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packages_versions.tab
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"Package" "Version" "Depends" "Imports"
"affy" "1.62.0" "R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)" "affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils, zlibbioc"
"affyio" "1.54.0" "R (>= 2.6.0)" "zlibbioc, methods"
"affyQCReport" "1.62.0" "Biobase (>= 1.13.16), affy, lattice" "affy, affyPLM, Biobase, genefilter, graphics, grDevices,
lattice, RColorBrewer, simpleaffy, stats, utils, xtable"
"AnnotationDbi" "1.46.1" "R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=
0.29.2), Biobase (>= 1.17.0), IRanges" "DBI, RSQLite, S4Vectors (>= 0.9.25)"
"arrayQualityMetrics" "3.40.0" "" "affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter,
graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter,
lattice, latticeExtra, limma, methods, RColorBrewer, setRNG,
stats, utils, vsn (>= 3.23.3), XML, svglite"
"Biobase" "2.44.0" "R (>= 2.10), BiocGenerics (>= 0.27.1), utils" "methods"
"BiocParallel" "1.18.0" "methods" "stats, utils, futile.logger, parallel, snow"
"biomaRt" "2.40.0" "methods" "utils, XML, RCurl, AnnotationDbi, progress, stringr, httr"
"clusterProfiler" "3.12.0" "R (>= 3.4.0)" "AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7),
ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue,
rvcheck, stats, tidyr, utils"
"convert" "1.60.0" "R (>= 2.6.0), Biobase (>= 1.15.33), limma (>= 1.7.0), marray,
utils, methods" NA
"DBI" "1.0.0" "R (>= 3.0.0), methods" NA
"DO.db" "2.9" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7)" "methods, AnnotationDbi"
"DOSE" "3.10.0" "R (>= 3.4.0)" "AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim
(>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils"
"enrichplot" "1.4.0" "R (>= 3.4.0)" "AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2,
ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices,
grid, gridExtra, igraph, methods, purrr, RColorBrewer,
reshape2, stats, UpSetR, utils"
"factoextra" "1.0.5" "R (>= 3.1.2), ggplot2 (>= 2.2.0)" "abind, cluster, dendextend, FactoMineR, ggpubr(>= 0.1.5),
grid, stats, reshape2, ggrepel, tidyr"
"FactoMineR" "1.41" "R (>= 3.0.0)" "car,cluster,ellipse,flashClust,graphics,grDevices,lattice,leaps,MASS,scatterplot3d,stats,utils"
"fgsea" "1.10.0" "R (>= 3.3), Rcpp" "data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
gridExtra, grid, fastmatch, Matrix, utils"
"geneplotter" "1.62.0" "R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate" "AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils"
"GEOquery" "2.52.0" "methods, Biobase" "httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma"
"ggplot2" "3.3.0" "R (>= 3.2)" "digest, glue, grDevices, grid, gtable (>= 0.1.1), isoband,
MASS, mgcv, rlang (>= 0.3.0), scales (>= 0.5.0), stats, tibble,
withr (>= 2.0.0)"
"GO.db" "3.8.2" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1)" "methods, AnnotationDbi"
"GOSemSim" "2.10.0" "R (>= 3.4.0)" "AnnotationDbi, GO.db, methods, utils"
"hgu133plus2.db" "3.2.3" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.34.3), org.Hs.eg.db
(>= 3.3.0)" "methods, AnnotationDbi"
"hgu95av2.db" "3.2.3" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.34.3), org.Hs.eg.db
(>= 3.3.0)" "methods, AnnotationDbi"
"HsAgilentDesign026652.db" "3.2.3" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.34.3), org.Hs.eg.db
(>= 3.3.0)" "methods, AnnotationDbi"
"illuminaHumanv4.db" "1.26.0" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.29.20),
org.Hs.eg.db (>= 3.1.2)" "methods, AnnotationDbi"
"limma" "3.40.0" "R (>= 2.3.0)" "grDevices, graphics, stats, utils, methods"
"marray" "1.62.0" "R (>= 2.10.0), limma, methods" NA
"MetaDE" "2.2.3" NA "survival, limma, samr, edgeR, DESeq2, impute, Biobase,
combinat"
"mouse4302.db" "3.2.3" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.34.3), org.Mm.eg.db
(>= 3.3.0)" "methods, AnnotationDbi"
"oligo" "1.48.0" "R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>=
1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12)" "affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1),
ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>=
1.0.0), splines, stats, stats4, utils, zlibbioc"
"org.Hs.eg.db" "3.8.2" "R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1)" "methods, AnnotationDbi"
"pheatmap" "1.0.12" "R (>= 2.0)" "grid, RColorBrewer, scales, gtable, stats, grDevices, graphics"
"RColorBrewer" "1.1-2" "R (>= 2.0.0)" NA
"sdef" "1.7" "R (>= 2.10)" "graphics,grDevices,stats,utils"
"simpleaffy" "2.60.0" "R (>= 2.0.0), methods, utils, grDevices, graphics, stats,
BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6),
genefilter, gcrma" "methods, utils, grDevices, graphics, stats, BiocGenerics,
Biobase, affy, genefilter, gcrma"
"UpSetR" "1.3.3" "R (>= 3.0)" "ggplot2, gridExtra, plyr, utils, stats, methods, grDevices,
scales"
"VennDiagram" "1.6.20" "R (>= 2.14.1), grid (>= 2.14.1), futile.logger" NA
"WriteXLS" "4.1.0" NA "utils"
"XML" "3.98-1.19" "R (>= 2.13.0), methods, utils" NA
"stats" "3.6.3" NA "utils, grDevices, graphics"
"utils" "3.6.3" NA NA