R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=
0.29.2), Biobase (>= 1.17.0), IRanges
R (>= 3.6.0), methods, utils, graphics, stats, parallel
R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13),
IRanges, XVector (>= 0.23.2)
R (>= 2.10), methods, Biobase (>= 2.5.5), marray
R (>= 3.1.2), methods, grid, graphics, stats, grDevices
R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid
R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>=
0.27.1), S4Vectors (>= 0.21.7), IRanges (>= 2.17.3),
BiocParallel
BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice
S4Vectors (>= 0.9.25), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
R (>= 2.7.0), methods, AnnotationDbi (>= 1.9.7)
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
R (>= 2.7.0), methods, AnnotationDbi (>= 1.43.1)
R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.25.3),
S4Vectors (>= 0.21.9)
R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.2.1), stats, methods, Rmpfr, gmp
R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>=
0.23.3)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 2.0.0), methods, utils, grDevices, graphics, stats,
BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6),
genefilter, gcrma
R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase,
DelayedArray (>= 0.3.20)
R (>= 3.2), mgcv, genefilter, BiocParallel
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils, zlibbioc
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), RCurl
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio, methods, ggplot2
methods, utils, graphics, stats, parallel
stats, utils, futile.logger, parallel, snow
bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
utils, XML, RCurl, AnnotationDbi, progress, stringr, httr
Biostrings, ipred, e1071, klaR, randomForest, class, tree,
nnet, rpart, party, foreign, Biobase, utils, stats, grDevices
graphics, stats, utils, methods, survival
AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7),
ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue,
rvcheck, stats, tidyr, utils
circlize (>= 0.4.5), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png
Biobase, ALL, graphics, stats, utils, cluster
methods, stats, utils, Biostrings, Biobase, dplyr, stringr,
purrr, ggplot2, data.table
genefilter, geneplotter, methods, MASS, RColorBrewer
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,
methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)
AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim
(>= 2.0.0), methods, qvalue, reshape2, S4Vectors, stats, utils
BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind,
tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils,
htmltools, htmlwidgets, RCurl
graphics, stats, utils, methods, locfit, Rcpp
AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2,
ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices,
grid, gridExtra, igraph, methods, purrr, RColorBrewer,
reshape2, stats, UpSetR, utils
methods, graphics, grDevices, stats, utils
data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
gridExtra, grid, fastmatch, Matrix, utils
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
S4Vectors (>= 0.9.42), AnnotationDbi, annotate, Biobase,
graphics, methods, stats, survival
AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils
stats, stats4, utils, RCurl, GenomeInfoDbData
httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma
ape, dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods,
purrr, rlang, rvcheck (>= 0.1.0), tidyr, tidytree (>= 0.2.4),
treeio (>= 1.7.3), utils
methods, slam, lpsymphony, fdrtool, BiocGenerics
IRanges, S4Vectors, GenomeInfoDb, BiocGenerics, methods,
Matrix, Rcpp
graphics, grDevices, methods, stats, utils
grDevices, graphics, stats, utils, methods
data.table, cometExactTest, RColorBrewer, NMF, methods,
wordcloud, grDevices, survival
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench, IHW
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, utils
XML, plyr, parallel, doParallel, foreach, iterators,
ProtGenerics
BiocGenerics (>= 0.27.1), Biobase (>= 2.17.8), methods,
graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7),
SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>=
1.23.2), ff, foreach, BiocManager, utils, S4Vectors (>=
0.9.25), RSQLite, DBI
methods, parallel, IRanges, GenomicRanges, GenomeInfoDb,
Biostrings, S4Vectors
grDevices, graphics, stats, methods, Biobase, gdsfmt,
GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf,
Matrix, dplyr, rlang, tidyr
stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
methods, utils, grDevices, graphics, stats, BiocGenerics,
Biobase, affy, genefilter, gcrma
graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3),
S4Vectors (>= 0.17.25), IRanges (>= 2.13.16), GenomeInfoDb (>=
1.13.1)
ape, MASS, grDevices, graphics, stats, utils
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma,
ape, dplyr, jsonlite, magrittr, methods, rlang, tibble,
tidytree (>= 0.2.3), utils
limma, matrixStats, locfit, stats, graphics
methods, utils, zlibbioc, BiocGenerics, S4Vectors, IRanges
tkWidgets (>= 1.19.0), affydata, widgetTools
hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,
rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,
org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit,
hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,
RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,
org.Hs.eg.db, reactome.db, AnnotationForge, graph,
EnsDb.Hsapiens.v75, BiocStyle, knitr
BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db
biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy,
hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens,
hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager
DESeq2, airway, knitr, rmarkdown, testthat
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
tools, tkWidgets, ALL, RUnit, golubEsets
Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,
AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,
DESeq2, MSnbase, annotate, RUnit
BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,
Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,
BiocStyle, knitr, batchtools, data.table
annotate, BiocStyle, knitr, rmarkdown, testthat
BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=
1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy
(>= 1.41.3), affydata (>= 1.11.5), RUnit
AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db,
prettydoc, ReactomePA, testthat
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg,
tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2,
glue, GenomicRanges
Matrix, HDF5Array, genefilter, SummarizedExperiment, airway,
pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit
testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW,
apeglm, ashr, tximport, tximportData, readr, pbapply, airway,
pasilla (>= 0.2.10)
prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat
BiocStyle, digest, knitr, rmarkdown, shiny
AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines
clusterProfiler, dplyr, knitr, org.Hs.eg.db, prettydoc
testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel, org.Mm.eg.db, limma, GEOquery
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
parallel, digest, crayon, RUnit, knitr, BiocGenerics
class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla,
RColorBrewer, BiocStyle, knitr
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db
GenomicRanges, Rsamtools, GenomicAlignments, BSgenome,
GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=
1.13.53), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,
DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14,
pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
BiocStyle
knitr, rmarkdown, BiocGenerics, testthat, covr
emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc,
rmarkdown, scales, testthat, tibble
vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS,
boot, rpart, mstate
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, testthat
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db,
gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines,
statmod (>= 1.2.2), vsn
knitr, rmarkdown, BSgenome, Biostrings, mclust, rjson
annotate, BiocGenerics, biomformat, knitr, gss, testthat (>=
0.8), vegan, interactiveDisplay
BiocStyle, knitr, rmarkdown, testthat, rgl
hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6,
pd.genomewidesnp.5, pd.mapping50k.hind240,
pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp,
genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6),
RUnit, human370v1cCrlmm, SNPchip, VanillaICE, crlmm
BiocGenerics, BiocStyle, knitr, multtest, rmarkdown, testthat
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, Rsamtools, VariantAnnotation
parallel, Matrix, RUnit, knitr, MASS, BiocGenerics
annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown,
digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit,
testthat
Hmisc, CPE, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
Biostrings, ggplot2, ggtree, knitr, phangorn, prettydoc,
testthat, tidyr
affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat
knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR
doMC, doMPI, doSNOW, doParallel, doRedis