forked from Isabelggayte/DEgenesHunter
-
Notifications
You must be signed in to change notification settings - Fork 4
/
Copy pathDESCRIPTION
126 lines (126 loc) · 4.08 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
113
114
115
116
117
118
119
120
121
122
123
124
125
126
Package: ExpHunterSuite
Title: Package For The Comprehensive Analysis Of Transcriptomic Data
Version: 1.7.2
Authors@R:
c(person(given = "James",
family = "Perkins",
role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-4108-096X")),
person(given = "Pedro",
family = "Seoane Zonjic",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-3020-1415")),
person(given = "Fernando",
family = "Moreno Jabato",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-7498-1962")),
person(given = "José",
family = "Córdoba Caballero",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-1821-5742")),
person(given = "Elena",
family = "Rojano Rivera",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-2678-710X")),
person(given = "Rocio",
family = "Bautista Moreno",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-1685-8119")),
person(given = "M. Gonzalo",
family = "Claros",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0002-0112-3550")),
person(given = "Isabel",
family = "Gonzalez Gayte",
role = c("aut"),
email = "[email protected]"),
person(given = "Juan Antonio",
family = "García Ranea",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0003-0327-1837"))
)
Description: The ExpHunterSuite implements a comprehensive protocol for the analysis of transcriptional data using established *R* packages and combining their results. It covers all key steps in DEG detection, CEG detection and functional analysis for RNA-seq data. It has been implemented as an R package containing functions that can be run interactively. In addition, it also contains scripts that wrap the functions and can be run directly from the command line.
Depends: R (>= 4.1.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
biocViews: GeneExpressionWorkflow
Suggests:
optparse,
PerformanceAnalytics,
naivebayes,
reshape2,
org.Hs.eg.db,
org.Mm.eg.db,
testthat (>= 3.0.0)
VignetteBuilder: knitr
Imports:
ReactomePA (>= 1.46.0),
limma (>= 3.58.0),
edgeR (>= 4.0.15),
NOISeq (>= 2.46.0),
biomaRt (>= 2.58.0),
topGO (>= 2.54.0),
diffcoexp (>= 1.22.0),
DT (>= 0.30),
ggplot2 (>= 3.4.4),
stringr (>= 1.5.0),
WGCNA (>= 1.72.1),
dplyr (>= 1.1.3),
BiocGenerics (>= 0.48.0),
enrichplot (>= 1.22.0),
rmarkdown (>= 2.25),
stats (>= 4.3.1),
Biobase (>= 2.62.0),
DESeq2 (>= 1.42.0),
ROCR (>= 1.0.11),
data.table (>= 1.14.8),
knitr (>= 1.44),
magrittr (>= 2.0.3),
SummarizedExperiment (>= 1.32.0),
miRBaseVersions.db (>= 1.1.0),
grDevices (>= 4.3.1),
graphics (>= 4.3.1),
utils (>= 4.3.1),
BiocParallel (>= 1.36.0),
MKinfer (>= 1.1),
matrixStats (>= 1.0.0),
ggupset (>= 0.3.0),
rlang (>= 1.1.1),
plyr (>= 1.8.9),
tidyr (>= 1.3.0),
GO.db (>= 3.18.0),
Matrix (>= 1.6.1.1),
fastcluster (>= 1.2.3),
DOSE (>= 3.28.0),
heatmaply (>= 1.5.0),
EnhancedVolcano (>= 1.20.0),
ggrepel (>= 0.9.4),
clusterProfiler (>= 4.11.0),
GenomicRanges (>= 1.54.0),
GenomicFeatures (>= 1.54.0),
tximport (>= 1.30.0),
annotatr (>= 1.28.0),
ggridges (>= 0.5.4),
FactoInvestigate (>= 1.8),
FactoMineR (>= 2.9),
cowplot (>= 1.1.1),
S4Vectors (>= 0.40.0),
OUTRIDER (>= 1.20.0),
MatrixGenerics (>= 1.14.0),
GenomeInfoDb (>= 1.38.0),
yaml (>= 2.3.7),
rtracklayer (>= 1.62.0),
AnnotationDbi (>= 1.64.0),
htmlreportR (>= 1.0.0)
Config/testthat/edition: 3