Merge pull request #185 from satijalab/release/0.5.0

Version 0.5.0

DESCRIPTION

@@ -1,40 +1,46 @@
 Package: Azimuth
 Type: Package
 Title: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data
-Version: 0.4.6
-Date: 2022-08-23
+Version: 0.5.0
+Date: 2023-04-06
 Authors@R: c(
   person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
   person(given = "Charlotte", family = "Darby", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0003-2195-5300")),
   person(given = "Yuhan", family = "Hao", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-1810-0822")),
+  person(given = "Austin", family = "Hartman", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-7278-1852')),
   person(given = "Paul", family = "Hoffman", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
   person(given = "Jaison", family = "Jain", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
+  person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-8628-5056')),
   person(given = "Rahul", family = "Satija", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-9448-8833")),
   person("Satija Lab and Collaborators", role = "fnd")
   )
-Description: What the package does (one paragraph).
+Description: Azimuth uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery). 
 URL: https://github.com/satijalab/azimuth
 BugReports: https://github.com/satijalab/azimuth/issues
 License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 biocViews:
 Remotes:
   immunogenomics/presto,
+  satijalab/seurat-data,
   mojaveazure/seurat-disk,
-  satijalab/seurat-data
+  stuart-lab/signac@seurat5
 Depends:
   R (>= 4.0.0)
 Imports:
+  BSgenome.Hsapiens.UCSC.hg38,
   DT (>= 0.15),
+  EnsDb.Hsapiens.v86,
   future (>= 1.19.1),
   ggplot2 (>= 3.3.2),
   glmGamPoi (>= 1.0.0),
   googlesheets4 (>= 0.2.0),
   hdf5r (>= 1.3.2),
   htmltools (>= 0.5.0),
   httr (>= 1.4.2),
+  JASPAR2020, 
   jsonlite (>= 1.7.0),
   Matrix (>= 1.2.18),
   methods,
@@ -43,16 +49,17 @@ Imports:
   Rcpp (>= 1.0.7),
   rlang (>= 0.4.8),
   scales (>= 1.1.1),
-  Seurat (>= 4.0.0),
+  Seurat (>= 5.0.0),
   SeuratDisk,
-  SeuratObject,
+  SeuratObject (>= 5.0.0),
   SeuratData,
   shiny (>= 1.5.0),
   shinyBS (>= 0.61),
   shinydashboard (>= 0.7.1),
   shinyjs (>= 2.0.0),
   stats,
   stringr (>= 1.4.0),
+  TFBSTools,
   tools,
   utils,
   plotly,

Dockerfile

@@ -1,7 +1,9 @@
-FROM satijalab/seurat:4.1.0
+FROM satijalab/seurat:5.0.0
 
 RUN apt-get update
 RUN apt-get install -y libv8-dev
+RUN apt-get install -y libbz2-dev
+RUN apt-get install -y liblzma-dev
 
 RUN mkdir lzf
 WORKDIR /lzf
@@ -16,10 +18,12 @@ ENV HDF5_PLUGIN_PATH=/lzf
 
 COPY Rprofile.site /usr/local/lib/R/etc/Rprofile.site
 
-RUN R --no-echo -e "BiocManager::install(c('glmGamPoi'))"
-RUN R --no-echo -e "install.packages(c('DT', 'future', 'ggplot2',  'googlesheets4', 'hdf5r', 'htmltools', 'httr', 'patchwork', 'rlang', 'shiny', 'shinyBS', 'shinydashboard', 'shinyjs', 'stringr', 'withr'), repo='https://cloud.r-project.org')"
-RUN R --no-echo -e "remotes::install_github(c('immunogenomics/presto', 'mojaveazure/seurat-disk', 'satijalab/seurat-data'), dependencies = FALSE)"
+RUN R --no-echo -e "BiocManager::install(c('BSgenome.Hsapiens.UCSC.hg38', 'glmGamPoi', 'GenomeInfoDb', 'GenomicRanges', 'TFBSTools', 'JASPAR2020', 'EnsDb.Hsapiens.v86', 'IRanges', 'Rsamtools', 'S4Vectors'), force = TRUE)"
 
+RUN R --no-echo -e "install.packages('sp', repos='http://cran.us.r-project.org')"
+RUN R --no-echo -e "install.packages('Matrix', repos='http://R-Forge.R-project.org')"
+RUN R --no-echo -e "install.packages(c('data.table', 'DT', 'future', 'ggplot2',  'googlesheets4', 'hdf5r', 'htmltools', 'httr', 'patchwork', 'rlang', 'shiny', 'shinyBS', 'shinydashboard', 'shinyjs', 'Signac', 'stringr', 'withr'), repo='https://cloud.r-project.org')"
+RUN R --no-echo -e "remotes::install_github(c('immunogenomics/presto', 'mojaveazure/seurat-disk', 'satijalab/seurat-data'), dependencies = FALSE)"
 
 ARG AZIMUTH_VER=unknown
 RUN echo "$AZIMUTH_VER"

NAMESPACE

@@ -8,38 +8,65 @@ S3method(ReferenceVersion,AzimuthData)
 S3method(ReferenceVersion,Seurat)
 S3method(RunAzimuth,Seurat)
 S3method(RunAzimuth,character)
+S3method(RunAzimuthATAC,Seurat)
+S3method(RunAzimuthATAC,character)
 S3method(SetColorMap,AzimuthData)
 S3method(SetColorMap,Seurat)
 export(AzimuthApp)
+export(AzimuthBridgeReference)
 export(AzimuthReference)
+export(Connect)
 export(ConvertGeneNames)
 export(CreateAzimuthData)
 export(CreateColorMap)
 export(GetColorMap)
 export(GetPlotRef)
+export(LoadBridgeReference)
 export(LoadFileInput)
+export(LoadH5ADobs)
 export(LoadReference)
 export(ReferenceVersion)
 export(RunAzimuth)
+export(RunAzimuthATAC)
+export(SaveAzimuthReference)
 export(SetColorMap)
 export(ValidateAzimuthReference)
 exportClasses(AzimuthData)
+import(BSgenome.Hsapiens.UCSC.hg38)
+importFrom(BSgenome.Hsapiens.UCSC.hg38,BSgenome.Hsapiens.UCSC.hg38)
+importFrom(BiocGenerics,width)
 importFrom(DT,DTOutput)
 importFrom(DT,dataTableProxy)
 importFrom(DT,renderDT)
 importFrom(DT,selectRows)
+importFrom(EnsDb.Hsapiens.v86,EnsDb.Hsapiens.v86)
+importFrom(GenomeInfoDb,seqlevelsStyle)
+importFrom(GenomeInfoDb,seqnames)
+importFrom(GenomeInfoDb,standardChromosomes)
+importFrom(GenomicRanges,granges)
+importFrom(GenomicRanges,makeGRangesFromDataFrame)
+importFrom(IRanges,findOverlaps)
+importFrom(JASPAR2020,JASPAR2020)
+importFrom(Matrix,sparse.model.matrix)
 importFrom(Matrix,sparseMatrix)
+importFrom(S4Vectors,queryHits)
+importFrom(S4Vectors,subjectHits)
 importFrom(Seurat,Assays)
 importFrom(Seurat,AverageExpression)
+importFrom(Seurat,CreateAssayObject)
 importFrom(Seurat,DietSeurat)
 importFrom(Seurat,DimPlot)
 importFrom(Seurat,FeaturePlot)
+importFrom(Seurat,FindBridgeTransferAnchors)
 importFrom(Seurat,FindClusters)
 importFrom(Seurat,FindNeighbors)
 importFrom(Seurat,FindTransferAnchors)
+importFrom(Seurat,GetAssayData)
 importFrom(Seurat,IntegrateEmbeddings)
 importFrom(Seurat,LabelClusters)
 importFrom(Seurat,LoadAnnoyIndex)
+importFrom(Seurat,Loadings)
+importFrom(Seurat,MapQuery)
 importFrom(Seurat,MappingScore)
 importFrom(Seurat,MinMax)
 importFrom(Seurat,NoLegend)
@@ -60,11 +87,13 @@ importFrom(SeuratData,LoadData)
 importFrom(SeuratDisk,Connect)
 importFrom(SeuratObject,"DefaultAssay<-")
 importFrom(SeuratObject,"Idents<-")
+importFrom(SeuratObject,"Loadings<-")
 importFrom(SeuratObject,"Misc<-")
 importFrom(SeuratObject,"Tool<-")
 importFrom(SeuratObject,AddMetaData)
 importFrom(SeuratObject,Assays)
 importFrom(SeuratObject,Cells)
+importFrom(SeuratObject,CheckDots)
 importFrom(SeuratObject,CreateSeuratObject)
 importFrom(SeuratObject,DefaultAssay)
 importFrom(SeuratObject,Embeddings)
@@ -76,11 +105,28 @@ importFrom(SeuratObject,Key)
 importFrom(SeuratObject,Loadings)
 importFrom(SeuratObject,Misc)
 importFrom(SeuratObject,Reductions)
+importFrom(SeuratObject,RenameAssays)
 importFrom(SeuratObject,RenameCells)
 importFrom(SeuratObject,SetAssayData)
 importFrom(SeuratObject,Tool)
 importFrom(SeuratObject,VariableFeatures)
 importFrom(SeuratObject,as.Neighbor)
+importFrom(Signac,AddMotifs)
+importFrom(Signac,Annotation)
+importFrom(Signac,CreateChromatinAssay)
+importFrom(Signac,Extend)
+importFrom(Signac,FeatureMatrix)
+importFrom(Signac,FindMotifs)
+importFrom(Signac,FindTopFeatures)
+importFrom(Signac,Fragments)
+importFrom(Signac,GRangesToString)
+importFrom(Signac,GeneActivity)
+importFrom(Signac,GetGRangesFromEnsDb)
+importFrom(Signac,RunChromVAR)
+importFrom(Signac,RunSVD)
+importFrom(Signac,RunTFIDF)
+importFrom(TFBSTools,getMatrixSet)
+importFrom(data.table,as.data.table)
 importFrom(future,future)
 importFrom(future,plan)
 importFrom(future,resolved)
@@ -131,6 +177,7 @@ importFrom(plotly,plotlyOutput)
 importFrom(plotly,renderPlotly)
 importFrom(plotly,toWebGL)
 importFrom(presto,wilcoxauc)
+importFrom(rhdf5,h5read)
 importFrom(rlang,"%||%")
 importFrom(scales,hue_pal)
 importFrom(shiny,Progress)

NEWS.md

@@ -1,3 +1,10 @@
+# Azimuth 0.5.0 (2023-11-04)
+
+## Changes
+- Azimuth ATAC
+  - Functionality added to `RunAzimuth()` ([vignette here](https://satijalab.github.io/azimuth/articles/run_azimuth_tutorial.html#scatac-seq-queries)), to `AzimuthApp`, and to the [Azimuth Website](https://azimuth.hubmapconsortium.org/) to support sc/snATAC-seq queries. 
+- Compatibility with Seurat v5
+
 # Azimuth 0.4.6 (2022-08-23)
 
 ## Changes