcombo"; version="1.8.0"; sha256="0lg1afphjsi7ni5a92njhkgphcq5cdcjlp1r3rxzav90zwz6c7fc"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr rvcheck]; }; + seqplots = derive2 { name="seqplots"; version="1.24.0"; sha256="0ydl46w9aixaaflxpcg3h2f8v9m90xqwv9yvzyr3j3b62gmrhg5i"; depends=[BiocManager Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; }; + seqsetvis = derive2 { name="seqsetvis"; version="1.6.0"; sha256="1jyv4w5f1x2pgbvmclrbf69bgrln7xkj3k60r73dg9nzp31h6dnr"; depends=[data_table eulerr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma pbapply png RColorBrewer Rsamtools rtracklayer S4Vectors]; }; + sesame = derive2 { name="sesame"; version="1.4.0"; sha256="0ym7wad9n2da2zm1navnqgbwin9qxag0666h36bmnz4zk8i984lj"; depends=[BiocParallel DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS matrixStats preprocessCore R6 randomForest S4Vectors sesameData wheatmap]; }; + sevenC = derive2 { name="sevenC"; version="1.6.0"; sha256="164qny66zzs4q04zv6y4ybpbdpqc428055pgnqq21cw07psymlfm"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; }; + sevenbridges = derive2 { name="sevenbridges"; version="1.16.1"; sha256="0icqjg198dihic9czw3p408w9fxhfh3z0gcc142jisw3bk1nwz0d"; depends=[curl docopt dplyr httr jsonlite objectProperties S4Vectors stringr uuid yaml]; }; + shinyMethyl = derive2 { name="shinyMethyl"; version="1.22.0"; sha256="0c4v1gdmz6s1hz06jrr3j669c4zi2msivrck09vw4ah7m5swx8c1"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; }; + shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.24.0"; sha256="1ab5qvz1brp4sx62nfw0rrlxka7zskkdpkmr75g3fdnbqpn6c4qi"; depends=[mixtools rTANDEM shiny xtable]; }; + sigFeature = derive2 { name="sigFeature"; version="1.4.0"; sha256="03y3nj6qfwrcbx3yh8yfb2hsrgs0wdkxqdp06gn4c2rqhz1mzl7h"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; }; + sigPathway = derive2 { name="sigPathway"; version="1.54.0"; sha256="057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb"; depends=[]; }; + sigaR = derive2 { name="sigaR"; version="1.34.0"; sha256="1a34mj08w42pm3ij3kydiipccn10rhn6pl1ms4pxa4bvw1ja8ynj"; depends=[Biobase CGHbase corpcor igraph limma marray MASS mvtnorm penalized quadprog snowfall]; }; + siggenes = derive2 { name="siggenes"; version="1.60.0"; sha256="03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4"; depends=[Biobase multtest scrime]; }; + sights = derive2 { name="sights"; version="1.12.0"; sha256="06xh4mqxmw2f6lpq4phxbpjax0lvsbqdj2z6r8z015w7zxnilgp1"; depends=[ggplot2 lattice MASS qvalue reshape2]; }; + signatureSearch = derive2 { name="signatureSearch"; version="1.0.3"; sha256="1f2428996apz15nhsq0w4hhcmmg4z3jrfgn33dy8mnh9rvapxn9h"; depends=[AnnotationDbi BiocParallel clusterProfiler data_table DelayedArray DOSE dplyr ExperimentHub fastmatch fgsea ggplot2 GSEABase HDF5Array magrittr Matrix qvalue Rcpp readr reshape2 rhdf5 RSQLite scales SummarizedExperiment visNetwork]; }; + signeR = derive2 { name="signeR"; version="1.12.0"; sha256="0nw20w2645995pa0jg911gxir2n7ih6d3d45csh3vk5dmy2imwmh"; depends=[BiocGenerics Biostrings class GenomeInfoDb GenomicRanges IRanges nloptr NMF PMCMR Rcpp RcppArmadillo VariantAnnotation]; }; + signet = derive2 { name="signet"; version="1.6.0"; sha256="02iff3zcbm27aav4llblwm248njr9sg44y8sd0pxkwb2yb297593"; depends=[graph igraph RBGL]; }; + sigsquared = derive2 { name="sigsquared"; version="1.18.0"; sha256="15f8ra46dx1hhz1z2a46m562v54clnrql8sm9g50rs427hmmbrj0"; depends=[Biobase survival]; }; + similaRpeak = derive2 { name="similaRpeak"; version="1.18.0"; sha256="1x5r6mkcnv6j6q5d0z7p7aqsaycsmcp07j9dbmgjiflin10h939n"; depends=[R6]; }; + simpleaffy = derive2 { name="simpleaffy"; version="2.62.0"; sha256="18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs"; depends=[affy Biobase BiocGenerics gcrma genefilter]; }; + simulatorZ = derive2 { name="simulatorZ"; version="1.20.0"; sha256="1mhpvyglzcc62hzq3ahwjc5jzilgv5waw21r3m7qn3zj9z45gfdf"; depends=[Biobase BiocGenerics CoxBoost gbm GenomicRanges Hmisc SummarizedExperiment survival]; }; + sincell = derive2 { name="sincell"; version="1.18.0"; sha256="17ns1mq3xwdzp33rfz6ak4cq5wa3bx624hbxshxxw7hl1ak9kscb"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; }; + singleCellTK = derive2 { name="singleCellTK"; version="1.6.0"; sha256="0yw40xprfaa7vz9dw3rmqxdm6vf1qicncx74m4v37glnjvb0k7cd"; depends=[AnnotationDbi ape Biobase celda circlize cluster colourpicker ComplexHeatmap data_table DelayedArray DESeq2 DT enrichR ggplot2 ggtree gridExtra GSVA GSVAdata limma MAST matrixStats multtest plotly RColorBrewer reshape2 Rtsne S4Vectors shiny shinyalert shinyBS shinycssloaders shinyjs shinythemes SingleCellExperiment SummarizedExperiment sva umap]; }; + singscore = derive2 { name="singscore"; version="1.6.0"; sha256="1jdaj16jjssd763fpbmjrlrldan3a6l6z5a96hb8nd08mvwmmd4g"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape reshape2 S4Vectors SummarizedExperiment tidyr]; }; + sitePath = derive2 { name="sitePath"; version="1.2.3"; sha256="0fs6vqpjabxjyb01pwhzqvzmdff2wk0y9i6hb9rrmxi2q3rdzbgz"; depends=[ape Rcpp seqinr]; }; + sizepower = derive2 { name="sizepower"; version="1.56.0"; sha256="05gmwnxzrf43l5qv4nrbapy26m2m890mshq7bmgkx7h9a8mxz5zr"; depends=[]; }; + skewr = derive2 { name="skewr"; version="1.18.0"; sha256="0i6i2r07kfif1vn78p975yj8f5mkzvarvcgm41fiah22dnq3v2fv"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; }; + slalom = derive2 { name="slalom"; version="1.8.0"; sha256="0c22sknb0s40hz8hpsvn7z3ha1lm465q00awnbmqaidargciqb5r"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; }; + slingshot = derive2 { name="slingshot"; version="1.4.0"; sha256="09w70jihn0w8mpafw0f2qr3cwjyqm040svl4fr4i3s2zmiszg848"; depends=[ape igraph matrixStats princurve SingleCellExperiment SummarizedExperiment]; }; + slinky = derive2 { name="slinky"; version="1.4.0"; sha256="00qijpa4qwns2afv1pw8fb8njay180hglpy503dqjrm55xc75bax"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; }; + snapCGH = derive2 { name="snapCGH"; version="1.56.0"; sha256="152n5lnnw5limvslryavmg5f2w75axvv6ha8yipwglm2y4ydp7m6"; depends=[aCGH cluster DNAcopy GLAD limma tilingArray]; }; + snm = derive2 { name="snm"; version="1.34.0"; sha256="0bh2pi7rny7d4b9viswm9ypsj0sk7sns60mcyjdp90vzl0lmw7xx"; depends=[corpcor lme4]; }; + snpStats = derive2 { name="snpStats"; version="1.36.0"; sha256="1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh"; depends=[BiocGenerics Matrix survival zlibbioc]; }; + soGGi = derive2 { name="soGGi"; version="1.18.0"; sha256="1f6jgy0hk7n4i4akfgg6vqbcjix4g4rdp0mscm5nvs9anzmsgrxv"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + sojourner = derive2 { name="sojourner"; version="1.0.1"; sha256="1rgk23360sshk70lj960ys3k7xbh02rs6czhd5crksrvs0pd6cfp"; depends=[boot dplyr EBImage fitdistrplus ggplot2 gridExtra lattice MASS mclust minpack_lm mixtools mltools nls2 pixmap plyr R_matlab Rcpp reshape2 rlang rtiff sampSurf scales shiny shinyjs sp truncnorm]; }; + sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.10.0"; sha256="0nf85w327rzx8azk4x45bkfg4pjzjyikmghbsfk8ym4n499br1l1"; depends=[MASS MCMCpack optparse tmvtnorm]; }; + sparsenetgls = derive2 { name="sparsenetgls"; version="1.4.0"; sha256="0d5yvfpwrjs6sgcaihspar7g1byf35qfgsrcnsl78mxkciqdzcdc"; depends=[glmnet huge MASS Matrix parcor]; }; + specL = derive2 { name="specL"; version="1.20.0"; sha256="1q0vwsyb5pdaxpq6k9x3lpjmwpk1wyf1wy76jrii0vrkb493kb2g"; depends=[DBI protViz RSQLite seqinr]; }; + spikeLI = derive2 { name="spikeLI"; version="2.46.0"; sha256="1kzlqjnqid65sp0lf7hj1bsiq1b5jrwkivrl63gqrsrhshhpa00y"; depends=[]; }; + spkTools = derive2 { name="spkTools"; version="1.42.0"; sha256="0zg27bmh5allar9hw1bq9a89nmnl2ngf8fzn0nphcslvzqfwq43s"; depends=[Biobase gtools RColorBrewer]; }; + splatter = derive2 { name="splatter"; version="1.10.1"; sha256="00j37dphf3vsrg6ji127czrza29g5h0p1p808v2r7asdynsd1253"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats rlang S4Vectors scales scater SingleCellExperiment SummarizedExperiment]; }; + splicegear = derive2 { name="splicegear"; version="1.58.0"; sha256="1smcpmglqqk0984arwc5c6gr8fv89yin2qz0xl3gmdz9wyi7cy1m"; depends=[annotate Biobase XML]; }; + splineTimeR = derive2 { name="splineTimeR"; version="1.14.0"; sha256="1hmbcpil8y06fkvx923psw66kiy5f6r1laga99jacjm6m0flkyj9"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; }; + splots = derive2 { name="splots"; version="1.52.0"; sha256="13yqwf0ms6r1g4ixpwl3z5vmyz8nq1ql9x74mi331x81ba4r6a4x"; depends=[RColorBrewer]; }; + spotSegmentation = derive2 { name="spotSegmentation"; version="1.60.0"; sha256="1j6nvswfz8wsjkdypx7hp63sf418mv5h4yl7cyafrq16bj269fhy"; depends=[mclust]; }; + srnadiff = derive2 { name="srnadiff"; version="1.6.0"; sha256="18v3rl9jc0pvv45jrssgcz6rlq48hw56q1wjgf1mjxhripc0m50n"; depends=[BiocManager BiocParallel BiocStyle DESeq2 devtools GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + ssPATHS = derive2 { name="ssPATHS"; version="1.0.0"; sha256="1vwj3v229ryqpc89ylvb8k4i1ylx7x4bpcdf2z67p3jzzcnsff03"; depends=[dml MESS ROCR SummarizedExperiment]; }; + sscore = derive2 { name="sscore"; version="1.58.0"; sha256="091fim8ivf431hhvma97qvpjsj0dqpv911x0ywdabdx2x3ajiqvz"; depends=[affy affyio]; }; + sscu = derive2 { name="sscu"; version="2.16.0"; sha256="1bk5pzl6az9cfvkqjiwpzbwz1xxxspql2vj2g6s70pn48q7cqfj5"; depends=[BiocGenerics Biostrings seqinr]; }; + ssize = derive2 { name="ssize"; version="1.60.0"; sha256="0bi0ia276mp63i36sf4lyyhljwmzgiaxfpcd8sm1x50cyh3x77wv"; depends=[gdata xtable]; }; + ssrch = derive2 { name="ssrch"; version="1.2.0"; sha256="0nzgq5kcqdnv5sqhy6nc88qhwrg97y02frd5ahhbviny1l08flfb"; depends=[DT shiny]; }; + ssviz = derive2 { name="ssviz"; version="1.20.0"; sha256="0qcryd8dml3rrbliyjhic0sdx311wczyivw2si8xvw12avgds37x"; depends=[Biostrings ggplot2 RColorBrewer reshape Rsamtools]; }; + staRank = derive2 { name="staRank"; version="1.28.0"; sha256="1a60wp9h7if46q6kd3y1nn9g6hm9fhja3dk43c5dvy36w1rbj95k"; depends=[cellHTS2]; }; + stageR = derive2 { name="stageR"; version="1.8.0"; sha256="1rfwx2m1m3zwmf3avahxz96m5pl2s4vqax35kwh1la7n1f6s40vk"; depends=[SummarizedExperiment]; }; + statTarget = derive2 { name="statTarget"; version="1.16.1"; sha256="015pf65ygggsxsww7bmsr2m1wrngd1lhkpwmg7f04nznzcc3lk0x"; depends=[impute pdist pls plyr randomForest ROC rrcov]; }; + stepNorm = derive2 { name="stepNorm"; version="1.58.0"; sha256="1xs4s1bnkzmcnw6s1ynxlg6ik8jm80gjpi5w745h3sbz359rzr0z"; depends=[marray MASS]; }; + strandCheckR = derive2 { name="strandCheckR"; version="1.4.0"; sha256="08wi4hhyll9kwcykkfwca036fy89476s99q70gslq05rxfg3jvq4"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + subSeq = derive2 { name="subSeq"; version="1.16.0"; sha256="177rx0cbzr6vr0yfjnzj4r3rb1gzrnvryvqbwv7mxy2akzczxagb"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; + supraHex = derive2 { name="supraHex"; version="1.24.0"; sha256="0hmj5nisd2pvcs7c38gb4x2v75jj5x1flaf4mfamy3qx0jvkhh8g"; depends=[ape hexbin MASS]; }; + survcomp = derive2 { name="survcomp"; version="1.36.1"; sha256="0baw6w7kn69v4swlycm61n1wdw6kav7m1ir47qvjgzanqlnxw7gc"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; + survtype = derive2 { name="survtype"; version="1.2.0"; sha256="04dw8a7siyshgr6y3gnhkaxdly5890cazz2cnlzdaicxl7qij111"; depends=[clustvarsel pheatmap SummarizedExperiment survival survminer]; }; + sva = derive2 { name="sva"; version="3.34.0"; sha256="1bzms6idx30s4nxl610zwa8rjxsyxb5pf3vxsdfmxg8j4pab9gh1"; depends=[BiocParallel genefilter limma matrixStats mgcv]; }; + swfdr = derive2 { name="swfdr"; version="1.12.0"; sha256="0zls12i05sq3qf18d64rcdmg6jp2rsg5kijax7z66zswj8schy3j"; depends=[]; }; + switchBox = derive2 { name="switchBox"; version="1.22.0"; sha256="0qrjn3ba1i9h497ybzn5xd1yrppdaimjcag8d1sb1v3lf99kxayf"; depends=[gplots pROC]; }; + switchde = derive2 { name="switchde"; version="1.12.0"; sha256="0fni2lh6ygazqkczwy4d26vy758k63lp7by5816pxwhs2gqrad9f"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; }; + synapter = derive2 { name="synapter"; version="2.10.0"; sha256="0pmk48zwzwf4vhwna0k7wr9ihzh66daplfq8mig72swrhv6a3f0z"; depends=[Biobase Biostrings cleaver knitr lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; }; + synergyfinder = derive2 { name="synergyfinder"; version="2.0.12"; sha256="0b324m92vpm6zjsxq9l0dip2ibxjc3py6qlv8lkgnr339h8863nk"; depends=[drc ggplot2 lattice nleqslv reshape2]; }; + synlet = derive2 { name="synlet"; version="1.16.0"; sha256="14wp0fs9054w32hj9999zg5pmj7c36fkg44axcd447f7ryd5ii9j"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; }; + systemPipeR = derive2 { name="systemPipeR"; version="1.20.0"; sha256="17r25v9wcglyma2v1c8fka80dm7fx86saxlsb2aprmwi4h3dhb0j"; depends=[annotate batchtools BiocGenerics Biostrings DESeq2 edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation yaml]; }; + tRNA = derive2 { name="tRNA"; version="1.4.0"; sha256="0yxww91q8p36wmsvpm60wnhc3l7bjpmb05a86xh3237hr3l1c8ik"; depends=[assertive BiocGenerics Biostrings GenomicRanges ggplot2 IRanges Modstrings S4Vectors scales stringr Structstrings XVector]; }; + tRNAdbImport = derive2 { name="tRNAdbImport"; version="1.4.0"; sha256="0g3zcphs3g0dn4kizhw3j3v389skgv1sckqrss80wz31qli2zc2x"; depends=[assertive BiocGenerics Biostrings GenomicRanges httr IRanges Modstrings S4Vectors stringr Structstrings tRNA xml2]; }; + tRNAscanImport = derive2 { name="tRNAscanImport"; version="1.6.0"; sha256="0a6f2bfqkjik25lqsgd00mxiw2gf75xkxb0f9pwlg13ab2hdk1dp"; depends=[assertive BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors stringr Structstrings tRNA XVector]; }; + tRanslatome = derive2 { name="tRanslatome"; version="1.24.0"; sha256="002ixhp0rfkidr1rdjxz6278ixa2vyd9a2yhd8hb5njam6hc6wbn"; depends=[anota Biobase DESeq edgeR GOSemSim gplots Heatplus limma org_Hs_eg_db plotrix RankProd sigPathway topGO]; }; + target = derive2 { name="target"; version="1.0.0"; sha256="1fcdg3axqgz5fdvzfv0qcsshibxijb3waa9whbm9gjk5qmvgmd2l"; depends=[BiocGenerics GenomicRanges IRanges matrixStats shiny]; }; + tenXplore = derive2 { name="tenXplore"; version="1.8.0"; sha256="005147m7pgy1163a1mgbhqz1xj6sz6nn7gz3x4426wniwm19libj"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; }; + ternarynet = derive2 { name="ternarynet"; version="1.30.0"; sha256="0ywgq00b9qyxsqdcrgdyvz0zk8ybb9gy3j3rkicbgxxpsa3cy3qf"; depends=[igraph]; }; + tigre = derive2 { name="tigre"; version="1.40.0"; sha256="1c4knji2wdl95464vb01pf3yhgx98sgr1ad389rjlbzlpnkaf3ad"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; }; + tilingArray = derive2 { name="tilingArray"; version="1.64.0"; sha256="0nzh19bci2vs7h77plaxnbc59jc1rhzdzdf90saf183c8rwgb5hk"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; }; + timecourse = derive2 { name="timecourse"; version="1.58.0"; sha256="08mhyvflnp49rmhkzjzbrgk17qi5889hrlssahxzkdn9snizlp5h"; depends=[Biobase limma marray MASS]; }; + timescape = derive2 { name="timescape"; version="1.10.0"; sha256="1xsrva4hgkjhlib7ij7kjfddbykwafljdfhwrgnmybr3rvsqa5vi"; depends=[dplyr gtools htmlwidgets jsonlite stringr]; }; + tkWidgets = derive2 { name="tkWidgets"; version="1.64.0"; sha256="0livknxr6w4vpnz3jnn3dgh9lir3d5hiwkyix9pmawqka1h21ig7"; depends=[DynDoc widgetTools]; }; + tofsims = derive2 { name="tofsims"; version="1.14.0"; sha256="15j5wdkil3f9ya6hcykv7ma1kf0dj6n3a3bhs804nmq26adh4grv"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; }; + topGO = derive2 { name="topGO"; version="2.38.1"; sha256="1kw9m2j67895k58lx9msc248pjwblp8clxwgsl01cql7sgi1xzlf"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; }; + topconfects = derive2 { name="topconfects"; version="1.2.0"; sha256="1j6g0s6h70cc9p3gyqyaf3syxbx9zskhn60p0kn05w1i72xlvccx"; depends=[assertthat ggplot2]; }; + topdownr = derive2 { name="topdownr"; version="1.8.0"; sha256="131417h29szrpq4nygxz3g19j71hlnsdvdng9p791q112xgqk7xr"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR ProtGenerics S4Vectors]; }; + trackViewer = derive2 { name="trackViewer"; version="1.22.1"; sha256="1d6xa8fmq5g9snrs324dvrnfrqpkjkv9jdal7fadad152mfq4p7n"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; }; + tracktables = derive2 { name="tracktables"; version="1.20.0"; sha256="198mivglr93g0qrn3zxkddrrc4hnwhja2xlhxyxmbvd9hggf5x2h"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; }; + tradeSeq = derive2 { name="tradeSeq"; version="1.0.1"; sha256="11svgkkjjpwagym1d6ivq4wkrgmlm7z32zjbsflffwmpzv4k6cg7"; depends=[BiocParallel clusterExperiment edgeR ggplot2 magrittr mgcv pbapply princurve RColorBrewer S4Vectors SingleCellExperiment slingshot SummarizedExperiment]; }; + transcriptR = derive2 { name="transcriptR"; version="1.14.0"; sha256="1v0q629ahm8awblmxm08lgvgp75spn2w6j4m896qhhqgn3h4w1nj"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; }; + transcriptogramer = derive2 { name="transcriptogramer"; version="1.8.0"; sha256="142wmbwf2inlp16pmpnq4f7ijmka3hl868r6f6lzhk1dnk4akmdv"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; }; + transite = derive2 { name="transite"; version="1.4.0"; sha256="18ij5a0iqxsnrv3ym0bbm1pkn4qf1lf6fhq9va7mbszwry1ad5z6"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; }; + traseR = derive2 { name="traseR"; version="1.16.0"; sha256="0x7awk8lj8bwgzbvx01r5r28v51lzmkwj4dhkqc1xs8ak03pslp1"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; }; + treeio = derive2 { name="treeio"; version="1.10.0"; sha256="1qhlw05y60g67l1bjdzjnznjvm5qbcici45npma1l1m8l5wylb8m"; depends=[ape dplyr jsonlite magrittr rlang tibble tidytree]; }; + trena = derive2 { name="trena"; version="1.8.0"; sha256="1pmapc42sspg1dbqaa4w68c3dvkzn5k59zmzir1i1dqvf4m7gqrx"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMySQL RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr xgboost]; }; + triform = derive2 { name="triform"; version="1.28.0"; sha256="12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9"; depends=[BiocGenerics IRanges yaml]; }; + trigger = derive2 { name="trigger"; version="1.32.0"; sha256="0nn20i3cdbg49p1v4an7dgv98dfpyl7h2nbpwjan3is9ardk520j"; depends=[corpcor qtl qvalue sva]; }; + trio = derive2 { name="trio"; version="3.24.2"; sha256="0qryhp17jawinblj13ljnphin84slfz37w2ripfpv9dicy05d5ir"; depends=[LogicReg siggenes survival]; }; + triplex = derive2 { name="triplex"; version="1.26.0"; sha256="1i8m4bh1g3a0cldwxdhrlm42nd8llcdgb4b440wddzhng2b8lmyg"; depends=[Biostrings GenomicRanges IRanges S4Vectors XVector]; }; + tspair = derive2 { name="tspair"; version="1.44.0"; sha256="1knwh6l5clakxk5w3nqvz6kpaiapvp3d9n25drqn6hhh139mg0ys"; depends=[Biobase]; }; + tweeDEseq = derive2 { name="tweeDEseq"; version="1.32.0"; sha256="0v89w6hr6314i4hs9sgv7zxxqm49gskgl3m7sg4pc3valmkgiz68"; depends=[cqn edgeR limma MASS]; }; + twilight = derive2 { name="twilight"; version="1.62.0"; sha256="0sgn9ypni38asj96xa8046pwg2r5pqbmzxb86hm8g98ncmsrs6js"; depends=[Biobase]; }; + twoddpcr = derive2 { name="twoddpcr"; version="1.10.0"; sha256="0nm8x77xlapabgwwkr5w6gg267yn7mf5qj8xg8z2h7bcpr288gw6"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; + tximeta = derive2 { name="tximeta"; version="1.4.5"; sha256="0qgbyi4vjyyijldvpl8pqql465cclid1fkhg9g2ssd7szqpbr36l"; depends=[AnnotationDbi BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges jsonlite rappdirs S4Vectors SummarizedExperiment tibble tximport]; }; + tximport = derive2 { name="tximport"; version="1.14.2"; sha256="1avy0zhgnszmg0dr9w74yq9ml10kwdrrgcni2wysrd48zzskc1n0"; depends=[]; }; + uSORT = derive2 { name="uSORT"; version="1.12.0"; sha256="0y17hic5ilibh453algrpdkyzlz96p68118g49ady37hfvd6f73f"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; + unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.22.0"; sha256="1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj"; depends=[BiocGenerics HTqPCR]; }; + universalmotif = derive2 { name="universalmotif"; version="1.4.9"; sha256="1dfni8g21v9n58v3wp3r6midwzjfjn4986vi9g71iwvqqbacf7gf"; depends=[ape BiocGenerics Biostrings ggplot2 ggseqlogo ggtree MASS processx Rcpp RcppThread Rdpack rlang S4Vectors yaml]; }; + variancePartition = derive2 { name="variancePartition"; version="1.16.1"; sha256="02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g"; depends=[Biobase BiocParallel colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest progress reshape2 scales]; }; + vbmp = derive2 { name="vbmp"; version="1.54.0"; sha256="08clr46pmiv8v3x2vvzy2bax1sf9np2m3zsx0waj6gwz9c6d43ry"; depends=[]; }; + vidger = derive2 { name="vidger"; version="1.6.0"; sha256="064r31r67a4c5gqradfn0wdxkzld9s1qlyzhj0l9w3b9hqb32wcv"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; }; + viper = derive2 { name="viper"; version="1.20.0"; sha256="1ba1lyag3q0yhqvgx5y36ps548jdgipyx07ifgwcd5dm91nqcacj"; depends=[Biobase e1071 KernSmooth mixtools]; }; + vsn = derive2 { name="vsn"; version="3.54.0"; sha256="1naqzb2m0km8fzr6chf9z71sisrwviy1fdi9b3hn4i8p18b4kqzh"; depends=[affy Biobase ggplot2 lattice limma]; }; + vtpnet = derive2 { name="vtpnet"; version="0.26.0"; sha256="1s7wcn45bs2r3gg73vs3m6vkbqg44ixxz8i5hgd6l3dhha7rkfqq"; depends=[doParallel foreach GenomicRanges graph gwascat]; }; + vulcan = derive2 { name="vulcan"; version="1.8.0"; sha256="1n60fy4jql5ljqh9bg7193znns0m5hzmb35d2h6nx13wzlj1yf8q"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; }; + waddR = derive2 { name="waddR"; version="1.0.1"; sha256="1dm5z05cpx941hwx1d02cxpvbyyjbwj9agg3fi5rcd4cq13iixh1"; depends=[arm BiocFileCache BiocParallel Rcpp RcppArmadillo SingleCellExperiment]; }; + wateRmelon = derive2 { name="wateRmelon"; version="1.30.0"; sha256="0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; }; + wavClusteR = derive2 { name="wavClusteR"; version="2.20.0"; sha256="0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; }; + waveTiling = derive2 { name="waveTiling"; version="1.28.0"; sha256="0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"; depends=[affy Biobase Biostrings GenomeGraphs GenomicRanges IRanges oligo oligoClasses preprocessCore waveslim]; }; + weaver = derive2 { name="weaver"; version="1.52.0"; sha256="0c47i05d57gwimjnnppngzl2jm7ipw6d4ha3apnzm0l6flh8x85c"; depends=[codetools digest]; }; + webbioc = derive2 { name="webbioc"; version="1.58.0"; sha256="1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62"; depends=[affy annaffy Biobase BiocManager gcrma multtest qvalue vsn]; }; + widgetTools = derive2 { name="widgetTools"; version="1.64.0"; sha256="1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5"; depends=[]; }; + wiggleplotr = derive2 { name="wiggleplotr"; version="1.10.1"; sha256="1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; }; + xcms = derive2 { name="xcms"; version="3.8.2"; sha256="0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g"; depends=[Biobase BiocGenerics BiocParallel IRanges lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; }; + xmapbridge = derive2 { name="xmapbridge"; version="1.44.0"; sha256="0ibaibdw8rjpirlp0x7hrjc7jhckw3inzymgqpnb9d6psaiwcvwq"; depends=[]; }; + xps = derive2 { name="xps"; version="1.46.0"; sha256="1i1hj84x6bfhrwjia3nfbcjkk8ynlb48avjrnpb3zzvx5mh35arw"; depends=[]; }; + yamss = derive2 { name="yamss"; version="1.12.1"; sha256="12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; }; + yaqcaffy = derive2 { name="yaqcaffy"; version="1.46.0"; sha256="0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz"; depends=[simpleaffy]; }; + yarn = derive2 { name="yarn"; version="1.12.0"; sha256="0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; }; + zFPKM = derive2 { name="zFPKM"; version="1.8.0"; sha256="1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; }; + zinbwave = derive2 { name="zinbwave"; version="1.8.0"; sha256="14vs1385sfr1jjjycd48xz82zr39ypxa44yg5mlvh61fifd3whr7"; depends=[BiocParallel edgeR genefilter Matrix SingleCellExperiment softImpute SummarizedExperiment]; }; + zlibbioc = derive2 { name="zlibbioc"; version="1.32.0"; sha256="1xh7qan0w62mzsmanbx9vcj6ygdfhzw1abaxijkq7f4nh5w87idj"; depends=[]; }; } diff --git a/pkgs/development/r-modules/bioc-workflows-packages.nix b/pkgs/development/r-modules/bioc-workflows-packages.nix new file mode 100644 index 0000000000000..ce845c539e934 --- /dev/null +++ b/pkgs/development/r-modules/bioc-workflows-packages.nix @@ -0,0 +1,36 @@ +# This file is generated from generate-r-packages.R. DO NOT EDIT. +# Execute the following command to update the file. +# +# Rscript generate-r-packages.R bioc-workflows >new && mv new bioc-workflows-packages.nix + +{ self, derive }: +let derive2 = derive { biocVersion = "3.10"; }; +in with self; { + BgeeCall = derive2 { name="BgeeCall"; version="1.2.1"; sha256="0v9aj4nlgx9yj2n2wpispjwlvg53b8x8mz6fnnnn73fyh0pplzmm"; depends=[biomaRt Biostrings GenomicFeatures jsonlite rhdf5 rtracklayer tximport]; }; + BiocMetaWorkflow = derive2 { name="BiocMetaWorkflow"; version="1.8.1"; sha256="1zdvnf5f5zdxpaxqn4z1dvv6qszrf6p2hr81jcnsmrl5nwbjv2jy"; depends=[]; }; + CAGEWorkflow = derive2 { name="CAGEWorkflow"; version="1.2.0"; sha256="0xbkbp0aw1vvkp7fq41qbh2mgxypj6y41vk7fzjx06hwhbjaqwdv"; depends=[CAGEfightR nanotubes]; }; + EGSEA123 = derive2 { name="EGSEA123"; version="1.10.0"; sha256="1bhpj102ncbkyx04kgmdj06r1fy9fxvc3zzi97mizn0vysvldihc"; depends=[edgeR EGSEA illuminaio limma]; }; + ExpressionNormalizationWorkflow = derive2 { name="ExpressionNormalizationWorkflow"; version="1.12.0"; sha256="0p8d1bcnzjxc1l8sbrs18jpdr8h08gx7mi69z5l3a7fq3wxv4lcy"; depends=[Biobase limma lme4 matrixStats pvca snm sva vsn]; }; + RNAseq123 = derive2 { name="RNAseq123"; version="1.10.0"; sha256="083j9rv39bhfzz4rvmv0ydiq9m9yahmmdk9n9gc733f884p79kin"; depends=[edgeR Glimma gplots limma Mus_musculus RColorBrewer]; }; + RnaSeqGeneEdgeRQL = derive2 { name="RnaSeqGeneEdgeRQL"; version="1.10.0"; sha256="0pj2wrnhsb609cw37x5jqjdk2gsv7njiibnrhw76gz1gasjyq15p"; depends=[edgeR GO_db gplots org_Mm_eg_db]; }; + SingscoreAMLMutations = derive2 { name="SingscoreAMLMutations"; version="1.2.0"; sha256="0ipjf3nia3cjfza81l6xqgb4gpzwd0zcsvp248pd1p9s8sgmrb0y"; depends=[dcanr edgeR ggplot2 gridExtra GSEABase mclust org_Hs_eg_db plyr reshape2 rtracklayer singscore SummarizedExperiment TCGAbiolinks]; }; + TCGAWorkflow = derive2 { name="TCGAWorkflow"; version="1.10.1"; sha256="1kknq2ffqz454g84pbpq7d92bg1namcnj1rznb5j3g7vgd5x7rr8"; depends=[AnnotationHub biomaRt BSgenome_Hsapiens_UCSC_hg19 c3net ChIPseeker circlize clusterProfiler ComplexHeatmap downloader DT ELMER gaia GenomeInfoDb GenomicRanges ggplot2 ggthemes knitr maftools minet motifStack MotIV pander pathview pbapply rGADEM RTCGAToolbox SummarizedExperiment TCGAbiolinks TCGAWorkflowData]; }; + annotation = derive2 { name="annotation"; version="1.10.0"; sha256="0dkbvznymbfsxsh2j5xd49hlz7fgl56wdikppc9518q725dxg650"; depends=[AnnotationHub biomaRt BSgenome BSgenome_Hsapiens_UCSC_hg19 Homo_sapiens org_Hs_eg_db org_Mm_eg_db Organism_dplyr TxDb_Athaliana_BioMart_plantsmart22 TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene TxDb_Mmusculus_UCSC_mm10_ensGene VariantAnnotation]; }; + arrays = derive2 { name="arrays"; version="1.12.0"; sha256="1kly63prhqnlf2dx5bhjgcfkx943aj63wrknbdncy9zgllfmlgx8"; depends=[]; }; + chipseqDB = derive2 { name="chipseqDB"; version="1.10.0"; sha256="07gx6mxx2q4l99w9gjh76zbi6vn0a7rvl1ah2ps7bav65x0s7sb3"; depends=[]; }; + csawUsersGuide = derive2 { name="csawUsersGuide"; version="1.2.0"; sha256="011qg7mg7svpr7rsgianb1zd9a8aqmf4dlzx32csd1kbl78dsl21"; depends=[]; }; + cytofWorkflow = derive2 { name="cytofWorkflow"; version="1.10.2"; sha256="1bys33nb3l2jhqw3snkrnzj9dlnyfz143jhzz9p6llzclj64z4d7"; depends=[BiocStyle CATALYST cowplot diffcyt HDCytoData knitr readxl uwot]; }; + eQTL = derive2 { name="eQTL"; version="1.10.0"; sha256="047dq3icd9zqsy4l1kirx2w4022zigwm5pgsn9501d3jx40yp1sn"; depends=[bibtex biglm data_table doParallel foreach GenomeInfoDb GGdata GGtools knitcitations lumi lumiHumanAll_db rmeta S4Vectors scatterplot3d SNPlocs_Hsapiens_dbSNP144_GRCh37 snpStats yri1kgv]; }; + generegulation = derive2 { name="generegulation"; version="1.10.0"; sha256="1izvc9nm7iczxci8ybgdgzgcgi1c5j9c2ws7j80xblnn058nv2sh"; depends=[Biostrings BSgenome_Scerevisiae_UCSC_sacCer3 GenomicFeatures MotifDb motifStack org_Sc_sgd_db S4Vectors seqLogo TxDb_Scerevisiae_UCSC_sacCer3_sgdGene]; }; + highthroughputassays = derive2 { name="highthroughputassays"; version="1.10.0"; sha256="1i5z1f8s1iwll2m49xvkgzgf8bl11v2lpx8sgfbnfilhclxgig78"; depends=[flowCore flowStats flowWorkspace]; }; + liftOver = derive2 { name="liftOver"; version="1.10.0"; sha256="1lnc9q0wpn9xrbxcwvv7h2ihl93qy860vr9xlyx9nb5h0jsv4x66"; depends=[BiocGenerics GenomicRanges gwascat Homo_sapiens rtracklayer]; }; + maEndToEnd = derive2 { name="maEndToEnd"; version="2.6.0"; sha256="1f5nd5b9h71a478b8z57g64lihb3z6nvkzf9z78g9yphzqikmwdh"; depends=[ArrayExpress arrayQualityMetrics Biobase clusterProfiler dplyr genefilter geneplotter ggplot2 gplots hugene10sttranscriptcluster_db limma matrixStats oligo oligoClasses openxlsx pd_hugene_1_0_st_v1 pheatmap RColorBrewer ReactomePA Rgraphviz stringr tidyr topGO]; }; + methylationArrayAnalysis = derive2 { name="methylationArrayAnalysis"; version="1.10.0"; sha256="1ddbgg8q4bhiaypci3z4gllpqwynrvm340s4l7s6n99f3fb94avz"; depends=[BiocStyle DMRcate FlowSorted_Blood_450k Gviz IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest knitr limma matrixStats minfi minfiData missMethyl RColorBrewer rmarkdown stringr]; }; + proteomics = derive2 { name="proteomics"; version="1.10.0"; sha256="1hcl4g3adwyq1sns2nq56zx8rcd55fab7pvj09wkr939yxcn4bnx"; depends=[hpar MLInterfaces MSGFplus MSnbase MSnID mzID mzR pRoloc pRolocdata rols rpx]; }; + recountWorkflow = derive2 { name="recountWorkflow"; version="1.10.0"; sha256="0l4ia2nfiphkxhp3w0ds3mx402nv789b8s64c28fvrha1fak33wj"; depends=[bumphunter clusterProfiler derfinder derfinderPlot DESeq2 edgeR GenomicFeatures GenomicRanges gplots limma org_Hs_eg_db recount regionReport rtracklayer]; }; + rnaseqDTU = derive2 { name="rnaseqDTU"; version="1.6.0"; sha256="12nsgyh53dasczwp1s9yra8h6g2fh1fy61fk64ngjzjjvgrzav3g"; depends=[DESeq2 devtools DEXSeq DRIMSeq edgeR rafalib stageR]; }; + rnaseqGene = derive2 { name="rnaseqGene"; version="1.10.0"; sha256="0jf9rndz16db6i6ps69qnng4i9bkiarkrdcq4n9jc6qcr6jdg6mn"; depends=[airway AnnotationDbi apeglm BiocStyle DESeq2 dplyr fission genefilter ggbeeswarm ggplot2 glmpca Gviz hexbin magrittr org_Hs_eg_db pheatmap PoiClaClu RColorBrewer ReportingTools RUVSeq sva tximeta vsn]; }; + sequencing = derive2 { name="sequencing"; version="1.10.0"; sha256="0p7kz40idfakkpixdkpk9djcsy3a5wgxbjiqbnh8gkv3z6k49wia"; depends=[AnnotationHub BiocParallel Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges RNAseqData_HNRNPC_bam_chr14 Rsamtools rtracklayer ShortRead VariantAnnotation]; }; + simpleSingleCell = derive2 { name="simpleSingleCell"; version="1.10.1"; sha256="0jv6d6fcr0w5kdvc9xgb8bb8lw6a8hja9m25c1gs3vqpnq6pfkv1"; depends=[]; }; + variants = derive2 { name="variants"; version="1.10.0"; sha256="168mkkbbqznyvxibzxhn3n3207936v5qfyrfqj9qik8bcrkc93qf"; depends=[BSgenome_Hsapiens_UCSC_hg19 cgdv17 org_Hs_eg_db PolyPhen_Hsapiens_dbSNP131 TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; +} diff --git a/pkgs/development/r-modules/build_packages.sh b/pkgs/development/r-modules/build_packages.sh new file mode 100755 index 0000000000000..b86c6af952805 --- /dev/null +++ b/pkgs/development/r-modules/build_packages.sh @@ -0,0 +1,27 @@ +#!/bin/sh +# args: names pkgs start end +pkgs=$1 +start=1 +if [[ $2 -gt 1 ]] ; then + start=$2 +fi + +end=100000 +if [[ $3 -ne 0 ]] ; then + end=$3 + echo "building from $start to $end" +fi + + +i=1 +trap "exit" INT +for pkg in $(cat $pkgs) +do + if [[ $i -ge $start && $i -le $end ]] ; then + echo "$i of $start to $end: Building ${pkg}" + nix build -f test-evaluation.nix rPackages.${pkg} + fi + let "i+=1" + +done + diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix index 44ff794654dd6..b290812b49452 100644 --- a/pkgs/development/r-modules/default.nix +++ b/pkgs/development/r-modules/default.nix @@ -1,4 +1,4 @@ -/* This file defines the composition for CRAN (R) packages. */ + /* This file defines the composition for CRAN (R) packages. */ { R, pkgs, overrides }: @@ -30,7 +30,12 @@ let urls = mkUrls (args // { inherit name version; }); }; inherit doCheck requireX; - propagatedBuildInputs = depends; + propagatedBuildInputs = depends ++ ( with pkgs; + # packages assumed very often by R package tools are added to buildInputs + (lib.optionals stdenv.isDarwin [ libiconv flock which ]) + ++ [ pkgs.gsl liblapack gmp.dev gtk2.dev bzip2.dev pkgs.pkgconfig + lzma icu.dev pcre.dev zlib.dev curl.dev libpng libtiff libjpeg + ]); nativeBuildInputs = depends; meta.homepage = mkHomepage (args // { inherit name; }); meta.platforms = R.meta.platforms; @@ -47,13 +52,17 @@ let "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ]; }; deriveBiocAnn = mkDerive { - mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html"; + mkHomepage = {name, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/data/annotation/html/${name}.html"; mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ]; }; deriveBiocExp = mkDerive { - mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html"; + mkHomepage = {name, biocVersion, ...}: "http://www.bioconductor.org/packages/${biocVersion}/data/experiment/html/${name}.html"; mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ]; }; + deriveBiocWrk = mkDerive { # not available on mirrors afaik + mkHomepage = {name, biocVersion, ...}: "https://www.bioconductor.org/packages/${biocVersion}/workflows/html/${name}.html"; + mkUrls = {name, version, biocVersion}: [ "https://www.bioconductor.org/packages/${biocVersion}/workflows/src/contrib/${name}_${version}.tar.gz"]; + }; deriveCran = mkDerive { mkHomepage = {name, snapshot, ...}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/"; mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ]; @@ -202,7 +211,7 @@ let defaultOverrides = old: new: let old0 = old; in let - old1 = old0 // (overrideRequireX packagesRequireingX old0); + old1 = old0 // (overrideRequireX packagesRequiringX old0); old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1); old3 = old2 // (overrideRDepends packagesWithRDepends old2); old4 = old3 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old3); @@ -216,269 +225,203 @@ let # `self` is `_self` with overridden packages; # packages in `_self` may depends on overridden packages. self = (defaultOverrides _self self) // overrides; + _self = { inherit buildRPackage; } // - import ./bioc-packages.nix { inherit self; derive = deriveBioc; } // + import ./bioc-packages.nix { inherit self; derive = deriveBioc; } // import ./bioc-annotation-packages.nix { inherit self; derive = deriveBiocAnn; } // import ./bioc-experiment-packages.nix { inherit self; derive = deriveBiocExp; } // - import ./cran-packages.nix { inherit self; derive = deriveCran; }; + import ./bioc-workflows-packages.nix { inherit self; derive = deriveBiocWrk; } // + import ./cran-packages.nix { inherit self; derive = deriveCran; }; # tweaks for the individual packages and "in self" follow packagesWithRDepends = { - FactoMineR = [ self.car ]; - pander = [ self.codetools ]; + # if R deps are missing for some reason, add them here. + tesseract = [ self.pdftools ]; + TextForecast = [ self.Rpoppler ]; + qmix = [ self.rstantools ]; # slow compile. Use linking and rstan? + cbq = [ self.rstantools ]; # slow compile. Use linking and rstan? + RBesT = [ self.rstantools ]; # slow compile. Use linking and rstan? }; - packagesWithNativeBuildInputs = { - abn = [ pkgs.gsl_1 ]; - adimpro = [ pkgs.imagemagick ]; - animation = [ pkgs.which ]; - audio = [ pkgs.portaudio ]; - BayesSAE = [ pkgs.gsl_1 ]; - BayesVarSel = [ pkgs.gsl_1 ]; - BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ]; - bigGP = [ pkgs.openmpi ]; - bio3d = [ pkgs.zlib ]; - BiocCheck = [ pkgs.which ]; - Biostrings = [ pkgs.zlib ]; - bnpmr = [ pkgs.gsl_1 ]; - cairoDevice = [ pkgs.gtk2.dev ]; - Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo.dev pkgs.x11 pkgs.fontconfig.lib ]; - Cardinal = [ pkgs.which ]; - chebpol = [ pkgs.fftw ]; - ChemmineOB = [ pkgs.openbabel pkgs.pkgconfig ]; - cit = [ pkgs.gsl_1 ]; - curl = [ pkgs.curl.dev ]; - data_table = [pkgs.zlib.dev] ++ lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; - devEMF = [ pkgs.xorg.libXft.dev pkgs.x11 ]; - diversitree = [ pkgs.gsl_1 pkgs.fftw ]; - EMCluster = [ pkgs.lapack ]; - fftw = [ pkgs.fftw.dev ]; - fftwtools = [ pkgs.fftw.dev ]; - Formula = [ pkgs.gmp ]; - gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ]; - git2r = [ pkgs.zlib.dev pkgs.openssl.dev pkgs.libssh2.dev pkgs.libgit2 pkgs.pkgconfig ]; - GLAD = [ pkgs.gsl_1 ]; - glpkAPI = [ pkgs.gmp pkgs.glpk ]; - gmp = [ pkgs.gmp.dev ]; - graphscan = [ pkgs.gsl_1 ]; - gsl = [ pkgs.gsl_1 ]; - haven = [ pkgs.libiconv pkgs.zlib.dev ]; - h5vc = [ pkgs.zlib.dev ]; - HiCseg = [ pkgs.gsl_1 ]; - imager = [ pkgs.x11 ]; - iBMQ = [ pkgs.gsl_1 ]; - igraph = [ pkgs.gmp pkgs.libxml2.dev ]; - JavaGD = [ pkgs.jdk ]; - jpeg = [ pkgs.libjpeg.dev ]; - jqr = [ pkgs.jq.dev ]; - KFKSDS = [ pkgs.gsl_1 ]; - kza = [ pkgs.fftw.dev ]; - magick = [ pkgs.imagemagick.dev ]; - ModelMetrics = lib.optional stdenv.isDarwin pkgs.llvmPackages.openmp; - mvabund = [ pkgs.gsl_1 ]; - mwaved = [ pkgs.fftw.dev ]; - ncdf4 = [ pkgs.netcdf ]; - nloptr = [ pkgs.nlopt pkgs.pkgconfig ]; - odbc = [ pkgs.unixODBC ]; - outbreaker = [ pkgs.gsl_1 ]; - pander = [ pkgs.pandoc pkgs.which ]; - pbdMPI = [ pkgs.openmpi ]; - pbdNCDF4 = [ pkgs.netcdf ]; - pbdPROF = [ pkgs.openmpi ]; - pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ]; - pdftools = [ pkgs.poppler.dev ]; - phytools = [ pkgs.which ]; - PKI = [ pkgs.openssl.dev ]; - png = [ pkgs.libpng.dev ]; - proj4 = [ pkgs.proj ]; - protolite = [ pkgs.protobuf ]; - qtbase = [ pkgs.qt4 ]; - qtpaint = [ pkgs.qt4 ]; - R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; - RAppArmor = [ pkgs.libapparmor ]; - rapportools = [ pkgs.which ]; - rapport = [ pkgs.which ]; - readxl = [ pkgs.libiconv ]; - rcdd = [ pkgs.gmp.dev ]; - RcppCNPy = [ pkgs.zlib.dev ]; - RcppGSL = [ pkgs.gsl_1 ]; - RcppZiggurat = [ pkgs.gsl_1 ]; - reprex = [ pkgs.which ]; - rgdal = [ pkgs.proj.dev pkgs.gdal ]; - rgeos = [ pkgs.geos ]; - rggobi = [ pkgs.ggobi pkgs.gtk2.dev pkgs.libxml2.dev ]; - Rglpk = [ pkgs.glpk ]; - RGtk2 = [ pkgs.gtk2.dev ]; - rhdf5 = [ pkgs.zlib ]; - Rhdf5lib = [ pkgs.zlib ]; - Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; - Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf ]; - rjags = [ pkgs.jags ]; - rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; - Rlibeemd = [ pkgs.gsl_1 ]; - rmatio = [ pkgs.zlib.dev ]; - Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ]; - Rmpi = [ pkgs.openmpi ]; - RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ]; - RNetCDF = [ pkgs.netcdf pkgs.udunits ]; - RODBC = [ pkgs.libiodbc ]; - rpanel = [ pkgs.bwidget ]; - rpg = [ pkgs.postgresql ]; - Rpoppler = [ pkgs.poppler ]; - RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ]; - RProtoBuf = [ pkgs.protobuf ]; - rPython = [ pkgs.python ]; - RSclient = [ pkgs.openssl.dev ]; - Rserve = [ pkgs.openssl ]; - Rssa = [ pkgs.fftw.dev ]; - rtiff = [ pkgs.libtiff.dev ]; - runjags = [ pkgs.jags ]; - RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ]; - rzmq = [ pkgs.zeromq3 ]; - SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ]; - sdcTable = [ pkgs.gmp pkgs.glpk ]; - seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ]; - seqinr = [ pkgs.zlib.dev ]; - seqminer = [ pkgs.zlib.dev pkgs.bzip2 ]; - sf = [ pkgs.gdal pkgs.proj pkgs.geos ]; - showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ]; - simplexreg = [ pkgs.gsl_1 ]; - spate = [ pkgs.fftw.dev ]; - ssanv = [ pkgs.proj ]; - stsm = [ pkgs.gsl_1 ]; - stringi = [ pkgs.icu.dev ]; - survSNP = [ pkgs.gsl_1 ]; - sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ]; - systemfonts = [ pkgs.fontconfig.dev pkgs.freetype.dev ]; - TAQMNGR = [ pkgs.zlib.dev ]; - tesseract = [ pkgs.tesseract pkgs.leptonica ]; - tiff = [ pkgs.libtiff.dev ]; - TKF = [ pkgs.gsl_1 ]; - tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ]; - topicmodels = [ pkgs.gsl_1 ]; - udunits2 = [ pkgs.udunits pkgs.expat ]; - units = [ pkgs.udunits ]; - V8 = [ pkgs.v8 ]; - XBRL = [ pkgs.zlib pkgs.libxml2.dev ]; - xml2 = [ pkgs.libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ pkgs.perl ]; - XML = [ pkgs.libtool pkgs.libxml2.dev pkgs.xmlsec pkgs.libxslt ]; - affyPLM = [ pkgs.zlib.dev ]; - bamsignals = [ pkgs.zlib.dev ]; - BitSeq = [ pkgs.zlib.dev ]; - DiffBind = [ pkgs.zlib ]; - ShortRead = [ pkgs.zlib.dev ]; - oligo = [ pkgs.zlib.dev ]; - gmapR = [ pkgs.zlib.dev ]; - Rsubread = [ pkgs.zlib.dev ]; - XVector = [ pkgs.zlib.dev ]; - Rsamtools = [ pkgs.zlib.dev ]; - rtracklayer = [ pkgs.zlib.dev ]; - affyio = [ pkgs.zlib.dev ]; - VariantAnnotation = [ pkgs.zlib.dev ]; - snpStats = [ pkgs.zlib.dev ]; + packagesWithNativeBuildInputs = with pkgs; { + BayesXsrc = [ readline.dev ncurses ]; + Cairo = [ libtiff libjpeg cairo.dev x11 fontconfig.lib ]; + ChemmineOB = [ openbabel ]; + FDX = [ fftw.dev ]; + GLPK = [ glpk ]; + JavaGD = [ jdk ]; + KRIG = lib.optional stdenv.isDarwin llvmPackages.openmp; + KSgeneral = [ fftw.dev ]; + LBLGXE = lib.optional stdenv.isDarwin llvmPackages.openmp; + MSGFplus = [ jdk ]; + ModelMetrics = lib.optional stdenv.isDarwin llvmPackages.openmp; + PKI = [ openssl.dev ]; + PoissonBinomial = [ fftw.dev ]; + PythonInR = [ python3 ncurses ]; + R2SWF = [ freetype.dev ]; + RAppArmor = [ libapparmor ]; + RGtk2 = [ gtk2.dev ]; + RMariaDB = [ libmysqlclient ]; + RMySQL = [ libmysqlclient openssl.dev ]; + RNetCDF = [ netcdf udunits ]; + RODBC = [ libiodbc ]; + RPostgreSQL = [ postgresql postgresql ]; + RProtoBuf = [ protobuf ]; + RSclient = [ openssl.dev ]; + RVowpalWabbit = [ boost ]; + Rblpapi = [ ]; # needs proprietary "Bloomberg LP api" lib + RcppCWB = [ ncurses.dev ]; + Rglpk = [ glpk ]; + Rhpc = [ openmpi ]; + Rhtslib = [ automake autoconf ] ; + Rmpfr = [ mpfr.dev ]; + Rmpi = [ openmpi ]; + Rserve = [ openssl ]; + V8 = [ v8 ]; + XBRL = [ libxml2.dev ]; + XML = [ libtool libxml2.dev xmlsec ]; + adimpro = [ imagemagick ]; + audio = [ portaudio ]; + bigGP = [ openmpi ]; + bioacoustics = [ fftw.dev ]; + cairoDevice = [ gtk2.dev ]; + data_table = lib.optional stdenv.isDarwin llvmPackages.openmp; + devEMF = [ xorg.libXft.dev x11 ]; + exactextractr = [ geos ]; + exifr = [ pkgs.perl ]; + gdalcubes = [ gdal proj.dev netcdf sqlite.dev ]; + gdtools = [ cairo.dev fontconfig.lib freetype ]; + gert = [ libgit2 ]; + git2r = [ openssl.dev libssh2.dev libgit2 ]; + glpkAPI = [ gmp glpk ]; + gmp = [ gmp.dev ]; + hdf5r = [ hdf5.dev]; + igraph = [ gmp libxml2.dev ]; + imager = [ x11 ]; + jpeg = [ libjpeg.dev ]; + jqr = [ jq.dev ]; + landsepi = [ gdal ]; + lwgeom = [ proj.dev geos ]; + magick = [ imagemagick.dev ]; + matchingMarkets = [ jdk ]; + mongolite = [ openssl cyrus_sasl ]; + mwaved = [ fftw.dev ]; + ncdf4 = [ netcdf ]; + odbc = [ unixODBC ]; + pander = [ pandoc ]; + pathfindR = [ jdk ]; + pbdMPI = [ openmpi ]; + pbdNCDF4 = [ netcdf ]; + pbdPROF = [ openmpi ]; + pcaL1 = [ clp ]; + poisbinom = [ fftw.dev ]; + proj4 = [ proj.dev ]; + protolite = [ protobuf ]; + qgg = lib.optional stdenv.isDarwin llvmPackages.openmp; + qtbase = [ qt5.dev ]; # patches/qtbase.patch still needed? don't think so. TODO: delete it. + qtpaint = [ qt5 ]; + rDEA = [ glpk] ; + rJava = [ jdk libzip ]; + rPython = [ (python3.withPackages(ps : with ps; [])) ncurses ]; # broken + rcdd = [ gmp.dev ]; + rcrypt = [ gnupg ]; + readtext = [ poppler.dev ]; + redux = [ hiredis ]; + rgdal = [ proj.dev gdal ]; + rgeos = [ geos ]; + rggobi = [ ggobi gtk2.dev libxml2.dev ]; + rjags = [ jags ]; + rpanel = [ bwidget ]; + rpg = [ postgresql ]; + rscala = [ scala ]; + runjags = [ jags ]; + rzmq = [ zeromq3 ]; + scModels = [ mpfr.dev ]; + sdcTable = [ glpk ]; + seewave = [ libsndfile.dev ]; + sf = [ gdal proj.dev geos ]; + showtext = [ freetype.dev ]; + specklestar = [ fftw.dev ]; + ssanv = [ proj.dev ]; + sysfonts = [ freetype.dev ]; + systemfonts = [ fontconfig.dev freetype.dev ]; + tesseract = [ pkgs.tesseract leptonica ]; + tkrplot = [ xorg.libX11 tk.dev ]; + uFTIR = [ gdal ]; + udunits2 = [ udunits expat ]; + units = [ udunits ]; + vapour = [ gdal ]; + websocket = [ pkgs.openssl.dev ]; + xml2 = [ libxml2.dev ] ++ lib.optionals stdenv.isDarwin [ perl ]; }; - packagesWithBuildInputs = { - # sort -t '=' -k 2 - gam = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; - quantreg = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; - rmutil = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; - robustbase = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; - SparseM = lib.optionals stdenv.isDarwin [ pkgs.libiconv ]; - svKomodo = [ pkgs.which ]; - nat = [ pkgs.which ]; - nat_templatebrains = [ pkgs.which ]; - pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.darwin.binutils ]; - RMark = [ pkgs.which ]; - RPushbullet = [ pkgs.which ]; - qtpaint = [ pkgs.cmake ]; - qtbase = [ pkgs.cmake pkgs.perl ]; - RcppEigen = [ pkgs.libiconv ]; - RCurl = [ pkgs.curl.dev ]; - R2SWF = [ pkgs.pkgconfig ]; - rggobi = [ pkgs.pkgconfig ]; - rgl = [ pkgs.libGLU pkgs.libGLU.dev pkgs.libGL pkgs.xlibsWrapper ]; - RGtk2 = [ pkgs.pkgconfig ]; - RProtoBuf = [ pkgs.pkgconfig ]; - Rpoppler = [ pkgs.pkgconfig ]; - XML = [ pkgs.pkgconfig ]; - cairoDevice = [ pkgs.pkgconfig ]; - chebpol = [ pkgs.pkgconfig ]; - fftw = [ pkgs.pkgconfig ]; - gdtools = [ pkgs.pkgconfig ]; - jqr = [ pkgs.jq.lib ]; - kza = [ pkgs.pkgconfig ]; - magick = [ pkgs.pkgconfig ]; - mwaved = [ pkgs.pkgconfig ]; - odbc = [ pkgs.pkgconfig ]; - openssl = [ pkgs.pkgconfig ]; - pdftools = [ pkgs.pkgconfig ]; - sf = [ pkgs.pkgconfig pkgs.sqlite.dev pkgs.proj.dev ]; - showtext = [ pkgs.pkgconfig ]; - spate = [ pkgs.pkgconfig ]; - stringi = [ pkgs.pkgconfig ]; - sysfonts = [ pkgs.pkgconfig ]; - systemfonts = [ pkgs.pkgconfig ]; - tesseract = [ pkgs.pkgconfig ]; - Cairo = [ pkgs.pkgconfig ]; - Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ]; - tcltk2 = [ pkgs.tcl pkgs.tk ]; - tikzDevice = [ pkgs.which pkgs.texlive.combined.scheme-medium ]; - rPython = [ pkgs.which ]; - gridGraphics = [ pkgs.which ]; - adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ]; - mzR = [ pkgs.netcdf ]; - cluster = [ pkgs.libiconv ]; - KernSmooth = [ pkgs.libiconv ]; - nlme = [ pkgs.libiconv ]; - Matrix = [ pkgs.libiconv ]; - mgcv = [ pkgs.libiconv ]; - minqa = [ pkgs.libiconv ]; - igraph = [ pkgs.libiconv ]; - ape = [ pkgs.libiconv ]; - expm = [ pkgs.libiconv ]; - mnormt = [ pkgs.libiconv ]; - pan = [ pkgs.libiconv ]; - phangorn = [ pkgs.libiconv ]; - quadprog = [ pkgs.libiconv ]; - randomForest = [ pkgs.libiconv ]; - sundialr = [ pkgs.libiconv ]; - ucminf = [ pkgs.libiconv ]; - glmnet = [ pkgs.libiconv ]; + packagesWithBuildInputs = with pkgs; { + BALD = [ jags ]; + CopulaCenR = [ pkgs.openssl.dev]; + CytoML = [ libxml2.dev ]; + HilbertVisGUI = [ gtkmm2.dev gnumake ]; + RAppArmor = [ libapparmor ]; + Rcplex = [ cplex ]; + RcppMeCab = [ mecab ]; + RmecabKo = [ mecab ] ; + Rpoppler = [ poppler.dev ]; + Rsymphony = [ doxygen graphviz subversion ]; + SparseM = lib.optionals stdenv.isDarwin [ ]; + SuperGauss = [ pkgs.fftw.dev] ; + TextForecast = [ poppler.dev ]; + adimpro = [ xorg.xdpyinfo ]; + av = [ libav ffmpeg-full ]; + baseflow = [ cargo ]; + bioacoustics = [ cmake soxr ]; + cld3 = [ protobuf ]; + clpAPI = [ CoinMP ]; + commonsMath = [ pkgs.commonsMath ]; + fftw = [ pkgs.fftw.dev ]; # uses doubles. other variations needed? + fftwtools = [ pkgs.fftw.dev ]; + gifski = [ pkgs.gifski ]; + gsl = [ pkgs.gsl]; + gsubfn = [ xorg.xdpyinfo x11 ]; + jqr = [ jq.lib ]; + libsoc = [ libxml2.dev ]; + mzR = [ netcdf ]; + nandb = [libtiff.dev ]; + nloptr = [ nlopt ]; + opencv = [ opencv4 ]; + openssl = [ pkgs.openssl.dev ]; + pbdZMQ = lib.optionals stdenv.isDarwin [ darwin.binutils ]; + pdftools = [ poppler_data poppler.dev libjpeg.dev]; + qpdf = [ libjpeg.dev ]; + qtbase = [ cmake perl ]; + qtpaint = [ cmake ]; + redland = [ librdf_redland ]; + rgl = [ libGLU libGLU.dev libGL xlibsWrapper ]; + rrd = [ rrdtool ]; + rsvg = [ librsvg.dev ]; + salso = [ cargo ]; + sf = [ sqlite.dev proj.dev ]; + sodium = [ libsodium.dev ]; + ssh = [ libssh ]; + tcltk2 = [ tcl tk ]; + tikzDevice = [ texlive.combined.scheme-medium ]; + webp = [ libwebp ]; + xslt = [ libxslt.dev libxml2.dev ]; }; - packagesRequireingX = [ - "accrual" - "ade4TkGUI" - "analogue" - "analogueExtra" + # TODO: some of these have been removed from the upstream source. delete them. + packagesRequiringX = [ "AnalyzeFMRI" "AnnotLists" "AnthropMMD" - "aplpack" - "asbio" "AtelieR" "BAT" - "bayesDem" "BCA" - "betapart" "BiodiversityR" - "bio_infer" - "bipartite" - "biplotbootGUI" - "blender" - "cairoDevice" "CCTpack" - "cncaGUI" - "cocorresp" "CommunityCorrelogram" - "confidence" - "constrainedKriging" "ConvergenceConcepts" - "cpa" "DALY" - "dave" + "DSpat" "Deducer" "DeducerPlugInExample" "DeducerPlugInScaling" @@ -486,158 +429,193 @@ let "DeducerSurvival" "DeducerText" "Demerelate" - "detrendeR" - "dgmb" "DivMelt" - "dpa" - "DSpat" - "dynamicGraph" - "dynBiplotGUI" + "ENiRG" "EasyqpcR" "EcoVirtual" - "ENiRG" - "exactLoglinTest" - "fat2Lpoly" - "fbati" "FD" - "feature" - "FeedbackTS" "FFD" - "fgui" - "fisheyeR" - "fit4NM" - "forams" - "forensim" + "FeedbackTS" "FreeSortR" - "fscaret" - "fSRM" - "gcmr" - "geomorph" - "geoR" - "georob" "GGEBiplotGUI" - "gnm" "GPCSIV" + "GUniFrac" "GrammR" "GrapheR" "GroupSeq" - "gsubfn" - "GUniFrac" - "gWidgets2RGtk2" - "gWidgets2tcltk" - "gWidgetsRGtk2" - "gWidgetstcltk" "HH" + "HierO" "HiveR" - "ic50" - "iDynoR" - "in2extRemes" - "iplots" - "isopam" "IsotopeR" + "JFE" "JGR" "KappaGUI" - "likeLTD" - "logmult" "LS2Wstat" "MareyMap" - "memgene" "MergeGUI" - "metacom" - "Meth27QC" "MetSizeR" + "Meth27QC" "MicroStrategyR" - "migui" - "miniGUI" "MissingDataGUI" - "mixsep" "MplusAutomation" - "mpmcorrelogram" - "mritc" - "multgee" - "multibiplotGUI" "OligoSpecificitySystem" - "onemap" "OpenRepGrid" - "paleoMAS" - "pbatR" "PBSadmb" "PBSmodelling" "PCPS" - "pez" - "phylotools" - "picante" "PKgraph" - "plotSEMM" - "plsRbeta" - "plsRglm" "PopGenReport" - "poppr" - "powerpkg" "PredictABEL" - "prefmod" "PrevMap" "ProbForecastGOP" - "qtbase" - "qtpaint" - "r4ss" + "RHRV" + "RNCEP" + "RQDA" + "RSDA" + "RSurvey" "RandomFields" - "rareNMtests" - "rAverage" "Rcmdr" - "RcmdrPlugin_coin" - "RcmdrPlugin_depthTools" "RcmdrPlugin_DoE" "RcmdrPlugin_EACSPIR" "RcmdrPlugin_EBM" - "RcmdrPlugin_EcoVirtual" "RcmdrPlugin_EZR" + "RcmdrPlugin_EcoVirtual" "RcmdrPlugin_FactoMineR" "RcmdrPlugin_HH" "RcmdrPlugin_IPSUR" "RcmdrPlugin_KMggplot2" - "RcmdrPlugin_lfstat" "RcmdrPlugin_MA" - "RcmdrPlugin_mosaic" "RcmdrPlugin_MPAStats" + "RcmdrPlugin_ROC" + "RcmdrPlugin_SCDA" + "RcmdrPlugin_SLC" + "RcmdrPlugin_TeachingDemos" + "RcmdrPlugin_UCA" + "RcmdrPlugin_coin" + "RcmdrPlugin_depthTools" + "RcmdrPlugin_lfstat" + "RcmdrPlugin_mosaic" "RcmdrPlugin_orloca" "RcmdrPlugin_plotByGroup" "RcmdrPlugin_pointG" "RcmdrPlugin_qual" - "RcmdrPlugin_ROC" "RcmdrPlugin_sampling" - "RcmdrPlugin_SCDA" - "RcmdrPlugin_SLC" "RcmdrPlugin_sos" "RcmdrPlugin_steepness" "RcmdrPlugin_survival" - "RcmdrPlugin_TeachingDemos" "RcmdrPlugin_temis" - "RcmdrPlugin_UCA" + "RenextGUI" + "RunuranGUI" + "SOLOMON" + "SRRS" + "SSDforR" + "STEPCAM" + "SYNCSA" + "Simile" + "SimpleTable" + "StatDA" + "SyNet" + "TIMP" + "TTAinterfaceTrendAnalysis" + "TestScorer" + "VecStatGraphs3D" + "WMCapacity" + "accrual" + "ade4TkGUI" + "analogue" + "analogueExtra" + "aplpack" + "asbio" + "bayesDem" + "betapart" + "bio_infer" + "bipartite" + "biplotbootGUI" + "blender" + "cairoDevice" + "cncaGUI" + "cocorresp" + "confidence" + "constrainedKriging" + "cpa" + "dave" + "detrendeR" + "dgmb" + "dpa" + "dynBiplotGUI" + "dynamicGraph" + "exactLoglinTest" + "fSRM" + "fat2Lpoly" + "fbati" + "feature" + "fgui" + "fisheyeR" + "fit4NM" + "forams" + "forensim" + "fscaret" + "gWidgets2RGtk2" + "gWidgets2tcltk" + "gWidgetsRGtk2" + "gWidgetstcltk" + "gcmr" + "geoR" + "geomorph" + "georob" + "ggtern" + "gnm" + "gsubfn" + "iDynoR" + "ic50" + "in2extRemes" + "iplots" + "isopam" + "likeLTD" + "logmult" + "loon" + "memgene" + "metacom" + "migui" + "miniGUI" + "mixsep" + "mpmcorrelogram" + "mritc" + "multgee" + "multibiplotGUI" + "onemap" + "optbdmaeAT" + "optrcdmaeAT" + "paleoMAS" + "pbatR" + "pez" + "phylotools" + "picante" + "plotSEMM" + "plsRbeta" + "plsRglm" + "poppr" + "powerpkg" + "prefmod" + "qtbase" + "qtpaint" + "r4ss" + "rAverage" + "rMouse" + "rareNMtests" "recluster" "relimp" - "RenextGUI" "reshapeGUI" + "rfviz" "rgl" - "RHRV" "rich" - "RNCEP" - "RQDA" - "RSDA" - "RSurvey" - "RunuranGUI" + "rpanel" "simba" - "Simile" - "SimpleTable" - "SOLOMON" + "soptdmaeA" "soundecology" "spatsurv" "sqldf" - "SRRS" - "SSDforR" "statcheck" - "StatDA" - "STEPCAM" "stosim" "strvalidator" "stylo" @@ -645,79 +623,136 @@ let "svIDE" "svSocket" "svWidgets" - "SYNCSA" - "SyNet" "tcltk2" - "TestScorer" - "TIMP" "titan" "tkrgl" "tkrplot" "tmap" "tspmeta" - "TTAinterfaceTrendAnalysis" "twiddler" "vcdExtra" - "VecStatGraphs3D" "vegan" "vegan3d" "vegclust" - "WMCapacity" "x12GUI" + "xRing" ]; packagesToSkipCheck = [ + "HDCytoData" "Rmpi" # tries to run MPI processes "pbdMPI" # tries to run MPI processes + "x12GUI" + "regRSM" # tries to run MPI processes + "TabulaMurisData" + "dmdScheme" + "exifr" + "fulltext" + "ggtern" + "packagefinder" + "spi" + "wrswoR_benchmark" + "FlowSorted_CordBlood_450k" # impure test + "FlowSorted_CordBloodCombined_450k" # impure test + "DuoClustering2018" # impure test ]; # Packages which cannot be installed due to lack of dependencies or other reasons. brokenPackages = [ + # comments are hints/tags. many issues are fixable and the fix may apply to multiple packages. Have a go! + "AntMAN" # salso. Cargo related. + "ArrayExpressHTS" # Error: package or namespace load failed for 'ArrayExpressHTS' + "BRugs" # there is no openbugs, a dependency. + "ChoR" # maven, impure + "DBKGrad" # rpanel + "DriftBurstHypothesis" # compile error + "GRANBase" # impure + "GRANCore" # impure? + "GUIDE" # rpanel (bwidget) + "GeneBook" # impure? + "HierO" # similar to rpanel + "RBLpapi" # lib not available + "RGreenplum" # RPostgres + "RKEEL" # impure + "RKEELjars" # impure + "ROI_plugin_clp" # cplex + "ROI_plugin_cplex" # " # cplex. different errors on darwin and linux + "ROI_plugin_symphony" # symphony + "ROracle" # OCI + "RQuantLib" # no lib to link. wants QuantLib. + "RVideoPoker" # rpanel + "Rcplex" # needs cplex + "Rsymphony" # SYMPHONY + "SDD" # rpanel + "anomaly" # compile error + "bamboo" # unable to load R code in package 'rscala + "baseflow" # cargo (rust) config problem + "baseflow" # ld: cannot find -lrustlib + "bigGP" # ompi_mpi_init: ompi_rte_init faile + "biotools" # rpanel + "clustermq" # ERROR: dependency 'rzmq' is not available for package 'clustermq', but rzmq builds ok. + "cocktailApp" # ggtern. object 'expand_default' not found. + "commonsMath" # impure build + "cplexAPI" # CPLEX interactive optimizer not found + "cytofWorkflow" # impure build, maybe patch NAMESPACE + "dataone" # redland + "doMPI" # ompi_mpi_init: ompi_rte_init failed + "erpR" # rpanel + "expands" # impure. commonsMath + "freetypeharfbuzz" # impure? /download.sh "https://github.com/lionel-/freetypeharfbuzz/raw/v`cat version`/tools/freetype-2.9-patched.tar.gz" freetype-2.9-patched.tar.gz + "ggtern" # Error in get(x, envir = ns, inherits = FALSE) : object 'expand_default' not found. + "ggtern" # object 'expand_default' not found + "gifski" # Cargo + "googleformr" # impure? Could not resolve host: docs.google.com + "gpuR" # linker error. lib needed? + "h2o" # impure. cannot open URL 'http://s3.amazonaws.com/h2o-release/h2o/rel-yu/4/Rjar/h2o.jar.md5 + "kazaam" # ompi_mpi_init: ompi_rte_init failed + "kmcudaR" # rror: "NVCC not found; check CUDA install" + "lazytrade" # h2o impure? URL 'http://s3.amazonaws.com/h2o-release/h2o/rel-yu/4/Rjar/h2o.jar.md5 + "lgcp" # rpanel + "metaMix" # ompi_mpi_init: ompi_rte_init failed + "metaMix" # ompi_mpi_init: ompi_rte_init failed + "moc_gapbk" # ompi_mpi_init: ompi_rte_init failed + "moc_gapbk" # ompi_mpi_init: ompi_rte_init failed + "moveVis" # gifski + "nearfar" # impure? cannot open the connection to 'https://raw.githubusercontent.com/joerigdon/nearfar/master/angrist.csv' + "optBiomarker" # rpanel + "ora" # ROracle + "pbdBASE" # ompi_mpi_init: ompi_rte_init failed + "pbdSLAP" # ompi_mpi_init: ompi_rte_init failed + "permGPU" # nvcc not found. needs cudatoolkit most likely + "plfMA" # might be gtk2 related + "plot3logit" # ggtern + "rLindo" # needs lindo. + "rPython" # configure.ac needs a patch to work + "randstr" # cannot open the connection to 'https://www.random.org/quota/?format=plain'. + "rdflib" # redland + "redland" # needs lib configuration for librdf_redland + "regRSM" # ompi_mpi_init: ompi_rte_init failed + "rpanel" # Error in structure(.External(.C_dotTcl, ...), class = "tclObj") : [tcl] can't find package BWidget. + "rsparkling" # impure. relies on impure h2o + "salso" # Cargo + "sdols" # Cargo + "seeds" # rpanel + "shallot" # commonsMath + "shinyML" # h2o + "sismonr" # needs julia + "smovie" # rpanel + "soilphysics" # rpanel + "spate" # config issue + "spatstat_gui" # rpanel + "tesseract" # patch config + "vdiffr" # freetypeharfbuzz + "x12" # same as x12GUI? + "x12GUI" # ???? + "xRing" # rpanel (bwidget) + # possibly broken ... + # zooaRchGUI # byte compile takes a very long time. uses cpu, so not hung? maybe large, single threaded? + # uHMM # byte compile takes a very long time. uses cpu, so not hung? maybe large, single threaded? ]; otherOverrides = old: new: { - stringi = old.stringi.overrideDerivation (attrs: { - postInstall = let - icuName = "icudt52l"; - icuSrc = pkgs.fetchzip { - url = "http://static.rexamine.com/packages/${icuName}.zip"; - sha256 = "0hvazpizziq5ibc9017i1bb45yryfl26wzfsv05vk9mc1575r6xj"; - stripRoot = false; - }; - in '' - ${attrs.postInstall or ""} - cp ${icuSrc}/${icuName}.dat $out/library/stringi/libs - ''; - }); - - xml2 = old.xml2.overrideDerivation (attrs: { - preConfigure = '' - export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2 - patchShebangs configure - ''; - }); - - Cairo = old.Cairo.overrideDerivation (attrs: { - NIX_LDFLAGS = "-lfontconfig"; - }); - - curl = old.curl.overrideDerivation (attrs: { - preConfigure = "patchShebangs configure"; - }); - - ggbio = old.ggbio.overrideDerivation (attrs: { - patches = [ - (pkgs.fetchpatch { - url = "https://github.com/tengfei/ggbio/commit/b04a9840cf5c0bd0514db2536f2e610bbd364727.patch"; - sha256 = "blwtObyIYo1UBWz4nlmcJ8Nyw/n0qwmJrtwFWuoUyMg="; - }) - ]; - }); - - RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: { - patchPhase = "patchShebangs configure"; - }); - + data_table = old.data_table.overrideDerivation (attrs: { NIX_CFLAGS_COMPILE = attrs.NIX_CFLAGS_COMPILE + lib.optionalString stdenv.isDarwin " -fopenmp"; @@ -728,18 +763,16 @@ let + lib.optionalString stdenv.isDarwin " -fopenmp"; }); - rpf = old.rpf.overrideDerivation (attrs: { - patchPhase = "patchShebangs configure"; - }); - - BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: { - patches = [ ./patches/BayesXsrc.patch ]; - }); - Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: { patches = [ ./patches/Rhdf5lib.patch ]; }); + sodium = old.sodium.overrideDerivation ( attrs: { + preConfigure = '' + patchShebangs configure + ''; + }); + rJava = old.rJava.overrideDerivation (attrs: { preConfigure = '' export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/ @@ -754,12 +787,6 @@ let ''; }); - jqr = old.jqr.overrideDerivation (attrs: { - preConfigure = '' - patchShebangs configure - ''; - }); - pbdZMQ = old.pbdZMQ.overrideDerivation (attrs: { postPatch = lib.optionalString stdenv.isDarwin '' for file in R/*.{r,r.in}; do @@ -768,10 +795,6 @@ let ''; }); - qtbase = old.qtbase.overrideDerivation (attrs: { - patches = [ ./patches/qtbase.patch ]; - }); - Rmpi = old.Rmpi.overrideDerivation (attrs: { configureFlags = [ "--with-Rmpi-type=OPENMPI" @@ -790,11 +813,6 @@ let ]; }); - RAppArmor = old.RAppArmor.overrideDerivation (attrs: { - patches = [ ./patches/RAppArmor.patch ]; - LIBAPPARMOR_HOME = pkgs.libapparmor; - }); - RMySQL = old.RMySQL.overrideDerivation (attrs: { MYSQL_DIR="${pkgs.libmysqlclient}"; preConfigure = '' @@ -802,50 +820,34 @@ let ''; }); - devEMF = old.devEMF.overrideDerivation (attrs: { - NIX_CFLAGS_LINK = "-L${pkgs.xorg.libXft.out}/lib -lXft"; - NIX_LDFLAGS = "-lX11"; - }); - - slfm = old.slfm.overrideDerivation (attrs: { - PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack"; - }); - SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: { PKG_LIBS = "-L${pkgs.blas}/lib -lblas -L${pkgs.lapack}/lib -llapack"; }); - EMCluster = old.EMCluster.overrideDerivation (attrs: { - patches = [ ./patches/EMCluster.patch ]; - }); - - spMC = old.spMC.overrideDerivation (attrs: { - patches = [ ./patches/spMC.patch ]; - }); - openssl = old.openssl.overrideDerivation (attrs: { - PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; - PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto"; + NIX_CFLAGS_COMPILE="-I${pkgs.openssl.dev}/include"; + NIX_LDFLAGS="-rpath ${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto"; }); websocket = old.websocket.overrideDerivation (attrs: { - PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include"; - PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto"; + NIX_CFLAGS_COMPILE = "-I${pkgs.openssl.dev}/include"; + NIX_LDFLAGS = "-rpath ${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -lssl -lcrypto"; }); - + Rserve = old.Rserve.overrideDerivation (attrs: { patches = [ ./patches/Rserve.patch ]; configureFlags = [ "--with-server" "--with-client" ]; }); - + nloptr = old.nloptr.overrideDerivation (attrs: { - # Drop bundled nlopt source code. Probably unnecessary, but I want to be - # sure we're using the system library, not this one. - preConfigure = "rm -r src/nlopt_src"; + configureFlags = [ + "--with-nlopt-cflags=-I${pkgs.nlopt}/include" + "--with-nlopt-libs=${pkgs.nlopt}/lib" + ]; }); - + V8 = old.V8.overrideDerivation (attrs: { postPatch = '' substituteInPlace configure \ @@ -858,65 +860,42 @@ let patchShebangs configure ''; }); - - acs = old.acs.overrideDerivation (attrs: { - preConfigure = '' - patchShebangs configure - ''; - }); - + gdtools = old.gdtools.overrideDerivation (attrs: { preConfigure = '' patchShebangs configure - ''; + ''; NIX_LDFLAGS = "-lfontconfig -lfreetype"; }); - magick = old.magick.overrideDerivation (attrs: { - preConfigure = '' - patchShebangs configure - ''; - }); - - protolite = old.protolite.overrideDerivation (attrs: { - preConfigure = '' - patchShebangs configure - ''; - }); - + # not working rpanel = old.rpanel.overrideDerivation (attrs: { preConfigure = '' - export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}" + export TCLLIBPATH=". ${pkgs.bwidget}/lib/${pkgs.bwidget.libPrefix}" ''; - TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"; + #TCLLIBPATH="${pkgs.bwidget}/lib/${pkgs.bwidget.libPrefix}"; }); + # needs another patch in custom configure file RPostgres = old.RPostgres.overrideDerivation (attrs: { preConfigure = '' - export INCLUDE_DIR=${pkgs.postgresql}/include - export LIB_DIR=${pkgs.postgresql.lib}/lib + #export INCLUDE_DIR=${pkgs.postgresql}/include + #export LIB_DIR=${pkgs.postgresql.lib}/lib patchShebangs configure ''; }); - OpenMx = old.OpenMx.overrideDerivation (attrs: { - preConfigure = '' - patchShebangs configure - ''; + # TODO: needs patch like openssl + tesseract = old.tesseract.overrideDerivation (attrs: { + PKG_CFLAGS = "-I${pkgs.tesseract}/include -I${pkgs.leptonica}/include"; + PKG_LIBS = "-Wl,-rpath,${pkgs.tesseract}/lib -L${pkgs.tesseract}/lib"; + }); - odbc = old.odbc.overrideDerivation (attrs: { - preConfigure = '' - patchShebangs configure - ''; - }); - - x13binary = old.x13binary.overrideDerivation (attrs: { - preConfigure = '' - patchShebangs configure - ''; + xslt = old.xslt.overrideDerivation (attrs: { + preConfigure = "patchShebangs configure"; }); - + geojsonio = old.geojsonio.overrideDerivation (attrs: { buildInputs = [ cacert ] ++ attrs.buildInputs; }); @@ -926,23 +905,11 @@ let }); mongolite = old.mongolite.overrideDerivation (attrs: { + NIX_CFLAGS_COMPILE = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include"; + NIX_LDFLAGS = "-rpath ${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz"; preConfigure = '' patchShebangs configure - ''; - PKGCONFIG_CFLAGS = "-I${pkgs.openssl.dev}/include -I${pkgs.cyrus_sasl.dev}/include -I${pkgs.zlib.dev}/include"; - PKGCONFIG_LIBS = "-Wl,-rpath,${pkgs.openssl.out}/lib -L${pkgs.openssl.out}/lib -L${pkgs.cyrus_sasl.out}/lib -L${pkgs.zlib.out}/lib -lssl -lcrypto -lsasl2 -lz"; - }); - - ps = old.ps.overrideDerivation (attrs: { - preConfigure = "patchShebangs configure"; - }); - - rlang = old.rlang.overrideDerivation (attrs: { - preConfigure = "patchShebangs configure"; - }); - - systemfonts = old.systemfonts.overrideDerivation (attrs: { - preConfigure = "patchShebangs configure"; + ''; }); littler = old.littler.overrideAttrs (attrs: with pkgs; { @@ -957,6 +924,66 @@ let ''; }); + # broken. needs Cargo too + gifski = old.gifski.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + + #broken. needs config help + redland = old.redland.overrideDerivation (attrs: { + # NIX_CFLAGS_COMPILE = "-I${pkgs.librdf_redland}/include"; + # NIX_LDFLAGS = "-rpath ${pkgs.librdf_redland}/lib -L${pkgs.librdf_redland}/lib -lrdf -lredland"; + #PKGCONFIG_CFLAGS = "-I${pkgs.librdf_redland}/include"; + #PKGCONFIG_LIBS = "-WL -rpath,${pkgs.librdf_redland}/lib -L${pkgs.librdf_redland}/lib"; + preConfigure = "patchShebangs configure"; + }); + + xml2 = old.xml2.overrideDerivation (attrs: { + preConfigure = '' + export LIBXML_INCDIR=${pkgs.libxml2.dev}/include/libxml2 + patchShebangs configure + ''; + }); + + # Packages that only need patchShebangs ... not very "DRY". + DeLorean = old.DeLorean.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + OpenMx = old.OpenMx.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + RKorAPClient = old.RKorAPClient.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + RMariaDB = old.RMariaDB.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + Rblpapi = old.Rblpapi.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + RcppCWB = old.RcppCWB.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + RcppParallel= old.RcppParallel.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + acs = old.acs.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + av = old.av.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + cld3 = old.cld3.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + curl = old.curl.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + freetypeharfbuzz = old.freetypeharfbuzz.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + gert = old.gert.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + ijtiff = old.ijtiff.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + jqr = old.jqr.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + keyring = old.keyring.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + libsoc = old.libsoc.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + liquidSVM = old.liquidSVM.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + magick = old.magick.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + missSBM = old.missSBM.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + odbc = old.odbc.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + opencv = old.opencv.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + pdftools = old.pdftools.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + protolite = old.protolite.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + ps = old.ps.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + qmix = old.qmix.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + qtpaint = old.qtpaint.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + redux = old.redux.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + rlang = old.rlang.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + rpf = old.rpf.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + rpg = old.rpg.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + rrd = old.rrd.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + rsvg = old.rsvg.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + rzmq = old.rzmq.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + strex = old.strex.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + systemfonts = old.systemfonts.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + webp = old.webp.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + x13binary = old.x13binary.overrideDerivation (attrs: { preConfigure = "patchShebangs configure"; }); + }; -in - self +in self + diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R index 1586b5b16b3a1..4b24722a060d1 100755 --- a/pkgs/development/r-modules/generate-r-packages.R +++ b/pkgs/development/r-modules/generate-r-packages.R @@ -3,16 +3,18 @@ library(data.table) library(parallel) cl <- makeCluster(10) -biocVersion <- 3.8 +biocVersion <- "3.10" snapshotDate <- Sys.Date()-1 mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/") - , "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/") - , "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/") - , cran=paste0("http://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/") + , "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/") + , "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/") + , "bioc-workflows"=paste0("http://www.bioconductor.org/packages/", biocVersion, "/workflows/src/contrib/") #need a working url for workflows + , cran=paste0("http://mran.revolutionanalytics.com/snapshot/", snapshotDate, "/src/contrib/") ) mirrorType <- commandArgs(trailingOnly=TRUE)[1] +#mirrorType <- "bioc-workflows" stopifnot(mirrorType %in% names(mirrorUrls)) packagesFile <- paste(mirrorType, 'packages.nix', sep='-') readFormatted <- as.data.table(read.table(skip=8, sep='"', text=head(readLines(packagesFile), -1))) @@ -27,7 +29,8 @@ knownPackages <- sapply(knownPackages, gsub, pattern=".", replacement="_", fixed mirrorUrl <- mirrorUrls[mirrorType][[1]] nixPrefetch <- function(name, version) { prevV <- readFormatted$V2 == name & readFormatted$V4 == version - if (sum(prevV) == 1) + # if ( 1 == 0 ) # force everything. needed too often sadly + if (sum(prevV) == 1) # assume links point to immutable files. as.character(readFormatted$V6[ prevV ]) else { @@ -40,7 +43,6 @@ nixPrefetch <- function(name, version) { cmd <- paste0(cmd, " ; rm -rf '", tmp, "'") system(cmd, intern=TRUE) } - } formatPackage <- function(name, version, sha256, depends, imports, linkingTo) { diff --git a/pkgs/development/r-modules/generic-builder.nix b/pkgs/development/r-modules/generic-builder.nix index 76bf29abc17c6..8458182746eb7 100644 --- a/pkgs/development/r-modules/generic-builder.nix +++ b/pkgs/development/r-modules/generic-builder.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation ({ installPhase = '' runHook preInstall mkdir -p $out/library + echo "$rCommand CMD INSTALL $installFlags --configure-args="$configureFlags" -l $out/library ." $rCommand CMD INSTALL $installFlags --configure-args="$configureFlags" -l $out/library . runHook postInstall ''; diff --git a/pkgs/development/r-modules/get_names.sh b/pkgs/development/r-modules/get_names.sh new file mode 100755 index 0000000000000..d6cb31f51cd14 --- /dev/null +++ b/pkgs/development/r-modules/get_names.sh @@ -0,0 +1,4 @@ +#!/bin/sh +nix eval -f test-evaluation.nix "$1" > "$1" +sed -i "$1" -e 's/\[ //g' -e 's/ ]//g' -e 's/ /\n/g' -e 's/\"//g' + diff --git a/pkgs/development/r-modules/patches/EMCluster.patch b/pkgs/development/r-modules/patches/EMCluster.patch deleted file mode 100644 index afc9de3a95a91..0000000000000 --- a/pkgs/development/r-modules/patches/EMCluster.patch +++ /dev/null @@ -1,6 +0,0 @@ -diff -ru -x '*~' EMCluster_orig/src/Makevars EMCluster/src/Makevars ---- EMCluster_orig/src/Makevars 2013-07-05 02:43:25.000000000 +0900 -+++ EMCluster/src/Makevars 2014-10-25 18:10:19.190992120 +0900 -@@ -1 +1 @@ --PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS) -+PKG_LIBS = $(FLIBS) $(LAPACK_LIBS) $(BLAS_LIBS) diff --git a/pkgs/development/r-modules/patches/RAppArmor.patch b/pkgs/development/r-modules/patches/RAppArmor.patch deleted file mode 100644 index f2dc49bd47664..0000000000000 --- a/pkgs/development/r-modules/patches/RAppArmor.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff -ru -x '*~' RAppArmor_orig/configure RAppArmor/configure ---- RAppArmor_orig/configure 2013-12-17 11:23:00.000000000 +0900 -+++ RAppArmor/configure 2014-10-18 22:22:39.641341244 +0900 -@@ -1,15 +1,2 @@ --if [ ! -e /usr/include/sys/apparmor.h ] --then -- echo "sys/apparmor.h not found. Make sure libapparmor-dev is installed." -- exit 1 --fi -- --LIBFILE=$(/sbin/ldconfig -p | egrep -oh " [-_a-zA-Z0-9/]*/libapparmor.so(.1)?$") -- --if [ -z "$LIBFILE" ] --then -- echo "libapparmor.so not found. Make sure libapparmor-dev is installed." -- exit 1 --fi -- -+LIBFILE="$LIBAPPARMOR_HOME/lib/libapparmor.so.1" - echo "PKG_LIBS="$LIBFILE > src/Makevars diff --git a/pkgs/development/r-modules/patches/Rhdf5lib.patch b/pkgs/development/r-modules/patches/Rhdf5lib.patch index dcd9b61798bd1..dff4b4aa4340a 100644 --- a/pkgs/development/r-modules/patches/Rhdf5lib.patch +++ b/pkgs/development/r-modules/patches/Rhdf5lib.patch @@ -1,12 +1,13 @@ -diff --git a/configure b/configure -index e2d292e..b13c0db 100755 +diff -u --label a/configure --label b/configure --- a/configure +++ b/configure -@@ -2880,6 +2880,7 @@ $MAKE +@@ -3660,6 +3660,7 @@ + echo "building the hdf5 library..."; cd ../; - ## we add the '-w' flag to suppress all the warnings hdf5 prints +sed -i 's#/bin/mv#mv#' configure - ./configure --with-pic --enable-shared=no --enable-cxx \ - --with-szlib \ - CXX="${CXX}" CXFLAGS="${CXXFLAGS} -w" \ + ./configure --with-pic --enable-shared=no --enable-cxx --enable-hl \ + --with-szlib=${SZIP_HOME} --with-zlib=${ZLIB_HOME} \ + CXX="${CXX}" CXXFLAGS="${CXXFLAGS} ${CXXPICFLAGS}" \ + +Diff finished. Mon Mar 16 11:15:35 2020 diff --git a/pkgs/development/r-modules/patches/spMC.patch b/pkgs/development/r-modules/patches/spMC.patch deleted file mode 100644 index 04239d721c077..0000000000000 --- a/pkgs/development/r-modules/patches/spMC.patch +++ /dev/null @@ -1,8 +0,0 @@ -Only in spMC_orig: spMC -diff -ru -x '*~' spMC_orig/src/Makevars spMC/src/Makevars ---- spMC_orig/src/Makevars 2014-09-19 21:23:30.000000000 +0900 -+++ spMC/src/Makevars 2014-10-25 18:14:48.366954769 +0900 -@@ -1,2 +1,2 @@ - PKG_CFLAGS=$(SHLIB_OPENMP_CFLAGS) --PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(BLAS_LIBS) $(LAPACK_LIBS) $(FLIBS) -+PKG_LIBS=$(SHLIB_OPENMP_CFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) diff --git a/pkgs/development/r-modules/sample-devenv-shell.nix b/pkgs/development/r-modules/sample-devenv-shell.nix new file mode 100644 index 0000000000000..df43b088d4077 --- /dev/null +++ b/pkgs/development/r-modules/sample-devenv-shell.nix @@ -0,0 +1,517 @@ +# usage: $ nix-shell test-package-build.nix +let + pkgs = import ../../.. {}; + # want to avoid needing it at all, but we might find it necessary + conda = pkgs.conda.override { extraPkgs = with pkgs; [ + which # some conda packages rely on this + ]; }; + + rpkgs = with pkgs.rPackages; + [ # some packages we care about. edit freely. + AnnotationDbi + ballgown + DESeq2 + EnsDb_Hsapiens_v79 + EnsDb_Hsapiens_v86 + devtools + dplyr + genefilter + ggplot2 + HDF5Array + hdf5r + knitr + pheatmap + PythonInR + RColorBrewer + Rhdf5lib + readr + rhdf5 + rmarkdown + tidygenomics + tidyr + tximeta + tximport + vsn + xts + + # some bioconductor workflows -- new! + rnaseqGene + simpleSingleCell + RNAseq123 + annotation + rnaseqDTU + maEndToEnd + #cytofWorkflow # broken + + # # packagesWithNativeBuildInputs + # abn + # adimpro + # animation + # audio + # BayesSAE + # BayesVarSel + # BayesXsrc + # #bigGP + # bio3d + # BiocCheck + # Biostrings + # bnpmr + # cairoDevice + # Cairo + # Cardinal + # chebpol + # ChemmineOB + # cit + # curl + # data_table + # devEMF + # diversitree + # EMCluster + # fftw + # fftwtools + # Formula + # gdtools + # git2r + # GLAD + # glpkAPI + # gmp + # graphscan + # gsl + # haven + # h5vc + # HiCseg + # imager + # iBMQ + # igraph + # JavaGD + # jpeg + # jqr + # KFKSDS + # kza + # magick + # ModelMetrics + # mvabund + # mwaved + # ncdf4 + # nloptr + # odbc + # outbreaker + # pander + # pbdMPI + # pbdNCDF4 + # pbdPROF + # pbdZMQ + # pdftools + # phytools + # PKI + # png + # proj4 + # protolite + # qtbase + # qtpaint + # R2SWF + # RAppArmor + # rapportools + # rapport + # readxl + # rcdd + # RcppCNPy + # RcppGSL + # RcppZiggurat + # reprex + # rgdal + # rgeos + # rggobi + # Rglpk + # RGtk2 + # rhdf5 + # Rhdf5lib + # Rhpc + # Rhtslib + # rjags + # rJava + # Rlibeemd + # rmatio + # Rmpfr + # Rmpi + # RMySQL + # RNetCDF + # RODBC + # #rpanel + # rpg + # Rpoppler + # RPostgreSQL + # RProtoBuf + # rPython + # RSclient + # Rsamtools + # Rserve + # Rssa + # rtiff + # runjags + # RVowpalWabbit + # rzmq + # SAVE + # sdcTable + # seewave + # seqinr + # seqminer + # sf + # showtext + # simplexreg + # spate + # ssanv + # stsm + # stringi + # survSNP + # sysfonts + # systemfonts + # TAQMNGR + # #tesseract + # tiff + # TKF + # tkrplot + # topicmodels + # udunits2 + # units + # V8 + # XBRL + # xml2 + # XML + # affyPLM + # bamsignals + # BitSeq + # DiffBind + # ShortRead + # oligo + # gmapR + # Rsubread + # XVector + # rtracklayer + # affyio + # VariantAnnotation + # snpStats + + # # packagesWithBuildinputs + # Cairo + # KernSmooth + # Matrix + # R2SWF + # RCurl + # RGtk2 + # RMark + # RProtoBuf + # RPushbullet + # RcppEigen + # Rpoppler + # #Rsymphony + # SparseM + # XML + # adimpro + # ape + # cairoDevice + # chebpol + # cluster + # expm + # fftw + # gam + # gdtools + # glmnet + # gridGraphics + # igraph + # jqr + # kza + # magick + # mgcv + # minqa + # mnormt + # mwaved + # mzR + # nat + # nat_templatebrains + # nlme + # odbc + # openssl + # pan + # pbdZMQ + # pdftools + # phangorn + # qtbase + # quadprog + # quantreg + # rPython + # randomForest + # rggobi + # rgl + # rmutil + # robustbase + # sf + # showtext + # spate + # stringi + # sundialr + # svKomodo + # sysfonts + # systemfonts + # tcltk2 + # #tesseract + # tikzDevice + # ucminf + + # # packagesRequiringX + # AnalyzeFMRI + # ##AnnotLists + # AnthropMMD + # AtelieR + # BAT + # BCA + # BiodiversityR + # CCTpack + # CommunityCorrelogram + # ConvergenceConcepts + # ##DALY + # DSpat + # Deducer + # DeducerPlugInExample + # DeducerPlugInScaling + # DeducerSpatial + # DeducerSurvival + # DeducerText + # Demerelate + # DivMelt + # ENiRG + # EasyqpcR + # FD + # FFD + # FeedbackTS + # FreeSortR + # GGEBiplotGUI + # GPCSIV + # GUniFrac + # GrammR + # ##GrapheR + # ##GroupSeq + # HH + # HiveR + # IsotopeR + # JGR + # KappaGUI + # LS2Wstat + # MareyMap + # MergeGUI + # MetSizeR + # Meth27QC + # MicroStrategyR + # MissingDataGUI + # MplusAutomation + # OligoSpecificitySystem + # OpenRepGrid + # PBSadmb + # PBSmodelling + # PCPS + # PKgraph + # PopGenReport + # PredictABEL + # PrevMap + # ProbForecastGOP + # RHRV + # RNCEP + # RQDA + # RSDA + # RSurvey + # RandomFields + # Rcmdr + # RcmdrPlugin_DoE + # RcmdrPlugin_EACSPIR + # RcmdrPlugin_EBM + # RcmdrPlugin_EZR + # RcmdrPlugin_EcoVirtual + # RcmdrPlugin_FactoMineR + # RcmdrPlugin_HH + # RcmdrPlugin_IPSUR + # RcmdrPlugin_KMggplot2 + # RcmdrPlugin_MA + # RcmdrPlugin_MPAStats + # RcmdrPlugin_ROC + # RcmdrPlugin_SCDA + # RcmdrPlugin_SLC + # RcmdrPlugin_TeachingDemos + # RcmdrPlugin_UCA + # RcmdrPlugin_coin + # RcmdrPlugin_depthTools + # RcmdrPlugin_lfstat + # RcmdrPlugin_mosaic + # RcmdrPlugin_orloca + # RcmdrPlugin_plotByGroup + # RcmdrPlugin_pointG + # RcmdrPlugin_qual + # RcmdrPlugin_sampling + # RcmdrPlugin_sos + # RcmdrPlugin_steepness + # RcmdrPlugin_survival + # RcmdrPlugin_temis + # RenextGUI + # RunuranGUI + # SOLOMON + # SRRS + # SSDforR + # STEPCAM + # SYNCSA + # Simile + # SimpleTable + # StatDA + # SyNet + # TIMP + # TTAinterfaceTrendAnalysis + # TestScorer + # VecStatGraphs3D + # WMCapacity + # accrual + # ade4TkGUI + # analogue + # analogueExtra + # aplpack + # asbio + # bayesDem + # betapart + # bio_infer + # bipartite + # biplotbootGUI + # blender + # cairoDevice + # cncaGUI + # cocorresp + # confidence + # constrainedKriging + # cpa + # dave + # detrendeR + # dgmb + # dpa + # dynBiplotGUI + # dynamicGraph + # exactLoglinTest + # fSRM + # fat2Lpoly + # fbati + # feature + # fgui + # fisheyeR + # fit4NM + # forams + # forensim + # fscaret + # gWidgets2RGtk2 + # gWidgets2tcltk + # gWidgetsRGtk2 + # gWidgetstcltk + # gcmr + # geoR + # geomorph + # georob + # gnm + # gsubfn + # iDynoR + # ic50 + # in2extRemes + # iplots + # isopam + # likeLTD + # logmult + # memgene + # metacom + # migui + # miniGUI + # mixsep + # mpmcorrelogram + # mritc + # multgee + # multibiplotGUI + # onemap + # paleoMAS + # pbatR + # pez + # phylotools + # picante + # plotSEMM + # plsRbeta + # plsRglm + # poppr + # powerpkg + # prefmod + # qtbase + # qtpaint + # r4ss + # rAverage + # rareNMtests + # recluster + # relimp + # reshapeGUI + # rgl + # rich + # simba + # soundecology + # spatsurv + # sqldf + # statcheck + # stosim + # strvalidator + # stylo + # svDialogstcltk + # svIDE + # svSocket + # svWidgets + # tcltk2 + # titan + # tkrgl + # tkrplot + # tmap + # tspmeta + # twiddler + # vcdExtra + # vegan + # vegan3d + # vegclust + # #x12GUI + # # otherOverrides no duplicates + # RcppArmadillo + # SamplerCompare + # spMC + # openssl + # websocket + # acs + # OpenMx + # x13binary + # geojsonio + # rstan + # ps + # mongolite + # rlang + # littler + ]; + + my_r = pkgs.rWrapper.override { packages = rpkgs; }; + my_rstudio = pkgs.rstudioWrapper.override { packages = rpkgs;}; + +in + pkgs.mkShell { + buildInputs = with pkgs; + [ + # conda # uncomment if you require conda + my_r # don't need this if you are only using rstudio + my_rstudio + + # uncomment next two if you are writing docs + # texlive.combined.scheme-full + # pandoc + + # add command line tool here + samtools + hisat2 + bowtie2 + ]; + # saves a step if you are using conda + # shellHook ="exec conda-shell"; + } + + diff --git a/pkgs/development/r-modules/test-evaluation.nix b/pkgs/development/r-modules/test-evaluation.nix index 2ca0d42c6db4f..8067de50acbf0 100644 --- a/pkgs/development/r-modules/test-evaluation.nix +++ b/pkgs/development/r-modules/test-evaluation.nix @@ -1,21 +1,452 @@ # Run +# Test expression evaluation # -# nix-build test-evaluation.nix --dry-run +# $ nix build -f test-evaluation.nix rWrapper --dry-run +# +# Test building part of the packages set +# +# $ nix build -f test-evaluation.nix bioc_workflows --show-trace --verbose # # to test whether the R package set evaluates properly. +# To play with this in nix repl... + +# nix-repl> pkgs = import ../../.. {} +# nix-repl> p = import ./test-evaluation.nix +# nix-repl> builtins.typeOf p +# ... +# nix-repl> builtins.attrNames p.notMarkedBroken # for example + + + let config = { allowBroken = true; allowUnfree = true; + allowUnsupportedSystem = true; }; inherit (import ../../.. { inherit config; }) pkgs; + packagesList = pkgs.lib.filter pkgs.lib.isDerivation (pkgs.lib.attrValues pkgs.rPackages); + + opengl_names = [ + "rgl" + "abcdeFBA" + "afCEC" + "alphashape3d" + "animalTrack" + "bcROCsurface" + "BiodiversityR" + "bios2mds" + "BiplotGUI" + "bpca" + "brainR" + "ChaosGame" + "clippda" + "ConsRank" + "CoopGame" + "corregp" + "depth" + "DGVM3D" + "DiceView" + "DirichletReg" + "edrGraphicalTools" + "eegkit" + "etasFLP" + "fCI" + "FieldSim" + "foodweb" + "frontiles" + "gdimap" + "GENEAsphere" + "gensphere" + "geoelectrics" + "geomorph" + "GGEBiplotGUI" + "GPoM" + "hiPOD" + "hyper_fit" + "hypervolume" + "kml3d" + "lba" + "longitudinalData" + "LSAfun" + "Maeswrap" + "MDSGUI" + "metadynminer3d" + "mgcViz" + "molaR" + "mtk" + "mvmesh" + "nat" + "nat_nblast" + "nat_templatebrains" + "NeatMap" + "optBiomarker" + "plot3Drgl" + "qpcR" + "qtlc" + "QuantifQuantile" + "R330" + "RadOnc" + "RcmdrPlugin_RiskDemo" + "RcmdrPlugin_TeachingDemos" + "Rknots" + "ROCS" + "Rpdb" + "SEERaBomb" + "snpReady" + "sphereplot" + "TTMap" + "VecStatGraphs3D" + "AFM" + "AIG" + "analogueExtra" + "Anthropometry" + "archiDART" + "Arothron" + "barplot3d" + "BIGL" + "Biocomb" + "biplotbootGUI" + "Blaunet" + "brainKCCA" + "clusterSim" + "cncaGUI" + "colourvision" + "cops" + "corr2D" + "cowbell" + "cpr" + "crs" + "cubing" + "curvHDR" + "DeSousa2013" + "DiffusionRgqd" + "DiffusionRimp" + "DiffusionRjgqd" + "Directional" + "directPA" + "drugCombo" + "dti" + "ecdfHT" + "EMMIXcskew" + "EvolutionaryGames" + "feature" + "fingerPro" + "fsbrain" + "gbp" + "geoviz" + "gge" + "gMOIP" + "GPareto" + "GrammR" + "graphscan" + "HiveR" + "hmgm" + "homals" + "HUM" + "iCheck" + "iSDM" + "JointNets" + "KarsTS" + "kernhaz" + "KernSmoothIRT" + "lidR" + "LMERConvenienceFunctions" + "LOST" + "matlib" + "mcca" + "MDSMap" + "Morpho" + "morphomap" + "MSQC" + "multibiplotGUI" + "nanop" + "neuroim" + "NNS" + "nonlinearTseries" + "NPCirc" + "OceanView" + "OCNet" + "OMICsPCA" + "OpenRepGrid" + "OptimalDesign" + "orthoDr" + "pca3d" + "phylocurve" + "predict3d" + "prim" + "RAINBOWR" + "rase" + "rayshader" + "Rcade" + "rcosmo" + "RDRToolbox" + "restlos" + "retistruct" + "rglwidget" + "rLiDAR" + "RockFab" + "rotations" + "RoundAndRound" + "Rpolyhedra" + "Rquake" + "scpm" + "SDD" + "shapes" + "shinyRGL" + "SimEUCartelLaw" + "smoothAPC" + "sNPLS" + "spherepc" + "sppmix" + "StatDA" + "stpp" + "stR" + "Surrogate" + "symbolicDA" + "tensorsparse" + "tkrgl" + "tolerance" + "TreeLS" + "treespace" + "trinROC" + "TSCS" + "ungroup" + "vegan3d" + "vennplot" + "viewshed3d" + "x3ptools" + ]; + + java_names = [ + "rJava" + "AGread" + "AntAngioCOOL" + "AWR_KMS" + "AWR_Athena" + "arulesNBMiner" + "bartMachine" + "bartMachineJARs" + "BridgeDbR" + "causalMGM" + "CollapsABEL" + "collUtils" + "corehunter" + "deisotoper" + "edeR" + "ENVISIONQuery" + "extraTrees" + "gaggle" + "glmulti" + "GreedyExperimentalDesign" + "GreedyExperimentalDesignJARs" + "helloJavaWorld" + "InSilicoVA" + "iplots" + "ISM" + "JGR" + "mallet" + "MSIseq" + "mwa" + "Onassis" + "paxtoolsr" + "qCBA" + "rCBA" + "rcdklibs" + "rChoiceDialogs" + "Rdrools" + "Rdroolsjars" + "REPPlab" + "rGroovy" + "RH2" + "RJDBC" + "rJPSGCS" + "RJSDMX" + "rJython" + "rkafka" + "rkafkajars" + "rmcfs" + "RMOA" + "RNCBIEUtilsLibs" + "RNetLogo" + "RSCAT" + "rviewgraph" + "SBRect" + "scagnostics" + "SELEX" + "sjdbc" + "spcosa" + "streamMOA" + "venneuler" + "xlsxjars" + "ArrayExpressHTS" + "AWR" + "AWR.Athena" + "AWR.Kinesis" + "AWR.KMS" + "awsjavasdk" + "BACA" + "BASiNET" + "BEACH" + "beastier" + "blkbox" + "boilerpipeR" + "CADStat" + "CAMTHC" + "CBSr" + "ChoR" + "coreNLP" + "DatabaseConnector" + "DatabaseConnectorJars" + "debCAM" + "DecorateR" + "Deducer" + "dialr" + "dialrjars" + "dsa" + "esATAC" + "expands" + "fsdaR" + "G2Sd" + "gMCP" + "hive" + "jdx" + "joinXL" + "jsr223" + "llama" + "mailR" + "matchingMarkets" + "mdendro" + "mleap" + "MLMOI" + "mutossGUI" + "Myrrix" + "Myrrixjars" + "NoiseFiltersR" + "OnassisJavaLibs" + "openNLP" + "openNLPdata" + "OpenStreetMap" + "PortfolioEffectEstim" + "PortfolioEffectHFT" + "prcbench" + "Rbgs" + "rcdk" + "RDAVIDWebService" + "ReQON" + "RFreak" + "RGMQL" + "RJDemetra" + "RKEA" + "RKEAjars" + "RKEEL" + "rmelting" + "RMOAjars" + "rMouse" + "rrepast" + "RWeka" + "RWekajars" + "RxnSim" + "SqlRender" + "subspace" + "tabulizer" + "tabulizerjars" + "textmining" + "TSsdmx" + "wordnet" + "XLConnect" + "xlsx" + ]; + + # R with everything. Use --dry-run options to test evaluation. + # Otherwise "we're going to need a bigger box" rWrapper = pkgs.rWrapper.override { - packages = pkgs.lib.filter pkgs.lib.isDerivation (pkgs.lib.attrValues pkgs.rPackages); + packages = packagesList; }; + inherit (pkgs) lib; + inherit (lib) subtractLists filterAttrs getAttrs; + inherit (builtins) attrNames getAttr; + isBroken = (n: v: (lib.attrByPath ["meta" "broken"] false v)); + findBroken = s : lib.filterAttrs isBroken s; + findNotBroken = s : lib.filterAttrs (n: v: ! (isBroken n v) ) s; + + # broken and notbroken denotes the value of the meta.broken attribute + + fakeDerive = x1: x2: x2; + fakeSelf = {}; + importPkgNames = s: import s { self = fakeSelf; derive = fakeDerive; }; + + + inherit (pkgs) rPackages; + r_names = (attrNames rPackages); + + r_broken_names = attrNames (findBroken rPackages) ++ java_names ++ opengl_names; + r_notbroken_names = subtractLists r_broken_names r_names; + + bioc_names = attrNames (importPkgNames ./bioc-packages.nix); + bioc_notbroken_names = subtractLists r_broken_names bioc_names; + + bioc_annotation_names = attrNames (importPkgNames ./bioc-annotation-packages.nix); + bioc_annotation_notbroken_names = subtractLists r_broken_names bioc_annotation_names; + + bioc_experiment_names = attrNames (importPkgNames ./bioc-experiment-packages.nix); + bioc_experiment_notbroken_names = subtractLists r_broken_names bioc_experiment_names; + + bioc_workflows_names = attrNames (importPkgNames ./bioc-workflows-packages.nix); + bioc_workflows_notbroken_names = subtractLists r_broken_names bioc_workflows_names; + + cran_names = attrNames (importPkgNames ./cran-packages.nix); + cran_notbroken_names = subtractLists r_broken_names cran_names; + + + # not broken ones.. + bioc_pkgs = getAttrs bioc_notbroken_names rPackages; + bioc_annotation_pkgs = getAttrs bioc_annotation_notbroken_names rPackages; + bioc_experiment_pkgs = getAttrs bioc_experiment_notbroken_names rPackages; + bioc_workflows_pkgs = getAttrs bioc_workflows_notbroken_names rPackages; + cran_pkgs = getAttrs cran_notbroken_names rPackages; + in - rWrapper + +{ rpkgs = pkgs.rPackages; + inherit + # package sets + rWrapper # BIG! ~18K packages + rPackages # SAME + bioc_pkgs + bioc_annotation_pkgs + bioc_experiment_pkgs + bioc_workflows_pkgs + cran_pkgs # ~15K packages + + # names + r_names + r_notbroken_names + r_broken_names + bioc_names + bioc_notbroken_names + bioc_annotation_names + bioc_annotation_notbroken_names + bioc_experiment_names + bioc_experiment_notbroken_names + bioc_workflows_names + bioc_workflows_notbroken_names + cran_names + cran_notbroken_names + + # special names to test bug fixes + opengl_names + java_names + + # helper functions + isBroken + findBroken + findNotBroken + + ;} + diff --git a/pkgs/tools/misc/xvfb-run/default.nix b/pkgs/tools/misc/xvfb-run/default.nix index 889ab823a9c07..f5c1cd4a40219 100644 --- a/pkgs/tools/misc/xvfb-run/default.nix +++ b/pkgs/tools/misc/xvfb-run/default.nix @@ -14,13 +14,14 @@ stdenv.mkDerivation { buildCommand = '' mkdir -p $out/bin cp ${xvfb_run} $out/bin/xvfb-run - + patch -p1 $out/bin/xvfb-run $patchfile chmod a+x $out/bin/xvfb-run patchShebangs $out/bin/xvfb-run wrapProgram $out/bin/xvfb-run \ --set FONTCONFIG_FILE "${fontsConf}" \ --prefix PATH : ${stdenv.lib.makeBinPath [ getopt xorgserver xauth which utillinux gawk coreutils ]} ''; + patchfile = stdenv.lib.optionalString stdenv.isDarwin ./patches/xvfb-run.patch; meta = with stdenv.lib; { platforms = platforms.linux; diff --git a/pkgs/tools/misc/xvfb-run/patches/xvfb-run.patch b/pkgs/tools/misc/xvfb-run/patches/xvfb-run.patch new file mode 100644 index 0000000000000..490d7660ca5a1 --- /dev/null +++ b/pkgs/tools/misc/xvfb-run/patches/xvfb-run.patch @@ -0,0 +1,30 @@ +diff --git a/trunk/xvfb-run b/trunk/xvfb-run +index 9d088c1c28e..bdc79ce917e 100644 +--- a/trunk/xvfb-run ++++ b/trunk/xvfb-run +@@ -156,7 +156,10 @@ if [ -z "$AUTHFILE" ]; then + fi + + # Start Xvfb. +-MCOOKIE=$(mcookie) ++mcookie=`dd if=/dev/urandom bs=16 count=1 2>/dev/null | hexdump -e \\"%08x\\"` ++MCOOKIE="$mcookie" ++ ++ + + if [ -z "$AUTO_DISPLAY" ]; then + # Old style using a pre-computed SERVERNUM +@@ -182,8 +185,12 @@ DISPLAY=:$SERVERNUM XAUTHORITY=$AUTHFILE "$@" 2>&1 + RETVAL=$? + set -e + +-# Kill Xvfb now that the command has exited. ++ ++# Kill Xvfb now that the command has exited, ++# but don't die if you can't kill a zombie. ++set +e + kill $XVFBPID ++set -e + + # Clean up. + XAUTHORITY=$AUTHFILE xauth remove ":$SERVERNUM" >"$ERRORFILE" 2>&1