-
Notifications
You must be signed in to change notification settings - Fork 27
/
DESCRIPTION
112 lines (112 loc) · 4 KB
/
DESCRIPTION
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
Package: mia
Type: Package
Version: 1.13.36
Authors@R:
c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-5064-0928")),
person(given = "Sudarshan A.", family = "Shetty", role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-7280-9915")),
person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-8563-8884")),
person(given = "Leo", family = "Lahti", role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-5537-637X")),
person(given = "Yang", family = "Cao", role = c("ctb")),
person(given = "Nathan D.", family = "Olson", role = c("ctb"),
email = "[email protected]"),
person(given = "Levi", family = "Waldron", role = c("ctb")),
person(given = "Marcel", family = "Ramos", role = c("ctb")),
person(given = "Héctor", family = "Corrada Bravo", role = c("ctb")),
person(given = "Jayaram", family = "Kancherla", role=c("ctb")),
person(given = "Domenick", family = "Braccia",
email = "[email protected]", role=c("ctb")),
person(given = "Basil", family = "Courbayre", role=c("ctb")),
person(given = "Muluh", family = "Muluh", role=c("ctb")),
person(given = "Giulio", family = "Benedetti", role=c("ctb")),
person(given = c("Moritz", "Emanuel"), family = "Beber",
email = "[email protected]", role = c("ctb"),
comment = c(ORCID = "0000-0003-2406-1978")),
person(given = "Nitesh", family = "Turaga", role=c("ctb")),
person(given = "Chouaib", family = "Benchraka", role=c("ctb")),
person(given = "Akewak", family = "Jeba", role=c("ctb")),
person(given = "Himmi", family = "Lindgren", role=c("ctb")),
person(given = "Noah", family = "De Gunst", role=c("ctb")),
person(given = "Théotime", family = "Pralas", role=c("ctb")),
person(given = "Shadman", family = "Ishraq", role=c("ctb")),
person(given = "Eineje", family = "Ameh", role=c("ctb")),
person(given = "Artur", family = "Sannikov", role=c("ctb")),
person(given = "Hervé", family = "Pagès", role=c("ctb")),
person(given = "Rajesh", family = "Shigdel", role=c("ctb")),
person(given = "Katariina", family = "Pärnänen", role=c("ctb")),
person(given = "Pande", family = "Erawijantari", role=c("ctb")),
person(given = "Danielle", family = "Callan", role=c("ctb")))
Title: Microbiome analysis
Description:
mia implements tools for microbiome analysis based on the
SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment
infrastructure. Data wrangling and analysis in the context of taxonomic data
is the main scope. Additional functions for common task are implemented such
as community indices calculation and summarization.
biocViews: Microbiome, Software, DataImport
License: Artistic-2.0 | file LICENSE
Encoding: UTF-8
LazyData: false
Depends:
R (>= 4.0),
SummarizedExperiment,
SingleCellExperiment,
TreeSummarizedExperiment (>= 1.99.3),
MultiAssayExperiment
Imports:
methods,
stats,
utils,
MASS,
ape,
decontam,
vegan,
BiocGenerics,
S4Vectors,
IRanges,
Biostrings,
DECIPHER,
BiocParallel,
DelayedArray,
DelayedMatrixStats,
scuttle,
scater,
DirichletMultinomial,
rlang,
dplyr,
tibble,
tidyr,
bluster,
MatrixGenerics,
mediation,
rbiom
Suggests:
testthat,
knitr,
patchwork,
BiocStyle,
yaml,
phyloseq,
dada2,
stringr,
biomformat,
reldist,
ade4,
microbiomeDataSets,
rmarkdown,
rhdf5,
topicmodels,
topicdoc,
NMF
URL: https://github.com/microbiome/mia
BugReports: https://github.com/microbiome/mia/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
VignetteBuilder: knitr