a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm,
genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots
methods, a4Core, a4Preproc, MLInterfaces, ROCR, pamr, glmnet,
varSelRF
R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata
R (>= 2.10),methods,Biobase,limma,affy (>=
1.22),preprocessCore,affycoretools
R (>= 3.2.0), grid, GenomicRanges, SummarizedExperiment (>=
0.2.0), GenomicAlignments
R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings,
hypergraph
R (>= 2.15.0), rnaSeqMap (>= 2.17.1), knitr, rgl, ggplot2,
gplots, parallel, doParallel, foreach,
VariantAnnotation,genefilter,statmod,xtable
R (>= 3.3.3), SummarizedExperiment(>= 1.1.6)
R (>= 3.3), GenomicRanges, cowplot, AneuFinderData
R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db
R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=
0.15.10), Biobase (>= 1.17.0), IRanges
R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges
(>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.7.10)
R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy,
lumi
methods, grDevices, stats, utils, parallel
R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
prettydoc, yaml
R (>= 3.0.0), Biostrings, GenomicAlignments, caTools,
GenomicRanges
R (>= 2.3.0), methods, GenomicRanges, abind, parallel
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase
R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr
R (>= 3.3), wateRmelon (>= 1.19.1), gdsfmt (>= 1.0.4),
methods, methylumi, minfi (>= 1.21.0), Biobase
magrittr (>= 1.5), ggplot2 (>= 1.0.0), lubridate (>= 1.3.3),
tidyr (>= 0.3.1), cgdsr, RCurl, XML
methods, utils, graphics, stats, parallel
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
limma, MASS, R(>= 2.10), Biobase, methods
R (>= 2.15.2), methods, S4Vectors, IRanges (>= 1.17.24),
GenomicRanges, SummarizedExperiment (>= 0.2.0), Formula
ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel,
Biobase
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 3.3), methods, BiocGenerics, GenomicRanges (>= 1.23.7),
SummarizedExperiment (>= 0.1.1), parallel
R (>= 3.3), IRanges, GenomicRanges, plyr, dplyr, magrittr
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 2.10), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23),
GenomeInfoDb, GenomicRanges, foreach, iterators, methods,
parallel, locfit
R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio
R (>= 2.14.0), Biobase, binom, methods, stats
BiocGenerics, Biobase, graphics, matter, methods, stats,
ProtGenerics
R (>= 2.14.1), Biobase, IRanges, methods, GenomicRanges
methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix
R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase,
utils
R (>= 2.10), RColorBrewer, Biobase, methods, genefilter,
splots, vsn, hwriter, locfit, grid
R (>= 2.15.0), RBGL, graph, methods, hash, ggplot2, RCurl,
Rgraphviz, XML
R (>= 2.10), methods, Biobase (>= 2.5.5), marray
R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall
R (>= 3.3), minfi, ChAMPdata (>= 2.6.0), FEM (>= 3.1),DMRcate,
Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest
R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter
Biobase, GenomicRanges (>= 1.13.3), Rsamtools (>= 1.13.1),
GenomicAlignments, methods, AnnotationDbi,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Homo.sapiens
Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors,
ensembldb, AnnotationFilter
R (>= 3.2), methods, grid, IRanges (>= 2.5.27), Biostrings,
GenomicRanges (>= 1.23.16), S4Vectors (>= 0.9.25), VennDiagram
R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19)
R (>= 2.10), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.9.25), IRanges (>= 1.99.1), GenomicRanges (>= 1.17.7),
ShortRead
R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25)
R (>= 3.1.0), GenomicRanges, methods, Biobase, MASS, graphics,
stats, changepoint
stats, utils, graphics, grDevices, datasets, base, biomaRt,
GenomicRanges, R (>= 3.1.0)
R (>= 3.3), GenomicRanges, ggplot2, chromstaRData
R (>= 3.0.3), methods, Biobase, BiocParallel
R (>= 2.15), BiocGenerics (>= 0.1.0), methods, BSgenome,
BSgenome.Drerio.UCSC.danRer7, GenomicRanges, seqinr, e1071
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.3), methods, SummarizedExperiment
R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats,
utils
R (>= 3.0), Biobase, methods, ff, oligoClasses, snow
R (>= 2.12), methods, utils, stats, graphics, parallel,
GenomicRanges
R (>= 2.10), methods, tools, stats, genefilter
brglm, doParallel, foreach, GenomicRanges, methods,
splitstackshape
R (>= 3.0.0), methods, VariantAnnotation, parallel, rjags,
ggplot2, gridExtra
R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>=
2.17.8), limma
R (>= 3.2.3), Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19, IRanges, Biostrings, S4Vectors
R, grid, utils, biomaRt, Gviz, psych, ggbio, trackViewer
R (>= 3.1.1), methods, topGO, GenomicRanges
R (>= 3.1.2), grid, graphics, stats, grDevices
R (>= 2.10), BiocGenerics, IRanges, GenomicRanges,
BiocParallel
R (>= 3.0), minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylationEPICmanifest
R (>= 2.14), igraph, shiny, arules, methods
R (>= 3.3.2), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer
R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0)
R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
R (>= 3.3.0), shiny, shinyjs, CRISPRseek
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
R (>= 3.4), GenomicRanges, SummarizedExperiment (>= 1.2.0),
BiocParallel
R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt
R (>= 3.3), shiny, ConsensusClusterPlus, RColorBrewer, gplots,
plyr, ggplot2, jsonlite, ape, WGCNA, RTCGAToolbox
R (>= 3.0.1), methods, biomaRt, grImport, grid, motifStack
R (>= 3.4), SummarizedExperiment, ggplot2
R (>= 3.3.0), shiny, ggvis, jsonlite, shinyjs
R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1),
stats, parallel
R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid
R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges,
GenomicRanges, SummarizedExperiment, Biostrings, VGAM,
VariantAnnotation (>= 1.13.44),
R (>= 3.4), methods, BiocGenerics, S4Vectors (>= 0.14.3),
IRanges, matrixStats
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice
S4Vectors (>= 0.9.25), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
BiocParallel, Biobase, SummarizedExperiment, IRanges (>=
2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11),
AnnotationDbi, RColorBrewer, S4Vectors
R (>= 3.3.0), GenomicRanges, SummarizedExperiment
R (>= 3.4), GenomicRanges, InteractionSet,
SummarizedExperiment
R (>= 3.2), GenomicRanges, IRanges, S4Vectors
R (>= 2.4.0), KEGG.db, prada, biomaRt, methods
R (>= 3.0.0), BSgenome.Mmusculus.UCSC.mm10, GenomicRanges,
VariantAnnotation
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
blockmodeling, gplots, testthat, R (>= 3.0.0)
isa2, Biobase (>= 2.17.8), AnnotationDbi, methods
R (>= 3.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
Homo.sapiens, ELMER.data
parallel,doParallel,foreach, SummarizedExperiment (>=
1.1.6),minfi (>= 1.22.0)
R (>= 3.1.2), grid, ComplexHeatmap (>= 1.11.1), GenomicRanges,
IRanges, locfit
R(>= 3.0.0), Biobase, GSEABase, pathview
BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.23.21),
GenomicFeatures (>= 1.23.18), AnnotationFilter (>= 0.99.7)
R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment
R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase
R (>= 3.4), SGSeq, Matrix, SummarizedExperiment
IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools
Rsamtools, GenomicFeatures (>= 1.14.5), rtracklayer,
GenomicAlignments
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 2.5.9)
utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData
(>= 1.1.4)
R (>= 3.2.0), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2
caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db,
AnnotationDbi
R (>= 3.0), methods, cgdsr (>= 1.1.30), coin (>= 1.0),
ggplot2, gridExtra, facopy.annot, grid
methods, LiquidAssociation, parallel, stats, Hmisc
R (>= 3.3.0), S4Vectors, IRanges, GenomicRanges, grid
R (>= 3.1),FNN, psych, gtools, zoo, rgl, grid, VennDiagram
R (>= 2.15.0), methods, Biobase, rrcov, flowCore
R (>= 2.10.0), methods, BiocGenerics, outliers, lattice,
flowViz, mvoutlier, bioDist, parody, RColorBrewer, latticeExtra
R (>= 2.10), flowCore, fda (>= 2.2.6), cluster, flowWorkspace,
ncdfFlow(>= 2.19.5)
R (>= 2.11.0), flowCore, flowViz,flowClust
R (>= 3.2), methods, flowCore, flowViz, flowStats
R (>= 3.0), GenomicRanges, ggplot2, DESeq2 (>= 1.9.11),
splines, methods, LSD
R (>= 2.14.0), ggplot2, TxDb.Hsapiens.UCSC.hg19.knownGene,
FunciSNP.data
R (>= 2.8.0), Biobase, coda, EBarrays, mgcv
R (>= 3.0.0), compiler, GA, graph, heatmap.plus, png,
Rgraphviz
Biobase, gCMAP (>= 1.3.0), methods, R (>= 3.4), Rook
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0),
methods, XML, RSQLite, MASS, Heatplus, RColorBrewer
R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges
survcomp, mclust, limma,biomaRt, iC10, AIMS, R (>= 2.10)
R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter
R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods
R (>= 3.3), Rsamtools (>= 1.18.2), SummarizedExperiment (>=
1.1.19), GenomicRanges (>= 1.23.16), methods
R (>= 2.10), methods, BiocGenerics (>= 0.15.3), S4Vectors (>=
0.13.13), IRanges (>= 2.5.36), GenomeInfoDb (>= 1.11.5),
GenomicRanges (>= 1.27.19), SummarizedExperiment (>= 1.5.3),
Biostrings (>= 2.37.1), Rsamtools (>= 1.21.4)
R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges
(>= 1.23.21), SummarizedExperiment, BiocParallel (>= 1.1.0),
Rsamtools (>= 1.17.29), rtracklayer (>= 1.25.3)
R (>= 3.4), S4Vectors (>= 0.7.21), GenomicRanges, methods,
BiocGenerics (>= 0.13.8)
R (>= 2.10), methods, RSQLite, DBI (>= 0.2-5), BiocGenerics
(>= 0.1.0), IRanges (>= 2.5.27), GenomeGraphs
R (>= 2.10), BiocGenerics (>= 0.11.3), GenomicRanges (>=
1.17.19), SummarizedExperiment (>= 1.1.6)
R(>= 3.3), randomForest, e1071, ggplot2, effsize, Biostrings,
rjags
methods, BiocGenerics, ggplot2 (>= 1.0.0)
R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel,
Homo.sapiens
R (>= 2.10.0), methods, BiocGenerics (>= 0.13.8), S4Vectors
(>= 0.7.21), Rsamtools, intervals (>= 0.13.1), ShortRead (>=
1.3.21), genomeIntervals (>= 1.25.1), grid
R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0)
R (>= 3.1.0), GenomicAlignments (>= 1.0.1), VariantAnnotation
R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2)
R (>= 2.15.1), methods, utils, GenomicRanges, Biostrings,
BSgenome, data.table
R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.9.25), IRanges
(>= 2.5.27), GenomeInfoDb, GenomicRanges (>= 1.23.16),
GenomicAlignments, rtracklayer
R (>= 3.3), penalized, Iso, survival, GSEABase, BiocGenerics,
Biobase, annotate, methods, graph,stats
shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5,
R(>= 2.10.0)
R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures,
AnnotationDbi
R (>= 3.1.2), grid, IRanges, GenomicRanges
R (>= 3.2.0), GenomicRanges, BiocGenerics
Rsamtools, GenomicFeatures, rtracklayer, GenomicAlignments,
GenomicRanges, ggplot2, grid, IRanges
R(>= 2.10.0), survival, coin, fpc, clusterRepro, impute,
randomForestSRC, sm, sigaR, Biobase
R (>= 3.4), methods, DelayedArray (>= 0.2.4), rhdf5
methods, BiocGenerics, S4Vectors (>= 0.11.6), IRanges (>=
2.7.11), GenomicRanges (>= 1.27.1), Biostrings (>= 2.41.3),
BSgenome, GenomicFeatures, VariantAnnotation (>= 1.19.3),
Rsamtools, GenomicAlignments, rtracklayer (>= 1.33.8),
GenomeInfoDb, SummarizedExperiment
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
Biostrings, GenomicAlignments, BiocParallel, hiAnnotator, R
(>= 3.0)
R (>= 2.15.0), methods, IRanges, GenomicRanges
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase,
S4Vectors, IRanges, methods, MASS, BSgenome, GenomeInfoDb (>=
1.1.3), GenomicRanges (>= 1.17.11)
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
Biobase, IRanges, GenomicRanges, RColorBrewer,
rtracklayer,graphics,GenomeInfoDb
R (>= 2.10), methods, Biobase, annotate, plotrix
R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
R(>= 3.2), methods, stats, graphics, grid, lattice, flowCore
graphics, grDevices, stats, utils, parallel, compiler, R (>=
3.2.3)
R (>= 3.1), methods, Biobase, GenomicRanges, GenomicFeatures,
S4Vectors
R (>= 3.2), methods, Biobase, BiocParallel
R (>= 2.14.0), plyr, ggbio, GenomicRanges
R (>= 3.4), GenomicRanges, SummarizedExperiment (>= 1.1.6)
R (>= 2.10), methods, BiocGenerics, grid
R (>= 3.4), GenomicRanges, Rsamtools, SummarizedExperiment,
edgeR, S4Vectors
R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest
xcms (>= 1.50.0), rsm, CAMERA, grDevices, graphics, stats,
utils
R (>= 2.12.0), MASS, Matrix, XML, digest, bitops
R (>= 3.1.0), methods, utils, stats, BiocGenerics (>= 0.21.1),
S4Vectors (>= 0.13.17)
R (>= 3.2), DiscriMiner, IRanges, S4Vectors (>= 0.9.25),
GenomicRanges, SummarizedExperiment (>= 1.1.6)
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (> 3.0.0),GenomicFeatures, ggplot2, Biobase
R (>= 3.4.0), methods, SummarizedExperiment (>= 0.2.0)
R (>= 3.4), regioneR, GenomicRanges, methods
R (>= 2.13.2), methods, graphics, fdrtool
R (>= 2.10.0), Biobase (>= 2.5.5), multtest, survival, affy
R (>= 2.10), convert, graph, limma, marray, methods
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
RUnit, BiocGenerics, BiocParallel, GenomicRanges,
SummarizedExperiment
R (>= 3.3.0), stats, gplots, gtools,graphics,base,
utils,grDevices
lattice, MASS, proto, foreign, gWidgets(>= 0.0-36),
gWidgetsRGtk2(>= 0.0-53), OTUbase, vegan, bpca
R (>= 2.15), grDevices, graphics, methods, stats, utils
R (>= 2.10.0), survival, Biobase, MASS, methods
R (>= 3.0.1), fdrtool, Category, BiocGenerics, methods,
cummeRbund, org.Hs.eg.db, MeSH.db, MeSH.AOR.db, MeSH.PCR.db,
MeSHDbi, MeSH.Hsa.eg.db, MeSH.Aca.eg.db, MeSH.Bsu.168.eg.db,
MeSH.Syn.eg.db, S4Vectors
R (>= 3.2.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
R (>= 2.13.0), EDASeq, DESeq, limma, qvalue
R (>= 3.3), metagenomeSeq (>= 1.17.1), methods, data.table,
Biobase, digest
R (>= 3.1.2), stringr, seqinr, gplots, Biostrings
R (>= 2.11.0), Biostrings(>= 2.4.8), plotrix,gsubfn,
grid,sqldf
R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb,
GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db
R (>= 3.3.0), GenomicRanges (>= 1.18.1), methods
R (>= 3.2.0), methods, grDevices, graphics, stats, utils,
GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools
Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
R (>= 3.0.2), MASS, plyr, reshape, Biobase, ggplot2
R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,
ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats,
cluster, marray, mclust, RColorBrewer, colorspace, igraph,
Rgraphviz, graph, annotate, Hmisc, fastICA, JADE
methods, BiocGenerics (>= 0.15.3), GenomicRanges,
SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>=
1.1.9)
R (>= 3.2), Biobase (>= 2.22.0), miRcompData
R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata,
KernSmooth
R (>= 2.9), methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools
R (>= 3.0.0), caret, DESeq2, Biobase, limma, randomForest,
edgeR
R (>= 2.13.0), methods, Biobase, xtable, limma, statmod,
lattice, vsn
R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges,
Biostrings
R (>= 2.15), Biostrings (>= 2.26), IRanges, seqLogo, parallel,
methods, grid, graphics, BSgenome, XVector,
BSgenome.Hsapiens.UCSC.hg19
R (>= 2.15.1), methods, grImport, grid, MotIV, ade4,
Biostrings
R (>= 3.1), methods, BiocGenerics (>= 0.7.1), Biobase (>=
2.15.2), mzR (>= 2.7.6), BiocParallel, ProtGenerics (>= 1.5.1)
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors
R (>= 2.14.0), flowCore(>= 1.37.15), RcppArmadillo, methods,
BH
R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
Biobase, affylmGUI, tkrplot, tkWidgets, IRanges, Rsamtools (>=
1.13.1), Biostrings, siggenes, chimera
R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10),
AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.23.31)
R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>=
1.23.15), Biobase, vegan
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 3.0.0), methods, Biobase, BiocGenerics,
R (>= 2.7.0), methods, utils, RSQLite, Biobase (>= 1.17.0),
AnnotationDbi (>= 1.3.12)
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.3.0), methods, ggplot2, gridExtra
R (>= 2.10), methods, BiocGenerics, Rcpp, Gviz
R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats,
ppiData, annotate (>= 1.17.4)
R (>= 3.0.1), IRanges, GenomicRanges, Biostrings (>= 2.26.3),
data.table, rTANDEM
R (>= 2.10), GO.db, KEGG.db, AnnotationDbi, annaffy, methods,
Biobase (>= 2.5.5)
R (>= 2.12.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2
R(>= 2.15.0), chipseq, IRanges, GenomicRanges
R (>= 2.10), flowCore, flowViz, lattice, latticeExtra
R (>= 3.1.0), methods, DBI (>= 0.5-1), RSQLite (>= 1.1),
BiocGenerics, S4Vectors
R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 3.2.0), methods, Rsamtools, GenomicRanges
biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb,
yeastExpData
R (>= 2.10), Biobase, RColorBrewer, grid, methods, rrcov
R (>= 2.14.0), GenomicAlignments, affy, RPA
R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
methods, annotate
R (>= 2.10), methods, WGCNA, MSnbase, flashClust
R (>= 3.2.2), methods, IRanges, biomaRt, BiocGenerics, httr,
plyr
R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods,
stats, utils, mclust, oligoClasses
R (>= 3.3), DNAcopy, VariantAnnotation (>= 1.14.1)
reshape, ggplot2, Biostrings, biovizBase, brew, xtable,
Rsamtools (>= 1.19.38), testthat
parallel, GenomicRanges (>= 1.13.3), Rbowtie
GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
R (>= 2.12.0), methods, VariantAnnotation, Biostrings, Biobase
R (>= 3.2.1), stats, methods, Rmpfr, gmp
R (>= 3.0.2), GenomicRanges, VariantAnnotation
R (>= 2.14.0), methods, GenomicRanges, Rsamtools, baySeq
R (>= 3.2), Biobase, rcdk, fingerprint, rcellminerData
R (>= 2.14.1), methods, graph, GOstats, ggplot2
R (>= 2.15.0), BiocGenerics (>= 0.1.0),
BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome,
ChIPpeakAnno
R (>= 2.15.0), methods, IRanges, PSICQUIC, AnnotationHub,
RCurl, shiny
memoise, GenomicRanges, BSgenome, rtracklayer, parallel
R (>= 3.4), SummarizedExperiment(>= 1.1.6), minfi (>= 1.22.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R (>= 3.0.0), methods, BiocGenerics (>= 0.8.0)
Rsamtools, GenomicRanges, IRanges, data.table, methods,
parallel
R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
R (>= 2.6.0), methods, utils, graph, grid
R (>= 3.1.2), GenomicRanges, IRanges, methods
R (>= 3.0.2), methods, GenomicRanges, abind
methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix,
grid, lattice
R (>= 2.15), methods, S4Vectors (>= 0.9.25), IRanges,
GenomicRanges, SummarizedExperiment, Rsamtools,
GenomicAlignments, rtracklayer
R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice
R (>= 3.3.0), edgeR, gplots, org.Mm.eg.db, GO.db
R (>= 2.11.0), methods, Biobase, Rsamtools, GenomicAlignments
R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25),
GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2),
gplots, gridExtra, limma, matrixStats, methods, illuminaio,
methylumi, plyr
R (>= 3.1.0), Biobase, ggplot2, limma, methods
R (>= 2.10), pracma, reshape, plotrix, microRNA, biomaRt,
Biostrings, Biobase, DBI
methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz
R (>= 3.1.1), affy, BiocGenerics, methods, phyloseq
methods, annotate (>= 1.21.0), graph (>= 1.21.0), Biobase,
RBGL (>= 1.17.0), XML (>= 2.4.0), hypergraph (>= 1.15.2),
AnnotationDbi
methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.21.6),
Biostrings (>= 2.37.1)
R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
R (>= 3.3), methods, GenomicRanges (>= 1.21.20)
R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>=
0.21.1)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 2.10), GO.db, RpsiXML, annotate, apComplex
R (>= 3.4), methods, SummarizedExperiment
R (>= 2.14.0), STRINGdb, methods, BiocGenerics, Biostrings,
IRanges, plyr, tcltk
R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
GenomicRanges, ShortRead, stats
R (>= 3.1), AnnotationDbi, GO.db, annotate
IRanges, GenomicRanges (>= 1.23.21), Rsamtools,
SummarizedExperiment, methods
methods, BiocGenerics (>= 0.3.2), shiny (>= 0.13.2), minfi (>=
1.18.2), IlluminaHumanMethylation450kmanifest, matrixStats, R
(>= 3.0.0)
rTANDEM (>= 1.3.5), shiny, mixtools, methods, xtable
BiocGenerics (>= 0.22.1), BiocParallel, Biostrings (>=
2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
methods, Biobase, multtest, splines, graphics
R (>= 2.0.0), methods, utils, grDevices, graphics, stats,
BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6),
genefilter, gcrma
R (>= 3.1), methods, BiocGenerics, Biobase,
SummarizedExperiment, survival, CoxBoost
R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
R (>= 3.1), GenomicRanges, Rsamtools, data.table, checkmate
R (>= 3.2.0), BiocGenerics, SummarizedExperiment
R (>= 3.1.0), VariantAnnotation, GenomicRanges, NMF
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 2.15.0), methods, cummeRbund, rtracklayer, VennDiagram,
RColorBrewer, plyr
methods,rbamtools (>= 2.14.3),refGenome (>=
1.6.0),Biobase,Biostrings (>= 2.28.0)
GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
Rgraphviz (>= 2.3.7)
R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines,
GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
R (>= 3.3.1), EBcoexpress, MASS, igraph, pvclust (>= 2.0-0),
gbm (>= 2.1.1), limma, DMwR (>= 0.4.1), matrixStats, Hmisc
R (>= 2.12), methods, qvalue, lattice, limma
R (>= 2.14), randomForest, MAclinical, tspair, pamr, snowfall,
glmpath, penalized, e1071, Biobase
R (>= 3.4), Biobase, BiocParallel, cluster, matrixStats,
stats, graphics, utils
R (>= 3.2), methods, GenomicRanges (>= 1.27.22), Biobase,
DelayedArray (>= 0.1.9)
R (>= 3.2), mgcv, genefilter, BiocParallel
R (>= 3.2.1), methods, GenomicRanges, Rsamtools (>= 1.20.4),
ggplot2, plyr, openxlsx
R (>= 2.15), methods, DESeq, DESeq2, edgeR, baySeq, ROC
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.3.0), methods, utils, ProtGenerics
graphite (>= 1.16), gRbase, graph, locfit, Rgraphviz
R (>= 3.1.0), grDevices, methods, GenomicRanges, grid
R (>= 2.15.0), methods, limma, sigPathway, samr, anota, DESeq,
edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus,
gplots, plotrix, Biobase
R (>= 2.15.2), methods, BiocGenerics, Biobase
methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8)
R (>= 3.0.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb
(>= 1.11.4), GenomicRanges (>= 1.27.6), SummarizedExperiment
(>= 1.5.3), Rsamtools (>= 1.23.10)
R (>= 3.0.0), methods, BiocGenerics (>= 0.13.8),
VariantAnnotation (>= 1.13.29)
S4Vectors (>= 0.9.25), IRanges (>= 1.99.2), GenomicRanges (>=
1.17.7), VariantAnnotation (>= 1.11.16), methods
R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel,
foreach
R (>= 2.10), Biobase, limma, methods, matrixStats, methylumi,
lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
illuminaio
R (>= 3.2), GenomicRanges (>= 1.23.16), Rsamtools
oligo, oligoClasses, Biobase, Biostrings, GenomeGraphs
R (>= 2.5.0), digest, tools, utils, codetools
R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
R (>= 2.14.0), methods, Biobase, BiocParallel (>= 1.8.0),
MSnbase (>= 2.1.10)
R (>= 2.10.0), Biobase (>= 2.5.5), methods, graphics
R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 3.3.0), GenomicRanges, ggplot2, grid
Biobase, graphics, grDevices, methods, multtest, stats, tcltk,
utils
Biobase, cluster, grDevices, graphics, methods, multtest,
stats, survival, splines, utils
bit, ffbase, DNAcopy, tilingArray, waveslim, cluster, aCGH,
snapCGH
AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGG.db (>= 1.8.1), methods,
multtest (>= 1.6.0), stats (>= 2.1.0)
affyio (>= 1.13.3), BiocInstaller, graphics, grDevices,
methods, preprocessCore, stats, utils, zlibbioc
affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi,
ggplot2, gplots, oligoClasses, ReportingTools, hwriter,
lattice, S4Vectors, edgeR, RSQLite, BiocGenerics
affxparser (>= 1.16.0), affy, graphics, methods, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, BiocInstaller,
R2HTML, xtable
affy, affyPLM, Biobase, genefilter, graphics, grDevices,
lattice, RColorBrewer, simpleaffy, stats, utils, xtable
S4Vectors, IRanges, GenomicRanges, SummarizedExperiment,
BiocParallel
methods, BiocGenerics, AnnotationDbi, BSgenome,
VariantAnnotation, Biostrings, S4Vectors (>= 0.9.25), IRanges,
Rsamtools, GenomicFeatures, Gviz, lattice, latticeExtra,
gridExtra, seqinr, GenomeInfoDb, nlme
Biostrings, IRanges, GenomicRanges, GenomicAlignments,
Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm,
splines, graph, RBGL, stringr, stats, methods, graphics,
GenomeInfoDb, S4Vectors
methods, log4r, tools, rjson, Biobase, graph
stats, DBI, limma, lumi, agricolae, RMySQL, DESeq2,
SummarizedExperiment, gplots, gage, S4Vectors
ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils,
plyr, DESeq2
methods, utils, grDevices, graphics, stats, foreach,
doParallel, BiocGenerics, S4Vectors, GenomeInfoDb, IRanges,
Rsamtools, bamsignals, DNAcopy, Biostrings, GenomicAlignments,
ggplot2, reshape2, ggdendro, ggrepel, ReorderCluster, mclust
DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice,
Rsamtools, genefilter, IRanges, BiocGenerics
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), RCurl
methods, utils, DBI, RSQLite, stats4, BiocGenerics, Biobase,
S4Vectors (>= 0.9.25), IRanges
utils, methods, grDevices, RSQLite, BiocInstaller,
AnnotationDbi (>= 1.31.19), S4Vectors, interactiveDisplayBase,
httr, yaml
GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics,
jsonlite, BiocInstaller, biocViews, AnnotationDbi, Biobase,
Biostrings, DBI, GEOquery, GenomeInfoDb, OrganismDbi, RSQLite,
rBiopaxParser, AnnotationForge, futile.logger (>= 1.3.0), XML,
RCurl
AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures,
GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges,
methods, org.Dm.eg.db, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, readr, regioneR, reshape2, rtracklayer,
S4Vectors, stats, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Rnorvegicus.UCSC.rn5.refGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene, utils
Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges,
Hmisc, IRanges, R2HTML, RColorBrewer, Rsamtools, ShortRead,
XML, biomaRt, edgeR, grDevices, graphics, methods, rJava,
stats, svMisc, utils, sendmailR, bitops
graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
affy, affyPLM (>= 1.27.3), beadarray, Biobase, Cairo (>=
1.4-6), genefilter, graphics, grDevices, grid, gridSVG (>=
1.4-3), Hmisc, hwriter, lattice, latticeExtra, limma, methods,
RColorBrewer, setRNG, stats, SVGAnnotation (>= 0.9-0), utils,
vsn (>= 3.23.3), XML
affy, Biobase, graphics, grDevices, limma, methods, stats,
utils, xtable
methods, foreach, S4Vectors (>= 0.9.25), DNAcopy, oligoClasses
(>= 1.21.3)
DESeq2, DEXSeq, GenomicRanges, GenomicFeatures, edgeR,
BiocGenerics, IRanges, GenomicAlignments, Gviz, S4Vectors,
AnnotationDbi, limma
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils
BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges,
GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid,
limma, Rsamtools, randomForest, rtracklayer, stats, stringr
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy,
reshape2, scales, coda, foreach, ggplot2, methods, utils,
graphics, stats
VariantAnnotation, Rsamtools, biomaRt, GenomicRanges,
S4Vectors, utils, stats, grDevices, graphics
GenomicRanges (>= 1.17.25), IRanges (>= 1.99.22), S4Vectors
(>= 0.9.39), RColorBrewer, splines, sva, limma, rtracklayer (>=
1.29.25), Biobase (>= 2.25.0), GenomeInfoDb
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges, zlibbioc
ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
magrittr, DT, lazyeval, ShortRead
utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva,
corpcor, moments, matrixStats, ggvis, d3heatmap, reshape2,
limma, grDevices, graphics, stats, methods, Matrix
SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices,
GenomicRanges, IRanges, Biostrings
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio
data.table, RCurl, digest, methods, stats, utils, dplyr,
graph, Biobase
dplyr (>= 0.4.3), htmlwidgets, Biobase, geNetClassifier,
AnnotationFuncs, org.Hs.eg.db, DOSE, clusterProfiler,
reactome.db, ReactomePA, plyr, grDevices, stats, utils,
DiagrammeR(>= 0.7), visNetwork, car, MASS (>= 7.3), gridExtra
(>= 2.0.0), AlgDesign (>= 1.1.7.3), psych (>= 1.4.8.11),
GPArotation (>= 2014.11.1), wordcloud (>= 2.5), markdown (>=
0.7.4), knitr (>= 1.8), ggdendro (>= 0.1.17), broom (>= 0.3.7),
pryr (>= 0.1), shiny (>= 0.13.2), jsonlite (>= 0.9.17),
shinyAce (>= 0.1), DT (>= 0.1), readr (>= 0.1.1), data.tree(>=
0.2.1), yaml(>= 2.1.13), scales(>= 0.2.5), curl(>= 0.9.1), covr
(>= 1.2.0), stringr (>= 1.0), tibble
biocViews (>= 1.33.7), BiocInstaller, graph, httr, tools,
optparse, codetools, methods, utils
methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, httr
Rgraphviz, geneplotter, graph, BiocGenerics, methods
org.Hs.eg.db, AnnotationDbi, reactome.db, graph, methods,
utils
stats, utils, futile.logger, parallel, snow
bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils,
yaml
Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit
BiocStyle, bookdown, rmarkdown, tools, stringr, httr, knitr,
utils
RCurl, rjson, rcdk (>= 3.3.2), foreach, doParallel,
Biostrings, GOSemSim, ChemmineR, fmcsR, pls, randomForest,
utils, stats, graphics, methods, org.Hs.eg.db, ChemmineOB
igraph (>= 1.0.1), AnnotationDbi, Biobase
Biostrings, ipred, e1071, klaR, randomForest, class, tree,
nnet, rpart, party, foreign, Biobase, utils, stats, grDevices
methods, e1071, randomForest, ropls, Biobase
BiocGenerics, Biobase, methods, grid, graphics, NMF
tmle, limma, foreach, parallel, doParallel, ggplot2,
wesanderson, magrittr, dplyr, stats, Matrix, methods,
SummarizedExperiment, superheat, SuperLearner, biotmleData
grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,
BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>= 1.99.28),
GenomeInfoDb (>= 1.5.14), GenomicRanges (>= 1.23.21),
SummarizedExperiment, Biostrings (>= 2.33.11), Rsamtools (>=
1.17.28), GenomicAlignments (>= 1.1.16), GenomicFeatures (>=
1.21.19), AnnotationDbi, VariantAnnotation (>= 1.11.4),
ensembldb (>= 1.99.13), AnnotationFilter (>= 0.99.8)
MASS, limma(>= 3.22.0), glmnet, Biobase, nem, graphics, stats,
utils
methods, BiocGenerics, Biobase, S4Vectors, IRanges,
GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer,
parallel, betareg, lokern, Formula, globaltest
beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8),
BiocGenerics, grDevices, stats, graphics
assertthat, methods, MASS, doParallel, parallel, e1071, earth,
foreach, randomForest, stats, IRanges, S4Vectors, data.table,
graphics
plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt,
Biostrings, parallel, utils, BSgenome.Hsapiens.UCSC.hg38,
rtracklayer, GenomicRanges, IRanges, S4Vectors, data.table
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
rtracklayer
IRanges (>= 2.5.17), GenomeInfoDb, scales, stats, graphics,
Biobase, locfit, gtools, data.table, S4Vectors, R.utils (>=
2.0.0), matrixStats (>= 0.50.0), permute, limma, DelayedArray
(>= 0.2.1), HDF5Array
BiocGenerics (>= 0.7.5), BiocStyle, Biobase, ggplot2,
WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra,
biovizBase, e1071, methods, grDevices, stats, utils
devtools, stringi, gtools, stats, utils, SummarizedExperiment,
Biostrings, IRanges
matrixStats, limma, doRNG, BiocGenerics, utils,
GenomicFeatures, AnnotationDbi
affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase
utils, Rsamtools, GenomicRanges (>= 1.23.16), IRanges (>=
2.5.27), data.table, beanplot, rtracklayer, som, VGAM
methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph
GSEABase, GSEAlm, tkrplot, geNetClassifier, RUnit, Formula,
rpart, survival, Biobase, phenoTest, circlize, plyr, graphics,
stats, utils
SNFtool, iCluster, survival, cluster, impute, limma,
ConsensusClusterPlus, grDevices
grid, irlba, lattice, signal, sp, stats4, utils
BiocGenerics, coda, EBarrays, gaga, gtools, GenomeInfoDb,
GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors
(>= 0.9.25), sqldf, survival, VGAM
flowCore, ggplot2, graphics, grDevices, grid, gridExtra,
matrixStats, methods, plotly, RColorBrewer, stats, utils
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCytoscape (>= 1.5.11)
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
prada, GSEABase, Category, stats4, BiocGenerics
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
topicmodels, slam, maptpx, igraph, xtable, gplots
Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
Biobase, CGHbase, CGHcall, methods, stats, utils
sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
limma,RPMM, DNAcopy, preprocessCore,impute, marray, wateRmelon,
plyr,goseq,missMethyl,
GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly
(>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat
BSgenome, Biobase, oligo (>= 1.11.31), oligoClasses(>=
1.17.39), ff, preprocessCore, methods, stats, Biostrings,
IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils,
limma, parallel, sva(>= 3.1.2)
BiocGenerics, zlibbioc, Rcpp (>= 0.11.0)
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra
matrixStats, MASS, Hmisc, Delaporte, methods, grDevices,
graphics, stats, utils
methods, readr, grid, Rsamtools, GenomeInfoDb,
GenomicAlignments, RColorBrewer, graphics, AnnotationDbi,
RCircos, org.Hs.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr,
BiocStyle, ArgumentCheck
AnnotationDbi, BiocGenerics, chipenrich.data (>= 1.11.4),
GenomeInfoDb, GenomicRanges, grDevices, grid, IRanges, lattice,
latticeExtra, methods, mgcv, org.Dm.eg.db, org.Dr.eg.db,
org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, parallel, plyr, rms,
rtracklayer, S4Vectors, stats, stringr, utils
methods, GenomeInfoDb, stats, BiocParallel, GenomicRanges (>=
1.14.4), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools (>=
1.16.1), IRanges (>= 1.6), S4Vectors (>= 0.8), biovizBase (>=
1.18), broom (>= 0.4), RColorBrewer (>= 1.1), dplyr (>= 0.5),
scales (>= 0.4.0), viridis (>= 0.3), hexbin (>= 1.27),
rmarkdown
BiocGenerics (>= 0.1.0), GO.db, biomaRt, BSgenome,
GenomicFeatures, GenomeInfoDb, matrixStats, AnnotationDbi,
limma, multtest, RBGL, graph, BiocInstaller, stats, regioneR,
DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments,
DelayedArray, SummarizedExperiment, Rsamtools
BiocGenerics (>= 0.11.3), S4Vectors (>= 0.1.0), IRanges (>=
1.99.17), Rsamtools (>= 1.17.28), GenomicAlignments (>=
1.1.16), chipseq (>= 1.12.0), gtools, BiocParallel, methods,
reshape2, Nozzle.R1, Biobase, grDevices, stats, utils,
GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Celegans.UCSC.ce6.ensGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene
AnnotationDbi, BiocGenerics, boot, DOSE (>= 3.0.0), IRanges,
GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2 (>=
2.2.0), gplots, graphics, grDevices, grid, gridBase, gtools,
methods, plotrix, dplyr, parallel, magrittr, RColorBrewer,
rtracklayer, S4Vectors, stats,
TxDb.Hsapiens.UCSC.hg19.knownGene, UpSetR, utils
methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges,
ShortRead
Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14),
graphics, grDevices, HilbertVis, ShortRead, stats, timsac,
utils
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
Biobase, GEOquery, frma, affy, bigmemory, biganalytics
Biobase (>= 2.17.8), graphics, grDevices, methods, stats,
IRanges, rtracklayer, GenomicRanges
methods, utils, grDevices, graphics, stats, foreach,
doParallel, S4Vectors, GenomeInfoDb, IRanges, reshape2,
Rsamtools, GenomicAlignments, bamsignals, mvtnorm
XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx,
circlize, graph, stats, utils, grDevices, graphics, methods,
biomaRt
bitops,gplots,grDevices,som,
dplyr,gridExtra,png,stringr,S4Vectors, IRanges,
GenomeInfoDb,graphics, stats, utils
methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor, RBGL
NMF, RColorBrewer, ape, phylobase, cluster, stats, limma,
dendextend, howmany, locfdr, matrixStats, graphics, parallel,
MAST
AnnotationDbi, ggplot2, GO.db, GOSemSim (>= 2.0.0), magrittr,
methods, plyr, qvalue, rvcheck, stats, stats4, tidyr, utils
methods, pracma, princurve, scatterplot3d, RColorBrewer,
grDevices, graphics, utils, stats
DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb,
S4Vectors, exomeCopy
Rcpp (>= 0.12.1), S4Vectors (>= 0.9.25), matrixStats,
RColorBrewer, gtools, combinat, IRanges, GenomeInfoDb,
GenomicRanges, methods, BiocGenerics, graphics, stats, coda,
SummarizedExperiment
S4Vectors, grDevices, stats, utils, NOISeq, IRanges,
Rsamtools, exomeCopy, foreach, ggplot2, plyr, openxlsx
methods, seqinr, yaml, rtfbs, gplots, mclust, gmp,
BiocGenerics (>= 0.13.8), IRanges, Biostrings, BSgenome,
biomaRt
RColorBrewer (>= 1.0.5), gplots (>= 2.8.0), graphics,
grDevices, methods, cluster, shiny, stats, utils, doParallel,
foreach, ggplot2, reshape2
methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, dplyr, devtools
colortools, hash, grDevices, gridExtra, rtracklayer, IRanges,
S4Vectors, GenomicRanges, ggplot2, stats, corrplot
methods, Rcpp, data.table, methods, RColorBrewer, scales,
grid, plyr, knitr, abind, clue, grDevices, utils, pdist
tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16),
gplots, gtools, gdata, caTools, grid, KernSmooth, MASS,
ggplot2, stringr, modeest, edgeR, limma, vioplot, methods
AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel,
grDevices, gplots, IRanges, GenomicFeatures, XVector,
methylPipe, GO.db, S4Vectors, GenomeInfoDb
rtracklayer, Rgraphviz, ggplot2, GenomicFeatures,
TxDb.Mmusculus.UCSC.mm9.knownGene, pcaMethods, reshape2,
pathview
methods, circlize (>= 0.3.4), GetoptLong, colorspace,
RColorBrewer, dendextend (>= 1.0.1), GlobalOptions (>= 0.0.10)
Biobase, ALL, graphics, stats, utils, cluster
GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods
grDevices, clue, cluster, gplots, IRanges, GenomicRanges,
S4Vectors, Rcpp, TSP, GenomicFiles, gtools, rtracklayer,
BiocParallel, DNAcopy, colorspace, reshape2, ggplot2, methods,
exomeCopy, GenomicAlignments, diagram
methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges,
GenomeInfoDb
matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges,
Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges,
CopyhelpeR, GenomeInfoDb, futile.logger
MASS, gplots, lattice, grDevices, graphics, stats
edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2
(>= 2.1.0), scales, HTSFilter, corrplot, HTSCluster (>= 2.0.8),
gridExtra, grDevices, graphics, stats, methods, compositions,
mvtnorm
maptpx, slam, plyr(>= 1.7.1), cowplot, gtools, flexmix,
picante, limma, parallel, reshape2, stats, utils, graphics,
grDevices
S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges,
GenomicAlignments, parallel, tools
parallel, genefilter, grDevices, stats, graphics
methods, corpcor, BiocParallel, ggplot2, plyr
parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges,
BSgenome, BiocParallel, hash
DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures,
BiocInstaller, BSgenome, AnnotationDbi, hash
AnnotationDbi, BiocParallel, Biostrings, methods,
GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices,
grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>=
0.9.38), utils
methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
matrixStats, VGAM, parallel, graphics, limma, beanplot
Rsamtools, edgeR, limma, GenomicFeatures, AnnotationDbi,
methods, S4Vectors, IRanges, GenomeInfoDb, BiocGenerics,
Rhtslib, stats
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges,
Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>=
2.26.3), GenomicFeatures (>= 1.17.13), biomaRt (>= 2.17.1),
stringr, RCurl, plyr, VariantAnnotation (>= 1.13.44),
rtracklayer, RSQLite, AnnotationDbi, AhoCorasickTrie, methods
plotrix, viridis, methods, shiny, graphics, stats, grDevices,
S4Vectors, flowCore, Biobase
tcltk, grDevices, graphics, utils, stats, Rtsne, e1071,
flowCore, gplots, colourpicker, VGAM, reshape2, ggrepel, shiny,
shinyFiles, vegan, Biobase, doParallel, parallel, pdist,
methods, destiny, FlowSOM(>= 1.4.0), igraph(>= 1.1.2), RANN(>=
2.5), Rcpp (>= 0.12.0)
flowCore, flowWorkspace (>= 3.21.10), openCyto (>= 1.11.3),
XML, data.table, flowUtils (>= 1.35.7), jsonlite, RBGL,
ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics, utils,
base64enc, plyr
DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap,
FactoMineR, corrplot, randomForest, e1071, caret, MASS,
lubridate, plsVarSel, kknn, FSelector, methods, stats, utils,
graphics, grDevices, reshape2
MSnbase, RColorBrewer,stats,preprocessCore,Cairo,png,
lattice,reshape2,gplots,pcaMethods,ggplot2,
limma,knitr,tmvtnorm,norm,impute, imputeLCMD, doParallel,
parallel, foreach,grDevices, graphics, openxlsx, utils, cp4p
(>= 0.3.5), scales, Matrix, vioplot, imp4p (>= 0.3),
highcharter, DAPARdata
methods, stats, utils, ggplot2, fdrtool, reshape2,
GenomicRanges, SummarizedExperiment, smoothmest, plyr, tidyr,
assertthat, S4Vectors, purrr, soGGi, ChIPpeakAnno
Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice,
BiocGenerics
bnlearn (>= 2.8), gtools, pcalg, RColorBrewer, plotrix, MASS
DT, ggplot2, RColorBrewer, annotate, gplots, AnnotationDbi,
DESeq2, DOSE, igraph, grDevices, graphics, stats, utils,
GenomicRanges, IRanges, S4Vectors, SummarizedExperiment,
stringi, reshape2, baySeq, d3heatmap, org.Hs.eg.db,
org.Mm.eg.db, limma, edgeR, clusterProfiler, V8, methods, sva,
shinydashboard, devtools, RCurl
methods, DBI, S4Vectors, IRanges, XVector
GenomicRanges, data.table, stringr, diffr, dplyr, methods,
rjson, utils, R.utils, foreach, withr, rtracklayer,
GenomeInfoDb, settings, filehash
checkmate, DESeq2, edgeR (>= 3.13.4), GenomicRanges, methods,
stats, SummarizedExperiment
graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL,
Rgraphviz, rrcov, NCIgraph
utils, methods, ggplot2, ggrepel, Nozzle.R1, coda, edgeR,
cluster, logging, dplyr, tidyr, reshape, pheatmap, grid,
gridExtra, knitr, grDevices, stats
graphics, grDevices, methods, stats, utils
AnnotationDbi (>= 1.27.9), BiocParallel, bumphunter (>=
1.9.2), derfinderHelper (>= 1.1.0), GenomeInfoDb (>= 1.3.3),
GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges
(>= 1.17.40), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>=
1.99.0), Rsamtools (>= 1.25.0), rtracklayer, S4Vectors (>=
0.9.38)
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3),
GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>=
1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28),
limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>=
0.9.38), scales, utils
genefilter, geneplotter, methods, MASS, RColorBrewer
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,
methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)
methods, graphics, grDevices, utils, stats, Matrix, Rcpp (>=
0.10.3), RcppEigen, Biobase, BiocGenerics, ggplot2, Hmisc, FNN,
VIM, proxy, igraph, smoother, scales, scatterplot3d
graph, igraph, RBGL, circlize, limma, edgeR, samr, EBSeq,
NBPSeq, DESeq, stats, grDevices, graphics, pheatmap, utils,
ggplot2, Matrix, jsonlite, tools, DESeq2, methods
BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
RColorBrewer, amap, edgeR, gplots, grDevices, limma,
GenomicAlignments, locfit, stats, utils, IRanges, zlibbioc,
lattice, systemPipeR, tools, Rcpp, dplyr, ggplot2,
BiocParallel, parallel, S4Vectors, Rsamtools, DESeq2, methods,
graphics, ggrepel
graphics, grDevices, minpack.lm (>= 1.0-4), stats, utils
Rsamtools, Rhtslib, Biostrings, BSgenome, rhdf5, edgeR, limma,
csaw, locfit, methods, IRanges, S4Vectors, GenomeInfoDb,
BiocGenerics, grDevices, graphics, stats, utils
methods, GenomicRanges, foreach, plyr, dplyr, reshape2,
ggplot2, matrixStats, Sushi, edgeR, locfit, statmod, biomaRt,
GenomeInfoDb, S4Vectors, IRanges, grDevices, graphics, stats,
utils, Biobase, readr, data.table, rtracklayer, pbapply, limma
Biobase, stats, biwt, gtools, MASS, tools
limma, missMethyl, GenomicRanges, parallel, methods, graphics,
plyr, Gviz, IRanges, stats, utils, S4Vectors
Matrix, MASS, RcppRoll, ggplot2, methods, mvtnorm, stats,
parallel
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, utils
annotate, annotationTools, biomaRt, Biobase, BiocGenerics,
corpcor, doParallel, foreach, fpc, hwriter, IRanges, iterators,
mclust, QTLRel, regress, rhdf5, Rsamtools, RUnit, XML
AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim
(>= 2.0.0), graphics, grDevices, grid, igraph, methods, qvalue,
reshape2, S4Vectors, scales, stats, stats4, utils
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
stats, Rcpp (>= 0.11.3), ggplot2, reshape2, GO.db,
org.Hs.eg.db, AnnotationDbi, graphics
Biobase (>= 2.31.3), BiocGenerics (>= 0.17.2), BiocParallel
(>= 1.5.1), biomaRt (>= 2.27.2), Biostrings (>= 2.39.3), DESeq
(>= 1.23.0), edgeR (>= 3.13.4), GenomeInfoDb (>= 1.7.3),
genomeIntervals (>= 1.27.0), GenomicAlignments (>= 1.7.3),
GenomicRanges (>= 1.23.16), SummarizedExperiment (>= 1.1.11),
graphics, IRanges (>= 2.5.27), LSD (>= 3.0), locfit, methods,
parallel, Rsamtools (>= 1.23.1), S4Vectors (>= 0.9.38),
ShortRead (>= 1.29.1), utils
Biobase, cluster, graphics, grDevices, lattice, methods, stats
BiocGenerics (>= 0.7.1), methods, graphics, grDevices, stats,
abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils
methods, graphics, BiocGenerics, IRanges (>= 1.13.9), DESeq,
aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings,
AnnotationDbi, GenomicFeatures, GenomicRanges
graphics, stats, utils, parallel, methods, ROCR, DESeq,
baySeq, snow, edgeR
methods, splines, sva, snm, jackstraw, qvalue(>= 1.99.0), MASS
R.utils, gplots, sna, wordcloud, igraph, pheatmap, edgeR,
DESeq2, clusterProfiler, S4Vectors, ggplot2, org.Hs.eg.db,
org.Mm.eg.db, limma, DOSE, AnnotationDbi
gplots, Biobase, GEOquery, limma, arrayQualityMetrics, impute,
RColorBrewer, zoo, igraph, plyr, Matrix, MASS, RCurl, affy
PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0),
limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5),
hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0),
safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap,
grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1)
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, gespeR,RcppAnnoy
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
tools, jsonlite, parallel, RCurl, tidyr, data.table, dplyr,
stringr, stringi
AnnotationDbi, ComplexHeatmap, DESeq2, EDASeq, GO.db,
KEGGREST, KEGGgraph, MASS, ReportingTools, Rgraphviz,
S4Vectors, SPIA, SummarizedExperiment, biocGraph, edgeR,
geneplotter, graph, hwriter, limma, methods, safe, topGO
methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb,
AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors,
AnnotationHub, Rsamtools, IRanges, ProtGenerics, Biostrings,
curl
S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment,
GenomeInfoDb, stats
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
BoolNet, e1071, gtools, stats, igraph, nem, utils, lattice,
latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph
epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4),
GenomicRanges, S4Vectors, IRanges
S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0),
OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb
git2r, epivizrServer, GenomeInfoDb, BiocGenerics,
GenomicFeatures, S4Vectors
edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr,
QuasiSeq, qvalue, reshape2, ROCR, scales, stringr
GenomicFiles (>= 1.5.2), rtracklayer, S4Vectors, BiocGenerics,
GenomicRanges, SummarizedExperiment, ggplot2, Biobase, shiny,
foreach, AnnotationDbi
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices
GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls,
limma, matrixStats, RBGL, prodlim, graph, methods, utils,
stats, doParallel, foreach, affxparser, GenomicRanges,
S4Vectors
methods, ExperimentHub, BiocInstaller, DBI, BiocCheck, httr,
curl
methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi
methods, graphics, grDevices, stats, utils
annotate, data.table, DOSE, FactoMineR, GO.db, GOstats,
graphite, igraph, S4Vectors, IRanges, MASS, nnet, reshape2,
Rgraphviz, scales
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
affy, MASS, Biobase (>= 1.13.41), methods, graphics
methods, graphics, stats, BiocGenerics, S4Vectors, IRanges
fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap,
grDevices, stats, utils
tcltk, graphics, grDevices, stats, utils
Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2,
RColorBrewer, png
data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
gridExtra, grid, fastmatch
methods, BiocGenerics, Biobase, tools, dplyr, IRanges,
Biostrings, S4Vectors, kebabs, igraph, Matrix, digest,
filehash, Rcpp, ggplot2, gtable, grid, reshape2, ggdendro,
BiocParallel, utils, stats
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
gplots, graphics, MASS, methods, SparseM, stats, utils
methods, Matrix, IRanges, GenomicRanges, parallel
ggplot2, flowCore, plyr, changepoint, knitr, reshape2,
RColorBrewer, scales, methods, graphics, stats, utils
methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid
BiocGenerics, MCMCpack, methods, Biobase, graph, RBGL,
ellipse, flowViz, flowCore, clue, mnormt
Biobase, BiocGenerics (>= 0.1.14), graph, graphics, methods,
rrcov, stats, utils, stats4, corpcor, Rcpp, matrixStats
flowCore, graphics, car, gplots, RFOC, GEOmap, methods,
grDevices
flowCore, flowViz, graphics, kza, methods, minpack.lm, gplots
Biobase, BiocGenerics (>= 0.1.6), graphics, grDevices,
methods, stats, stats4
Biobase, graphics, grDevices, methods, rrcov, stats, feature,
flowCore
rrcov,flowCore, graphics, methods, stats, utils
flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny,
methods, graphics, stats, utils
methods, BiocGenerics, geneplotter, flowCore, flowViz, IRanges
methods, flowCore (>= 1.32.0), stats, extremevalues
flowCore, ConsensusClusterPlus, BiocGenerics, tsne, XML,
flowUtils
BiocGenerics, MASS, flowViz, flowCore, fda (>= 2.2.6),
Biobase, methods, grDevices, graphics, stats, utils,
KernSmooth, lattice,ks
flowCore, methods, flowViz, stats, flowClust
Biobase, graphics, grDevices, methods, flowCore, flowMeans,
sfsmisc, rrcov, flowClust, flowMerge, stats
Biobase, graph, methods, stats, utils, corpcor, RUnit, XML,
flowCore (>= 1.32.0)
stats4, Biobase, flowCore, graphics, grDevices, grid,
KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer,
stats, utils, hexbin,IDPmisc
Biobase, BiocGenerics, graph, graphics, lattice, methods,
stats, stats4, utils, RBGL, XML, tools, gridExtra, Rgraphviz,
data.table, dplyr, latticeExtra, Rcpp, RColorBrewer, stringr,
scales, flowViz
RUnit, methods, ChemmineR, BiocGenerics, parallel
DESeq2, Biobase, Biostrings, GenomicRanges,
SummarizedExperiment, Rsamtools, ggbio, reshape2, rtracklayer,
fda, GenomicAlignments, gtools, Matrix
Biobase, MASS, DBI, affy, methods, oligo, oligoClasses,
preprocessCore, utils, BiocGenerics
Biobase, DBI, methods, preprocessCore, stats, utils
shiny, fda, doParallel, GenomicAlignments, Rcpp, methods,
foreach, parallel, GenomeInfoDb, Rsamtools, grDevices,
graphics, stats, RColorBrewer
methods, BiocGenerics, Biobase, S4Vectors, IRanges,
GenomicRanges, Rsamtools (>= 1.6.1), rtracklayer (>= 1.14.1),
ChIPpeakAnno (>= 2.2.0), VariantAnnotation, plyr, snpStats,
ggplot2 (>= 0.9.0), reshape (>= 0.8.4), scales
pls, matrixStats, minfi, methods,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb,
grDevices, graphics, stats
BiocGenerics, Biostrings, dplyr, GenomeInfoDb, GenomicRanges,
httr, IRanges, jsonlite, methods, purrr, VariantAnnotation
BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings,
BSgenome, GenomicRanges, Rsamtools, GenomicAlignments,
matrixStats, MASS, splines, grDevices, graphics, stats, methods
Biobase, methods, GSEAlm, Category, Matrix (>= 1.0.9),
parallel, annotate, genefilter, AnnotationDbi, DESeq,
grDevices, graphics, stats, utils, bigmemory, bigmemoryExtras
(>= 1.1.2)
brew, BiocGenerics, annotate, AnnotationDbi, graphics,
grDevices, GSEABase, hwriter, parallel, stats, utils, yaml
Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db,
rmarkdown, grDevices, graphics, stats, utils, parallel
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocInstaller
MASS, hypergea (>= 1.3.0), gplots, Rcpp (>= 0.11.3), graphics,
stats, utils
tcltk, ggplot2, methods, stats, grDevices, graphics, utils
graphics, grDevices, methods, stats, tcltk, utils, xtable
BiocGenerics, IRanges, GenomicRanges(>= 1.23.24),
GenomicFeatures, Biostrings, VariantAnnotation, rtracklayer,
S4Vectors, GenomeInfoDb, Biobase
utils, GenomicRanges, org.Hs.eg.db, BiocGenerics,
GenomeInfoDb, GenomicFeatures, IRanges, rtracklayer
S4Vectors (>= 0.9.42), AnnotationDbi, annotate, Biobase,
graphics, methods, stats, survival
snpStats, mvtnorm, GGtools, Rsamtools, igraph, kernlab,
FactoMineR, plspm, IRanges, GenomicRanges,
data.table,rioja,grDevices, graphics,stats,utils
plyr, graph, htmlwidgets, Rgraphviz, rjson, XML
AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils
S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser,
RColorBrewer, Biostrings
Biobase, MASS, graphics, stats, survival, limma
Biobase, BiocGenerics, GWASTools, gdsfmt, GenomicRanges,
graph, IRanges, S4Vectors, SeqArray, SeqVarTools, graphics,
grDevices, methods, stats, utils
gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats
Biostrings, BSgenome, data.table, GenomeInfoDb, GenomicRanges
(>= 1.23.26), GenomicAlignments, S4Vectors (>= 0.9.25),
ggplot2, gridBase, impute, IRanges, matrixStats, methods,
parallel, plotrix, plyr, readr, reshape2, Rsamtools (>=
1.25.2), seqPattern, rtracklayer, RUnit
stats, stats4, utils, RCurl, GenomeInfoDbData
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
stats, httr, xml2, jsonlite, utils, lazyeval, readr,
data.table, GenomicRanges, IRanges
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
XVector, Biostrings (>= 2.23.3), rtracklayer (>= 1.29.24),
biomaRt (>= 2.17.1), Biobase (>= 2.15.1)
GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25),
VariantAnnotation, GenomeInfoDb
Rsamtools, rtracklayer, GenomicRanges, IRanges, BiocGenerics
(>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid,
gridExtra, methods, igraph, S4Vectors (>= 0.13.13), dplyr,
Gviz, Biobase, graphics, stats, utils
utils, XML, IRanges (>= 2.3.23), BSgenome, GenomeInfoDb,
AnnotationHub
methods, BiocGenerics (>= 0.17.0), Rcpp (>= 0.11.2), IRanges
(>= 2.5.26), data.table
S4Vectors (>= 0.13.13), GenomeInfoDb (>= 1.1.3), IRanges (>=
2.5.12), methods, graphics
ggplot2, rtracklayer, BiocGenerics, GenomicRanges,
GenomeInfoDb, IRanges, methods, BiocParallel, Rtsne, graphics,
stats
AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField,
GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0),
grid, gridExtra, gtable, gtools, IRanges (>= 2.7.5), plyr (>=
1.8.3), reshape2, Rsamtools, scales, stats, utils, viridis
Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel,
parallel, foreach, reshape2, dplyr
limma, genefilter, Biobase, BiocGenerics, S4Vectors, IRanges,
Matrix, AnnotationDbi, digest, GenomicRanges,
SummarizedExperiment
grid, grDevices, graphics, stats, utils, gridExtra, scales,
reshape2, gtable, Hmisc, biovizBase (>= 1.23.3), Biobase,
S4Vectors (>= 0.13.13), IRanges, GenomeInfoDb (>= 1.1.3),
GenomicRanges (>= 1.21.10), SummarizedExperiment, Biostrings,
Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.16),
BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer (>=
1.25.16), GenomicFeatures (>= 1.17.13), OrganismDbi, GGally,
ensembldb (>= 1.99.13), AnnotationDbi, AnnotationFilter
plyr, scales, data.table, RColorBrewer, gridExtra
methods, utils, stats, BiocGenerics, snpStats, ff, Rsamtools,
AnnotationDbi, Biobase, bit, VariantAnnotation, hexbin,
rtracklayer, Gviz, stats4, S4Vectors (>= 0.9.25), IRanges,
GenomeInfoDb, GenomicRanges, iterators, Biostrings, ROCR,
biglm, ggplot2, reshape2
ape, grDevices, grid, magrittr, methods, rvcheck, tidyr, utils
methods, Biobase, Biostrings, graphics, grDevices, stats,
utils, IRanges (>= 2.3.23)
Biobase, changepoint, data.table, genefilter, graphics,
GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats
Biobase, edgeR, grDevices, jsonlite, methods, scater, stats,
S4Vectors, utils
S4Vectors (>= 0.13.13), IRanges, rtracklayer (>= 1.31.2),
GenomicFeatures (>= 1.17.13), Biostrings, VariantAnnotation (>=
1.11.4), tools, Biobase, BSgenome, GenomicAlignments (>=
1.1.9), BiocParallel
methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, DBI,
SparseM
Biostrings, GenomeInfoDb, GenomicRanges, IRanges, httr, rjson,
Rsamtools, S4Vectors (>= 0.9.25), Biobase, methods
AnnotationDbi, dendextend, doParallel, foreach, parallel,
org.Hs.eg.db, GO.db, Rcpp, stats, graphics,
MultiAssayExperiment, IRanges, S4Vectors
mgcv, graphics, stats, utils, AnnotationDbi,
GO.db,BiocGenerics
org.Hs.eg.db, AnnotationDbi, topGO, cluster, flexmix, RBGL,
graph, Matrix, corpcor, Rcpp
AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils
methods, stats, stats4, AnnotationDbi (>= 0.0.89), Biobase (>=
1.15.29), Category (>= 2.3.26), GO.db (>= 1.13.0), RBGL,
annotate (>= 1.13.2), graph (>= 1.15.15), AnnotationForge
plyr, grid, gProfileR, reshape2, limma, ggplot2, gtable
BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools,
ShortRead, rtracklayer, ggplot2
GenomicRanges, methods, BatchJobs, BBmisc, S4Vectors,
BiocGenerics, foreach, doParallel, bit, ff, rtracklayer,
ffbase, GenomicFiles, SummarizedExperiment
methods, snpStats, BiocGenerics, S4Vectors (>= 0.9.25),
IRanges, GenomeInfoDb, GenomicFiles, GenomicRanges,
SummarizedExperiment, VariantAnnotation, Biobase, BatchJobs,
gQTLBase, limma, mgcv, dplyr, AnnotationDbi, GenomicFeatures,
ggplot2, reshape2, doParallel, foreach, ffbase, BBmisc,
beeswarm, HardyWeinberg, graphics, stats, utils, shiny,
ldblock, plotly, erma
AnnotationDbi, graph, stats, utils, rappdirs
graphics, grDevices, reshape2, stats, utils
GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS,
parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4)
circlize (>= 0.3.3), GetoptLong, grDevices, utils
BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno,
data.table, matrixStats, BSgenome, parallel, IRanges (>=
2.5.5), S4Vectors (>= 0.9.6), GenomicAlignments (>= 1.7.3),
GenomeInfoDb, Rsamtools, hash, limma
XVector (>= 0.5.7), rtracklayer (>= 1.25.13), lattice,
RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5),
Biobase (>= 2.15.3), GenomicFeatures (>= 1.17.22), BSgenome (>=
1.33.1), Biostrings (>= 2.33.11), biovizBase (>= 1.13.8),
Rsamtools (>= 1.17.28), latticeExtra (>= 0.6-26), matrixStats
(>= 0.8.14), GenomicAlignments (>= 1.1.16), GenomeInfoDb (>=
1.1.3), BiocGenerics (>= 0.11.3), digest(>= 0.6.8)
methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges,
GenomeInfoDb, GenomicRanges, snpStats, Biostrings, Rsamtools,
rtracklayer, gQTLstats, Gviz, VariantAnnotation, AnnotationHub,
AnnotationDbi, GenomicFeatures, graph, ggbio, ggplot2,
SummarizedExperiment
graphics, stats, utils, methods, ncdf4, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
1.19.38), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
utils, tools, BiocGenerics, S4Vectors, IRanges
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, GenomeInfoDb
foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2,
scales, methods
methods, HilbertVis, png, grDevices, circlize (>= 0.3.3)
sonicLength, dplyr, BiocGenerics, GenomicRanges, rSFFreader,
readxl, methods
Biostrings, graphics, grDevices, rtracklayer, RColorBrewer,
Matrix, parallel, GenomeInfoDb
graphics, grDevices, stats, utils, BiocGenerics
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi,
biomaRt, RankProd
BiocGenerics (>= 0.2.0), S4Vectors (>= 0.9.25), IRanges (>=
1.21.39), GenomicRanges (>= 1.23.21), Rsamtools (>= 1.8.5),
Biostrings (>= 2.24.1), chipseq (>= 1.6.1), hwriter (>= 1.3.0),
Cairo (>= 1.5.5), GenomicFeatures (>= 1.9.31), BiocParallel,
parallel, tools, rtracklayer (>= 1.17.19), GenomicAlignments,
VariantTools (>= 1.7.7), GenomeInfoDb, SummarizedExperiment,
methods
edgeR (>= 3.9.14), DESeq2 (>= 1.10.1), DESeq (>= 1.22.1),
BiocParallel (>= 1.4.3), Biobase, utils, stats, grDevices,
graphics, methods
methods, grid, graph, hypergraph, Rgraphviz, stats4
stats, graphics, preprocessCore, grDevices, randomForest,
affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest,
scatterplot3d, utils
shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2,
ggplot2, scales, ROCR, dplyr, DT, limma, methods, UpSetR
DESeq2, SummarizedExperiment, GenomicRanges, IRanges,
S4Vectors, ggplot2 (>= 2.0.0), d3heatmap, pheatmap,
pcaExplorer, IHW, gplots, UpSetR, goseq, stringr, plyr, dplyr,
limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0),
shinydashboard, shinyBS, DT, rentrez, rintrojs, knitr,
rmarkdown, shinyAce, BiocParallel, grDevices, methods
biomaRt, ENVISIONQuery, AffyCompatible, R.methodsS3, utils
methods, slam, lpsymphony, fdrtool, BiocGenerics
tools, Biobase, hwriter, methods, vsn, stats, utils, e1071
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats,
ggfortify, grDevices, methods, Matrix, utils, graphics,
gridExtra, grid, lattice, Rsamtools, survival, BiocParallel,
GenomicAlignments, parallel
d3heatmap, shinyBS, shinyFiles, shinythemes, ggplot2
methods, data.table, RCurl, Rlabkey (>= 2.1.127), Biobase,
pheatmap, ggplot2, scales, stats, gtools, gplots, reshape2,
plotly, heatmaply (>= 0.7.0), rjson, rmarkdown
Biobase, BiocParallel, ComplexHeatmap, circlize, compiler,
cowplot, DESeq2, ggplot2, grDevices, knitr, Matrix, methods,
S4Vectors, stats, SummarizedExperiment, utils
AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr,
preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma,
BiocParallel
pROC, deSolve, rootSolve, compiler, preprocessCore,
GenomicFeatures, GenomicRanges, IRanges, BiocGenerics,
GenomicAlignments, Rsamtools, S4Vectors
IRanges, S4Vectors (>= 0.13.13), GenomeInfoDb, BiocGenerics,
methods, Matrix
interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer,
ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi
seqLogo, Biostrings, GenomicFeatures, IRanges, seqinr, limma,
graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL,
GenomicAlignments, BiocParallel, BiocGenerics
rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2,
methods, BiocGenerics, XVector, tibble, stats, BiocParallel,
bit64, stringr, utils
Rcpp, tkrplot, multtest, relimp, geneplotter, RColorBrewer,
Iso, IsoGene, ORCME, ORIClust, orQA, goric, ff, Biobase, jpeg
BiocGenerics (>= 0.7.5), DESeq2, reshape, tidyr, plyr, readr,
dplyr, RColorBrewer, gplots, methods, ggplot2, gtools,
gridExtra, grid, GGally
affxparser, DBI, GLAD, oligo, oligoClasses, stats
graphics, grDevices, stats, survival, utils
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify,
grDevices, methods, Matrix, BiocParallel,utils, stats
DESeq2 (>= 1.10.0), statmod, Hmisc, plotrix, stringr, Biobase
(>= 2.30.0), locfit, BiocGenerics (>= 0.7.5), BiocParallel,
genefilter, geneplotter, S4Vectors, IRanges, GenomicRanges
regioneR, GenomicRanges, Rsamtools, stats, graphics, memoise,
rtracklayer, GenomeInfoDb, S4Vectors, biovizBase, digest,
bezier
methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
utils, apcluster
AnnotationDbi,graph,DBI, graph, grDevices, methods, stats,
tools, utils
Biobase, graphics, grDevices, methods, stats, tools, utils
Matrix, snpStats, erma, VariantAnnotation, GenomeInfoDb,
Rsamtools, GO.db, GenomicFiles
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
grDevices, graphics, stats, utils, methods
limma, tcltk, BiocInstaller, tkrplot, R2HTML, xtable, gcrma,
AnnotationDbi
Rcpp (>= 0.11.0), DOSE, ggtree, gridExtra, ape, grid, png,
Biobase, sva, reshape2, utils, grDevices, org.Hs.eg.db,
clusterProfiler, ggplot2, ReactomePA
Rcpp (>= 0.12.2), RcppArmadillo, fpc, vegan, mclust,
apcluster, ggplot2, ellipse, limma, utils, statmod, MASS,
igraph, grDevices, graphics, fastcluster, ggdendro, zoo, stats,
amap, Rtsne, gmodels
Biobase, graphics, grDevices, methods, stats
Matrix, penalized, graphics, grDevices, stats
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table
cgdsr, parallel, stringr, reshape2, data.table, RColorBrewer,
methods, LowMACAAnnotation, BiocParallel, motifStack,
Biostrings
affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures,
GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv,
KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS,
graphics, stats, stats4, methods
BiocGenerics, stats4, graphics, stats, utils, MASS, Biobase,
quantreg, limma, affy, SparseM, vsn, zlibbioc
data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
Biostrings, phangorn, stringdist, UpSetR
parallel, Rcpp, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment, BiSeq
RColorBrewer, gplots, bbmle, statmod, grDevices, graphics,
stats
Biobase, graphics, grDevices, methods, stats, utils
VGAM, coda, BSgenome, BSgenome.Hsapiens.UCSC.hg19, S4Vectors,
methods, preprocessCore, GenomicAlignments, Rsamtools,
Biostrings, GenomicRanges, IRanges, VariantAnnotation,
SummarizedExperiment, GenomeInfoDb, rtracklayer, graphics,
stats, grDevices, utils, zlibbioc
data.table, ggplot2(>= 2.0), cowplot, cometExactTest,
RColorBrewer, NMF, ggrepel, methods, ComplexHeatmap, mclust,
VariantAnnotation, Biostrings, Rsamtools, rjson, grid,
DPpackage, wordcloud, grDevices, changepoint, gridExtra,
survival
Biobase, affy, methods, stats, utils, zlibbioc
multtest, clusterSim, apcluster, limma, e1071, AnnotationDbi,
methods, parmigene,igraph,reactome.db
Biobase, graphics, grDevices, venn, mclust, stats, utils, MASS
Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr,
stringr, abind, methods, parallel, reshape2, stats, stats4,
graphics, utils
methods, TFBSTools, IRanges, XVector, Biostrings
BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db,
org.Hs.eg.db, GGally, ggplot2, scales, cluster
e1071 (>= 1.5-12), pamr (>= 1.22), randomForest (>= 3.9-6),
RColorBrewer (>= 0.1-3), Biobase (>= 2.5.5), graphics,
grDevices, stats, utils
AnnotationDbi, DBI, GO.db, KEGG.db, cluster, Matrix
GenomicRanges, SNPassoc, limma, DMRcate, snpStats, vegan,
BiocGenerics, minfi, IRanges, S4Vectors, methods, doParallel,
parallel, ggplot2 (>= 2.0.0), sva, permute
GenomicRanges, Biostrings, graphics, gtools, IRanges, methods,
stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer,
preprocessCore
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, GOSemSim (>= 1.99.3), MeSH.db, methods, rvcheck
optimx, Formula, plyr, multtest, BiocParallel, ggplot2
KEGGgraph, mygene, hpar, org.Hs.eg.db, igraph, RCurl, biomaRt,
KEGGREST, AnnotationDbi,MWASTools, stats, graphics, utils
rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb,
GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP,
matrixStats
parallel, matrixStats, foreach, Matrix, gplots
edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots,
corrplot, vsn, brew, rjson, log4r
epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan,
GenomeInfoDb, phyloseq, httr
Biostrings, ca, graphics, grDevices, grid, gridBase, IRanges,
stats, utils
grDevices, stats, utils, lumi, methylumi, Gviz, genoset,
SummarizedExperiment, IRanges, GenomicRanges,
VariantAnnotation, rtracklayer, GenomicFeatures, annotate,
Biobase (>= 2.5.5), AnnotationDbi, genefilter, biomaRt,
methods, parallel
Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase,
grDevices, graphics, hexbin, matrixStats, minfi (>= 1.17.9),
methods, RColorBrewer, shiny, stats, SummarizedExperiment,
utils
methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors,
methods, ggplot2, gridExtra
IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>=
0.13.13), GenomeInfoDb, KernSmooth, qvalue, emdbook, Rsamtools,
gtools, fastseg, rtracklayer, mclust, Rcpp, R.utils, limma,
grDevices, graphics, stats, utils
foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute,
data.table, limma, R.matlab, digest
marray, gplots, IRanges, BiocGenerics, Gviz,
GenomicAlignments, Biostrings, parallel, data.table,
GenomeInfoDb, S4Vectors
BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
SummarizedExperiment, Biobase, graphics, lattice, annotate,
genefilter, AnnotationDbi, minfi, stats4, illuminaio
AnnotationDbi, Biobase, BiocParallel, data.table, edgeR,
futile.logger, ggplot2, GO.db, GOstats, gplots, graph,
graphics, grDevices, GSEABase, limma, matrixStats, mGSZ,
org.Hs.eg.db, RBGL, Rgraphviz, RJSONIO, stats, vegan
BiocGenerics, S4Vectors, preprocessCore, grDevices, methods,
grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses
methods, Formula, data.table, pracma, MCMCpack, coda, modeest,
testthat, Rcpp, scales, Kmisc
S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges,
beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma,
preprocessCore, illuminaio, matrixStats (>= 0.50.0), mclust,
genefilter, nlme, reshape, MASS, quadprog, data.table,
GEOquery, stats, grDevices, graphics, utils
methods, BiocGenerics, Biobase, S4Vectors (>= 0.9.25),
IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16),
SummarizedExperiment (>= 0.2.0), oligoClasses, DNAcopy, ff,
foreach, matrixStats, lattice, data.table, grid, stats, utils
utils, methods, graphics, KernSmooth, stats
graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi,
Rgraphviz
RCurl, httr, stringr, Hmisc, energy, entropy, Roleswitch,
gplots, glmnet, impute, limma, pcalg
DBI, RSQLite, stringr, sqldf, plyr, methods
graphics, grDevices, gridExtra, Matrix, parallel,
RColorBrewer, reshape, scales, utils
limma, minfi, methylumi, IlluminaHumanMethylation450kmanifest,
statmod, ruv, stringr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, org.Hs.eg.db,
AnnotationDbi, BiasedUrn, GO.db,
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
gdata, pls, sfsmisc, MASS, rpart, rda, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4
GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
Biobase, RJSONIO, stringr, reshape2, ggplot2, KEGGREST, plyr,
XML, RCurl, flexmix, Matrix, methods, tools
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, graphite, genefilter, BiocGenerics, gplots, GSEABase,
Biobase, parallel, corpcor, svd, cluster
parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>=
0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>=
2.0.0), matrixStats, densityClust, Rtsne, MASS, reshape2,
limma, dplyr, qlcMatrix, pheatmap, stringr, proxy, slam, stats
parmigene, randomForest, SummarizedExperiment, gplots,
circlize, RColorBrewer, HiveR, clusterProfiler, DOSE, Biobase,
limma, grDevices, graphics, TCGAbiolinks, GEOquery, stats,
RISmed, grid, utils
MASS, splines, lattice, IRanges, GenomicRanges,
GenomicAlignments, Rsamtools, GenomeInfoDb, S4Vectors
methods, compiler, grDevices, grImport, stringr, BiocGenerics,
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges,
Biostrings, BSgenome, rtracklayer, VariantAnnotation,
BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue
graphics, grid, methods, S4Vectors, IRanges (>= 1.13.5),
Biostrings (>= 1.24.0), lattice, rGADEM, utils
qtl, GenABEL, MASS, outliers, graphics, stats, utils
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
BSgenome, easyRNASeq, edgeR, GenomicAlignments,
GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges,
parallel, plyr, Rsamtools, R.utils, stats,
SummarizedExperiment, S4Vectors, utils
shiny, mzID (>= 1.2), MSGFplus, shinyFiles (>= 0.4.0), tools
plyr, IRanges, preprocessCore, vsn, grid, stats4, affy,
impute, pcaMethods, mzID (>= 1.5.2), MALDIquant (>= 1.16),
digest, lattice, ggplot2, S4Vectors, XML, Rcpp
MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach,
doParallel, parallel, methods, iterators, data.table, Biobase,
ProtGenerics, reshape2, dplyr, mzR
plyr, foreach, parallel, doSNOW, stringr, mzR, reshape2,
fastcluster, ggplot2, sapa
Rcpp, lme4, marray, limma, gplots, ggplot2, methods, grid,
ggrepel, preprocessCore, MSnbase, reshape2, survival,
minpack.lm, utils, grDevices, graphics, stats
methods, GenomicRanges (>= 1.25.93), BiocGenerics,
SummarizedExperiment (>= 1.3.81), S4Vectors, IRanges, Biobase,
reshape2, shinydashboard, shiny, stats, tidyr, UpSetR, utils
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
BiocGenerics, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, methods, utils
methods, parallel, doParallel, foreach, grDevices, graphics,
utils, SummarizedExperiment, stats
stats, parallel, BiocGenerics (>= 0.18.0), VariantAnnotation
(>= 1.18.1), reshape2 (>= 1.4.1), plyr (>= 1.8.3), ggplot2 (>=
2.1.0), pracma (>= 1.8.8), SummarizedExperiment (>= 1.2.2),
IRanges (>= 2.6.0), GenomeInfoDb (>= 1.8.1), Biostrings (>=
2.40.0), gridExtra (>= 2.2.1)
gProfileR, stringr, topGO, GOstats, annotate, AnnotationDbi,
graph
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, graphics, stats, utils
httr (>= 0.3), jsonlite (>= 0.9.7), S4Vectors, Hmisc, sqldf,
plyr
httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, GenomeInfoDb
XML, plyr, parallel, doParallel, foreach, iterators,
ProtGenerics
Biobase, BiocGenerics (>= 0.13.6), ProtGenerics
graphics, methods, baseline, signal, GenomicAlignments,
GenomeInfoDb, rtracklayer, SummarizedExperiment, limma,
trackViewer, stats, utils
BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
fda, CSAR, ICSNP
graph, KEGGgraph, methods, RBGL, RCytoscape, R.methodsS3
boot, e1071, graph, graphics, grDevices, methods, RBGL (>=
1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod,
plotrix, limma
Rcpp (>= 0.11.0), minet, randomForest, c3net, PCIT, GeneNet,
tools, pracma, Matrix, corpcor, fdrtool
glasso, mvtnorm, parcor, GeneNet, huge, CompQuadForm, ggm,
mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2
stats, Matrix, dplyr, doParallel, foreach, parallel,
sparseMVN, ggplot2, gridExtra, pROC
dmt, ggplot2, graph, igraph, parallel, plyr, qvalue,
RColorBrewer
methods, parallel, Xmisc (>= 0.2.1), rbamtools (>= 2.6.0),
changepoint (>= 2.1.1)
graphics, grDevices, marray, methods, nnet, stats
limma, mvtnorm, utils, methods, HTqPCR (>= 1.16.0)
methods, stats, utils, grDevices, parallel, GenomeInfoDb,
GenomicRanges, IRanges, Rcpp (>= 0.11), qvalue (>= 2.2),
bamsignals (>= 1.4), rtracklayer (>= 1.32)
Biobase, methods, BiocGenerics, graphics, stats
stats, IRanges, S4Vectors, graphics, methods
methods, BiocGenerics, S4Vectors (>= 0.9.39), IRanges (>=
2.5.27), Biobase, GenomicRanges (>= 1.23.16), Rsamtools, stats,
graphics, parallel
multtest (>= 1.7.3), graphics, grDevices, stats, akima
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
BiocGenerics (>= 0.3.2), 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, BiocInstaller, utils, S4Vectors (>=
0.9.25), RSQLite
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
smatr, ggplot2, ggrepel, nem
methods,Biobase,gtools,flowCore(>=
1.31.17),flowViz,ncdfFlow(>=
2.11.34),flowWorkspace,flowStats(>= 3.29.1),flowClust(>=
3.11.4),MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils
som, fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape,
biomaRt, Biobase, arules
Biobase, graphics, methods, stats, twilight
RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges,
GenomicFeatures, AnnotationDbi, methods, tools, utils,
BiocFileCache, dbplyr, DBI
Biobase, BiocInstaller, GenomicRanges, graph, IRanges, RBGL,
DBI, S4Vectors (>= 0.9.25), stats
e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR,
sva
limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db,
hgu133a.db, KEGG.db, nlme
matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit,
hexbin
methods, utils, Biobase, DBI, RSQLite, AnnotationDbi
graphics, grDevices, MASS, methods, pvclust, stats, utils,
RedeR
shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph,
stats, utils
MCMCpack, limma, corpcor, rmarkdown, knitr, pander,
matrixStats, reshape2, scales, ggplot2, rentrez, BatchQC, DT,
gtools, tidyr, plyr, dplyr, ape, phyloseq, shiny, grDevices,
stats, methods, XML, graphics, utils, alluvial, BiocStyle,
edgeR, preprocessCore, DESeq2
EMT, mclust, Matching, data.table, stats, grDevices, graphics,
utils
KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,
KEGGREST, methods, utils
httr, igraph, plyr, rjson, R.utils, data.table, jsonlite
cleaver (>= 1.3.6), Biobase, Biostrings, IRanges, S4Vectors,
mzID, mzR (>= 1.99.1), MSnbase (>= 1.15.5), Pviz, biomaRt,
GenomicRanges, rtracklayer, ensembldb (>= 1.99.13),
BiocParallel, AnnotationFilter
Biobase, BiocGenerics, BiocParallel (>= 1.3.13), parallel,
reshape2, grid, utils, cowplot, methods, limma, ggplot2,
gridExtra, grDevices, stats
DESeq2, SummarizedExperiment, GenomicRanges, IRanges,
S4Vectors, genefilter, ggplot2 (>= 2.0.0), d3heatmap, scales,
NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny
(>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce,
threejs, biomaRt, pheatmap, knitr, rmarkdown, tidyr, grDevices,
methods
AnnotationDbi, Biobase, Category, GO.db, graph, graphics,
GSEABase, KEGG.db, methods, ScISI, stats, stats4
ROTS, limma, affy, genefilter, preprocessCore,
aroma.affymetrix, aroma.core
limma, fields, GenomicRanges, ggplot2, plyr, tools, methods,
data.table
S4Vectors (>= 0.9.25), Rsamtools (>= 1.10.2), GenomicFeatures
(>= 1.19.8), biomaRt (>= 2.17.1), stringr, RCurl, Nozzle.R1,
VariantAnnotation (>= 1.7.28), rtracklayer, RSQLite, ggplot2,
AnnotationDbi, customProDB (>= 1.7.0), pheatmap
Biobase, piano, magicaxis, RColorBrewer, parallel, caTools,
methods, downloader, stats, utils, graphics, grDevices, lsa,
reshape2
survival, limma, Hmisc, gplots, Category, AnnotationDbi,
hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
SNPchip, hgu133a.db, HTSanalyzeR, ellipse
methods, car, nlme, nortest, MASS, logistf
Matrix, MASS, ggbio, GenomicRanges, GenomeInfoDb, supraHex,
scales, grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz,
lattice, caret, plot3D, stats
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea
methods, stats4, IRanges, GenomicRanges, graphics, grDevices,
stats, Rsamtools, GenomicAlignments, S4Vectors
bnlearn, C50, MASS, matrixStats, partykit, Rgraphviz, WGCNA,
GO.db, impute, preprocessCore, grDevices, graphics, stats,
utils, parallel, pheatmap (>= 1.0.8)
methods, PICS, graphics, grDevices, stats, Gviz, fda,
BSgenome, stats4, BiocGenerics, IRanges, S4Vectors
Biobase, flowCore, graphics, grDevices, lattice, MASS,
methods, robustbase, stats, utils, flowStats
Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2,
Biobase
BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray,
methods, quadprog, Rcsdp, stats, stats4, utils
Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils,
Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges,
Biostrings, BSgenome (>= 1.32.0)
Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma,
zlibbioc
stats, CompQuadForm, Matrix, survival, Biobase, GSEABase
Biobase, Category, graph, graphics, grDevices, lattice,
methods, RColorBrewer, stats
Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
Biobase, BiocGenerics, graphics, grDevices, grid, MASS,
methods, RColorBrewer, rrcov, stats4, utils
parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges,
Biobase, GenomeInfoDb, S4Vectors
diagram, stringr, ggplot2, reshape2, grDevices, matrixcalc,
stats, gplots, methods, utils, graphics
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, graphics, utils, grDevices, methods, pracma, maxLik,
Biobase, FNN, minpack.lm, BiocParallel, ropls
Biobase, mclust (>= 4.3), caret, e1071, sampling, class,
kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin,
BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS,
knitr, mvtnorm, gtools, plyr, ggplot2, biomaRt, utils,
grDevices, graphics
shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics,
utils, ggplot2
DAPAR (>= 1.8.7), DAPARdata, rhandsontable, data.table,
shinyjs, DT, shiny, shinyAce, highcharter, openxlsx
mzR (>= 2.3.2), MSnbase, Biostrings, GenomeInfoDb, utils,
Biobase, BiocInstaller, RCurl
rTANDEM, plyr, seqinr, Nozzle.R1, ggplot2, reshape2, parallel,
rpx, tidyr, dplyr, plotly, rmarkdown,
AnnotationHub, colourpicker, data.table, digest, dplyr, DT (>=
0.2), fastmatch, ggplot2, grDevices, highcharter (>= 0.5.0),
htmltools, httr, jsonlite, miscTools, plyr, R.utils, shinyjs,
stringr, stats, survival, Sushi, tools, utils, XML, methods
stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel,
biomaRt, BgeeDB, topGO, BiocInstaller, Biobase, labeling
Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses
GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer,
S4Vectors, data.table, grDevices, graphics, stats, utils,
SummarizedExperiment, GenomeInfoDb, Rsamtools, Biostrings,
rtracklayer, ggplot2, futile.logger, VGAM, edgeR, limma
biovizBase, Biostrings, GenomicRanges, IRanges, data.table,
methods
data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots,
Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub,
GenomicRanges, graph, grDevices, stats, utils
Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander,
S4Vectors
graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase
(>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0),
GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>=
0.50.2), R.utils (>= 2.3.0), Rsamtools (>= 1.20), BiocParallel
(>= 1.6.6),
methods, parallel, Matrix (>= 1.0), grid, annotate, graph (>=
1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi,
IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm,
qtl, Rgraphviz
reshape, ggplot2, Biostrings, biovizBase, graphics, methods,
plyr, stats
Biostrings, graphics, gtools, methods, stats, utils, HMMcopy,
rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges,
limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
methods, grDevices, graphics, utils, zlibbioc, BiocGenerics,
S4Vectors (>= 0.9.25), IRanges, BiocInstaller, Biobase,
Biostrings, BSgenome, Rsamtools (>= 1.19.38), GenomicFeatures
(>= 1.17.13), ShortRead (>= 1.19.1), GenomicAlignments,
BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles
methods, parallel, clues, ggplot2, pheatmap, clValid, igraph,
data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors,
IRanges, GenomeInfoDb, GenomicRanges, ggbio
methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf,
RColorBrewer
utils, grDevices, graphics, stats, tools, xtable, R2HTML,
TeachingDemos, BiocGenerics, S4Vectors (>= 0.9.25), IRanges,
XVector, GenomicRanges, SummarizedExperiment, biomaRt,
BSgenome, Rsamtools, ShortRead
BiocGenerics, IRanges, methods, S4Vectors, stats,
SummarizedExperiment
graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
BiocGenerics
S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
phastCons100way.UCSC.hg19, SummarizedExperiment, GenomicScores
methods, S4Vectors, IRanges, GenomeInfoDb, ggbio, ggplot2,
exomeCopy, SomaticSignatures, Rsamtools, shiny, VGAM, dplyr,
reshape2
utils, grDevices, stats, graphics, rgl, plotrix, S4Vectors,
IRanges, GenomeInfoDb, GenomicAlignments
biomaRt, AnnotationDbi, GenomicRanges,
BSgenome.Hsapiens.UCSC.hg19, GenomeInfoDb, Biostrings,
rtracklayer, org.Hs.eg.db, GenomicFeatures, genomation (>=
1.5.5), rmarkdown (>= 0.9.5), knitr (>= 1.12.3), BiocGenerics,
S4Vectors, stats, plotrix
plyr,DNAcopy,lattice,ggplot2,grid,shiny (>= 0.11.1),
limma,affy,mclust,TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Hs.eg.db,GenomicFeatures,GenomeInfoDb,GenomicRanges,AnnotationDbi,
parallel,IRanges,grDevices,aCGH
Rgraphviz, sfsmisc, graphics, methods, graph, grDevices,
flowType (>= 2.0.0)
stats, utils, methods, RCurl, rjson, foreach, doParallel,
Biostrings, GOSemSim, ChemmineR, fmcsR, rcdk (>= 3.3.8)
methods, httpuv (>= 1.3.2), Rcpp (>= 0.11.5), jsonlite (>=
0.9.15), BiocGenerics, igraph, base64enc
graphics, grDevices, methods, stats, MASS, rgl
assertive.base (>= 0.0-6), assertive.files (>= 0.0-2),
assertive.numbers (>= 0.0-2), assertive.properties (>= 0.0-3),
assertive.sets (>= 0.0-2), assertive.types (>= 0.0-2), Biobase
(>= 2.32.0), data.table (>= 1.9.6), dplyr (>= 0.5.0), magrittr
(>= 1.5), openxlsx (>= 3.0.0), pathological (>= 0.1-1),
reshape2 (>= 1.4.1), stats, stringi (>= 1.1.1),
SummarizedExperiment (>= 1.2.3), testthat (>= 1.0.2), tidyr (>=
0.6.0), utils
BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb,
GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer
(>= 1.35.3), S4Vectors, stats, utils
BiocGenerics, biomaRt, circlize, graphics, grDevices, methods,
rtracklayer, plyr, stats, utils
BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno,
graphics, IRanges (>= 1.13.5), multtest, stats, utils
memoise, GenomicRanges, BSgenome, rtracklayer, parallel,
graphics, stats, utils, GenomeInfoDb, IRanges
BiocStyle (>= 2.3.20), derfinder (>= 1.1.0), DEFormats,
DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1),
knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR,
rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment
glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats,
pbapply, utils, methods
graphics, stats, utils, methods, settings, BiocGenerics,
S4Vectors, Biostrings, GenomicRanges, IRanges, BiocParallel,
doParallel, parallel, foreach, caret, kernlab, ranger,
BSgenome, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
org.Hs.eg.db, impute, iterators
parallel, S4Vectors (>= 0.9.25), IRanges (>= 1.20.0),
GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
GenomicAlignments, rtracklayer, BSgenome, gplots, grid, MASS,
gsmoothr, edgeR (>= 3.4.0), DNAcopy, Ringo, aroma.affymetrix,
Rsolnp, cluster
Biobase,hwriter,Category,GOstats,limma(>=
3.17.5),lattice,AnnotationDbi,edgeR, annotate,PFAM.db,
GSEABase, BiocGenerics(>= 0.1.6), grid, XML, R.utils, DESeq2(>=
1.3.41), ggplot2, ggbio, IRanges
rJava, graphics, stats, utils, grDevices
Biostrings, IRanges, methods, graphics, seqLogo
rjson, GetoptLong (>= 0.0.9), RCurl, utils
gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment,
hash, AnnotationDbi
BiocGenerics, GenomeInfoDb, GenomicRanges, IRanges, reshape2,
GenomicFeatures, grid, plyr, S4Vectors, GenomicAlignments,
ggplot2, ggbio, Rsamtools, rtracklayer, data.table, sqldf
Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo
plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools,
utils, RSQLite
BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4
grid, gridExtra, reshape2, gplots, ggplot2, plotrix,
RColorBrewer, STRINGdb, MCL, linkcomm, hash, png, sqldf,
igraph, knitr, RITANdata
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb,
S4Vectors, BiocParallel, stats, graphics, methods, grDevices
Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
stats, methods, BiocGenerics, IRanges, Biobase, affxparser,
stats4
RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid,
hwriter, lattice, latticeExtra, limma, methods, splots (>=
1.13.12)
geneplotter, limma, biomaRt, car, splots, methods
Biostrings(>= 2.32.1), GenomicRanges(>= 1.16.4), Rsamtools(>=
1.16.1), rtracklayer(>= 1.24.2), GenomicAlignments(>= 1.5.12)
GenomicRanges , IRanges, edgeR, DESeq, DBI
affy, boot, impute, splines, graphics, qvalue, reshape2
methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges,
SummarizedExperiment, GenomicAlignments (>= 0.99.4),
rtracklayer, GenomeInfoDb
httr, progress, jsonlite, utils, Biobase
BiocGenerics, Biostrings, IRanges, methods, S4Vectors, knitr
(>= 1.7), BiocStyle, plyr, markdown, grid, reshape2, digest,
Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools,
GenomicAlignments, GenomicFiles
utils, BiocGenerics (>= 0.1.3), S4Vectors (>= 0.13.8), IRanges
(>= 2.3.7), XVector (>= 0.15.1), zlibbioc, bitops, BiocParallel
XML, assertthat, stringi, rvest, data.table, xml2, dplyr,
purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr,
scales
methods,XML,limma (>= 3.18),survival,RCircos,data.table (>=
1.9.4),RCurl,RJSONIO
RedeR, minet, snow, limma, data.table, car, IRanges, igraph,
S4Vectors
shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db
corrplot, MASS, stats, lattice, grDevices, gridExtra,
snowfall, psych, BiocParallel, grid, bladderbatch, reshape2
methods, utils, stats, stats4, BiocGenerics
graphics, methods, SparseM, stats, utils
methods, reshape2, scales, gridExtra, XML
graphics, stats, utils, methods, e1071, parallel, foreach,
doParallel, doRNG, shiny, ggplot2, pheatmap (>= 1.0.8), ROCR,
robustbase, rrcov, cluster, WriteXLS, Rcpp (>= 0.11.1), scater
biomaRt, BiocGenerics, data.table, dplyr, edgeR, ggbeeswarm,
grid, limma, Matrix, matrixStats, parallel, plyr, reshape2,
rhdf5, rjson, shiny, shinydashboard, stats, tximport, utils,
viridis
fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm,
SummarizedExperiment, grDevices, graphics, stats, S4Vectors,
scran
Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook,
rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods,
nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel
AnnotationDbi, GO.db, RpsiXML, annotate, methods,
org.Sc.sgd.db, utils
graphics, stats, utils, aroma.light, BiocParallel, class,
cluster, compositions, diptest, EDASeq, scran, edgeR, fpc,
gplots, grDevices, hexbin, limma, matrixStats, mixtools,
RColorBrewer, boot, shiny, miniUI, rhdf5, RUVSeq, DT, NMF,
ggplot2, plotly, reshape2, visNetwork, rARPACK
Biobase, stats, methods, utils, graphics, grDevices, Matrix,
edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, zoo, statmod,
splines, ggplot2, MASS, DT, viridis
sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer
Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils,
abind
ggplot2, shiny, topGO, segmented, reshape2, org.Hs.eg.db,
org.Mm.eg.db
nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
methods, parallel, S4Vectors, IRanges, GenomicRanges,
GenomeInfoDb, SummarizedExperiment, Biostrings,
VariantAnnotation
Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
methods, IRanges, BSgenome, digest, rtracklayer,
GenomicRanges, Biostrings, shiny (>= 0.13.0), DBI, RSQLite,
plotrix, fields, grid, kohonen, parallel, GenomeInfoDb, class,
S4Vectors, ggplot2, reshape2, gridExtra, jsonlite, DT (>=
0.1.0), RColorBrewer, Rsamtools, GenomicAlignments
grDevices, graphics, stats, methods, stringr, gdsfmt,
GenomicRanges, IRanges, S4Vectors, GWASExactHW,
VariantAnnotation, Biobase, logistf
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, liftr, uuid, dplyr, shiny (>= 0.13), miniUI (>=
0.1.1), rstudioapi (>= 0.5)
AnnotationDbi, BiocGenerics, Biostrings, GenomicAlignments,
GenomicFeatures, GenomeInfoDb, RUnit, S4Vectors (>= 0.9.39),
grDevices, graphics, igraph, parallel, rtracklayer, stats
Biobase, S4Vectors (>= 0.13.8), IRanges (>= 2.3.7),
GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6), hwriter,
methods, zlibbioc, lattice, latticeExtra,
corpcor (>= 1.6.2), graphics, igraph, limma, marray, MASS,
penalized, quadprog, snowfall, stats
BiocGenerics, Biostrings, BSgenome (>= 1.36.3), class,
graphics, grDevices, GenomicRanges, nloptr, methods, NMF,
stats, utils, VariantAnnotation, PMCMR
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, utils, grDevices, graphics, stats, BiocGenerics,
Biobase, affy, genefilter, gcrma
graphics, stats, gbm, Hmisc, S4Vectors, IRanges, GenomicRanges
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice,
methods, stats, BiocGenerics
scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2,
reactome.db, KEGG.db, BioNet, goseq, methods, IRanges, igraph,
Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics,
stats, utils
aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma,
methods, stats, tilingArray, utils
methods, graphics, lattice, grid, foreach, utils, Biobase,
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges,
SummarizedExperiment, oligoClasses (>= 1.31.1)
DESeq2, cluster, ggplot2, lattice, GenomeInfoDb, BiocParallel,
VariantAnnotation, BiocGenerics, IRanges, methods,
SummarizedExperiment, RColorBrewer, Biostrings, grDevices,
gridExtra, stats, grid, utils, reshape2, scales, S4Vectors
graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
methods, reshape2, ggplot2, S4Vectors, IRanges, GenomeInfoDb,
GenomicRanges, Biostrings, Rsamtools, GenomicAlignments,
rtracklayer, preprocessCore, chipseq, BiocParallel
S4Vectors, IRanges, GenomeInfoDb, Biostrings, ggplot2, ggbio,
reshape2, NMF, pcaMethods, Biobase, methods, proxy
stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack
networkD3, httr, igraph, utils, stats, miRNAtap, miRNAtap.db,
AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots,
grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks,
gdata
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
fitdistrplus, edgeR, stats, locfit, akima, Biobase, checkmate,
methods, utils, matrixStats, ggplot2, scales, BiocParallel
annotate, Biobase, graphics, grDevices, grid, methods, utils,
XML
methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>=
0.9.25), IRanges (>= 2.3.21), GenomeInfoDb, GenomicRanges (>=
1.23.21), GenomicFeatures, Rsamtools, GenomicAlignments, graph,
Rgraphviz
graphics, ggplot2, seqLogo, Biostrings, biomaRt,
GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz,
IRanges, S4Vectors, GenomeInfoDb, utils, plyr,
BSgenome.Mmusculus.UCSC.mm9
graphics, grDevices, methods, RColorBrewer, stats, utils
GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb,
Gviz, Rsolnp
SpidermiR, KEGGREST, org.Hs.eg.db, AnnotationDbi, e1071, ROCR,
grDevices, igraph
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
methods, graph, RBGL, parallel, BiocGenerics
png, sqldf, plyr, igraph, RCurl, methods, RColorBrewer,
gplots, hash, plotrix
data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99),
digest, Biobase
utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3),
S4Vectors (>= 0.13.13), IRanges (>= 2.7.2), GenomeInfoDb (>=
1.11.4)
ape, MASS, grDevices, graphics, stats, utils
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta
matrixStats, stats, graphics, utils, limma
methods, stats, SummarizedExperiment, edgeR, ggplot2, limma,
lmtest, parallel, pls
AnnotationDbi, mclust, GenomicRanges, IRanges, zoo, squash,
pls,rtracklayer,ROCR,verification
data.table, reshape2, grid, ggplot2, stats, grDevices,
graphics, utils
RColorBrewer, lattice, qvalue, multtest, utils, tools,
Biobase, knitr, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2),
rmarkdown (>= 1.0)
doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2
BiocGenerics, GenomicRanges, GenomicFeatures,
SummarizedExperiment, VariantAnnotation, rjson, ggplot2, grid,
limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap,
BatchJobs
graphics, grDevices, methods, stats, tcltk, utils
grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics,
reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot,
graphics, GenomicAlignments, Hmisc
downloader (>= 0.4), survminer, grDevices, gridExtra,
graphics, tibble, grid, GenomicRanges, XML (>= 3.98.0),
data.table, EDASeq (>= 2.0.0), edgeR (>= 3.0.0), jsonlite (>=
1.0.0), plyr, knitr, methods, biomaRt, ggplot2, ggthemes,
survival, stringr (>= 1.0.0), IRanges, scales, rvest (>=
0.3.0), stats, utils, selectr, S4Vectors, ComplexHeatmap (>=
1.10.2), R.utils, SummarizedExperiment (>= 1.4.0), genefilter,
ConsensusClusterPlus, readr, RColorBrewer, doParallel, dplyr,
GenomeInfoDb, GenomicFeatures, parallel, tools, xml2, httr (>=
1.2.1), matlab, circlize, ggrepel (>= 0.6.3)
shiny (>= 0.14.1), downloader (>= 0.4), grid, plotly, readr,
stringr (>= 1.1.0), SummarizedExperiment, ggrepel, data.table,
shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), pathview, ELMER (>=
1.2.1), clusterProfiler, parallel, TCGAbiolinks (>= 2.2.4),
shinyjs (>= 0.7), colourpicker, shinyBS (>= 0.61)
edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges,
SummarizedExperiment, GenomicAlignments, Rsamtools, e1071,
cluster, ggplot2, grid, grDevices, stats, utils, methods,
locfit
methods, AnnotationDbi, gplots, graphics, grDevices, stats,
utils, annotate, DBI, RSQLite
strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods,
stats
Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth,
graphics, grDevices, stats
R.utils, methods, Biobase, parallel, edgeR, DESeq2,
SummarizedExperiment, RBGL, DESeq, fields, limma,
TeachingDemos, KEGGgraph, qpgraph, clipper, AnnotationDbi,
doParallel
Biobase, biobroom, broom, data.table, doParallel, foreach,
futile.logger, ggplot2, grDevices, gridExtra, grid, knitr,
limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr,
purrr, RColorBrewer, RCurl, reshape2, rmarkdown, sme, splines,
stats, stringr, utils, VennDiagram, VGAM
IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base,
stringr, RColorBrewer, methods
GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz,
pbapply, Rsamtools, rtracklayer, S4Vectors, scales, tools,
IRanges, AnnotationDbi, grImport
BiocGenerics, caret, chipseq, e1071, GenomicAlignments,
GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2,
graphics, grDevices, IRanges, pROC, reshape2, Rsamtools,
rtracklayer, S4Vectors, stats, utils
BiocGenerics, S4Vectors (>= 0.9.25), IRanges, Rsamtools (>=
1.19.38), zlibbioc, gplots
ape, ggplot2, jsonlite, magrittr, methods, rvcheck
bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel,
iterators, RColorBrewer, circlize, cgdsr, igraph, grid,
gridExtra, xtable, gtable, scales, R.matlab, gRapHD, grDevices,
graphics, stats, utils, methods
ggplot2, shiny, plyr, grid, fastICA, igraph, combinat, mgcv,
mclust, gplots
AnnotationHub, BiocGenerics, BiocParallel, GenomicAlignments,
GenomeInfoDb, GenomicRanges, gtools, IRanges, methods,
Rsamtools (>= 1.14.3), rtracklayer, S4Vectors,
SummarizedExperiment, utils
methods, BiocGenerics (>= 0.3.2), S4Vectors, Hmisc, minqa,
stats, Biobase (>= 0.3.2), plyr, IRanges
AnnotationFilter, BiocGenerics (>= 0.19.1), BiocParallel,
Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges,
GGally, ggplot2, Gviz, limma, IRanges (>= 2.7.1), reshape2,
Rsamtools, S4Vectors (>= 0.11.11), SummarizedExperiment,
VariantAnnotation (>= 1.19.9)
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
DBI, stringr, RSQLite, R.utils, WriteXLS, stats, BiocParallel
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
Biobase, S4Vectors (>= 0.9.25), IRanges (>= 1.14.0),
oligoClasses (>= 1.31.1), foreach, matrixStats, data.table,
grid, lattice, methods, GenomeInfoDb (>= 1.11.4), crlmm, tools,
stats, utils, BSgenome.Hsapiens.UCSC.hg18
MASS, pbkrtest (>= 0.4-4), iterators, splines, colorRamps,
gplots, reshape2, lme4 (>= 1.1-10), doParallel, limma,
grDevices, graphics, utils, stats
utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.13.13), IRanges
(>= 2.3.25), XVector (>= 0.5.6), Biostrings (>= 2.33.5),
AnnotationDbi (>= 1.27.9), BSgenome (>= 1.37.6), rtracklayer
(>= 1.25.16), GenomicFeatures (>= 1.27.4)
utils, DBI, RSQLite (>= 1.0.0), Biobase, S4Vectors (>=
0.9.25), IRanges (>= 2.3.23), RBGL, graph, AnnotationDbi,
BiocParallel, Biostrings (>= 2.33.11), GenomeInfoDb (>= 1.3.6),
GenomicRanges (>= 1.19.13), SummarizedExperiment,
GenomicFeatures, Rsamtools (>= 1.17.8), BSgenome, Gviz, shiny,
GenomicScores
Rsamtools (>= 1.17.6), BiocGenerics, Biostrings, parallel,
GenomicFeatures (>= 1.17.13), Matrix, rtracklayer (>= 1.25.3),
BiocParallel, GenomeInfoDb, BSgenome, Biobase
mixtools, stats, parallel, e1071, KernSmooth
methods, affy, limma, lattice, ggplot2, hexbin
methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges (>=
2.5.27), Biostrings, foreach, GenomicFeatures, ggplot2, Hmisc,
mclust, rtracklayer, seqinr, stringr, wmtsa
methods, affy, preprocessCore, GenomicRanges, waveslim,
IRanges
multtest, qvalue, stats, utils, BiocInstaller
dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer,
cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb
pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr,
magrittr, roar
mzR (>= 1.1.6), BiocGenerics, ProtGenerics, lattice,
RColorBrewer, plyr, RANN, multtest, MassSpecWavelet (>= 1.5.2),
S4Vectors
Biobase, BiocGenerics, genefilter, graphics, grDevices,
gtools, MergeMaid, methods, stats, utils, mvtnorm
methods, zlibbioc, BiocGenerics, S4Vectors, IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
lsei, SomaticSignatures, VariantAnnotation, GenomeInfoDb,
reshape2, gridExtra, corrplot, dendextend, GetoptLong,
circlize, gtrellis, PMCMR, ComplexHeatmap, KEGGREST, grDevices
biomaRt, downloader, edgeR, gplots, graphics, limma,
matrixStats, preprocessCore, readr, RColorBrewer, stats,
quantro
IRanges, XVector, Biostrings, Rcpp, S4Vectors
S4Vectors (>= 0.13.8), IRanges, XVector, Biostrings
S4Vectors, IRanges, XVector, Biostrings, Rsamtools
R.oo (>= 1.20.0), R.utils (>= 2.4.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools
affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl
simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf,
genefilter, estrogen, annaffy, gcrma
testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown
knitr, testthat, alpineData, rtracklayer, ensembldb,
BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
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,
DBI (>= 0.2-4), RSQLite (>= 0.6-4), 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, Biostrings, affy, hgu95av2.db,
human.db0, org.Hs.eg.db, Homo.sapiens, hom.Hs.inp.db, GO.db,
BiocStyle, knitr
IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation,
Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge,
rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR,
Biostrings, SummarizedExperiment, ExperimentHub
RUnit, knitr, BiocStyle, grasp2db, BiocInstaller
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata,
hgu133atagcdf
simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy,
gcrma, hugene10sttranscriptcluster.db
RColorBrewer, crlmm, ff,
BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19,
lattice, latticeExtra, RUnit, BiocGenerics
RUnit, BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
motifStack, MotifDb, trackViewer
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
aCGH, affy, limma, snapCGH, beadarray, DNAcopy
BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations,
knitrBootstrap, testthat, ggplot2, rmarkdown
tools, tkWidgets, ALL, RUnit, golubEsets
limma, DESeq2, airway, ggplot2, plyr, GenomicRanges,
testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase,
SummarizedExperiment
BiocStyle, rmarkdown, testthat (>= 0.10.0)
RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, knitr,
devtools (>= 1.4.1)
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, GenomicRanges, AnnotationDbi,
oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase,
annotate, RUnit
WGCNA, testthat, knitr, rmarkdown, BiocStyle, GOSemSim,
GSEABase
BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,
Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, Rsamtools,
GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle,
knitr
annotate, BiocStyle, knitr, rmarkdown, testthat
cluster, parallel, GenomicFeatures, dynamicTreeCut,
Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene
rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
BioMark, RUnit, BiocGenerics, BiocStyle, golubEsets,
hu6800.db, knitr, rmarkdown
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
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,
EnsDb.Hsapiens.v75, RUnit
xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi
BiocInstaller, Biobase, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg38.masked,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,
BSgenome.Scerevisiae.UCSC.sacCer1,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
testthat, RUnit, doParallel, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6),
hgu95av2.db, KEGG.db, SNPchip, geneplotter, limma, lattice,
RUnit, org.Sc.sgd.db, GOstats, GO.db
knitr, methods, GO.db, KEGG.db, estrogen, org.Hs.eg.db,
hgu95av2.db, limma, affy, genefilter
crossmeta, knitr, rmarkdown, testthat, lydata
BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db,
Biobase, tools
ChemmineR, BiocStyle, knitr, knitcitations, knitrBootstrap
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB (>=
1.3.8), ChemmineDrugs, png,rmarkdown
argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat,
Rsamtools, GenomicInteractions, GenomicRanges, IRanges,
AnnotationHub
ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle,
gridExtra (>= 2.2), testthat
reactome.db, BSgenome.Ecoli.NCBI.20080805,
BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db,
BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7,
EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle,
rtracklayer, knitr, rmarkdown, BiocStyle, testthat,
trackViewer, motifStack, OrganismDbi
clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle,
rmarkdown, testthat
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
knitr, BiocStyle, testthat, biomaRt, ggbio
knitr, testthat, ReactomePA, RUnit, BiocGenerics,
AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db,
biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods,
Biostrings,Homo.sapiens
limma, edgeR, car, Rmixmod, ggplot2 (>= 2.2.0), gridExtra (>=
2.0.0), BiocStyle, pamr, sparsediscrim, PoiClaClu,
curatedOvarianData, parathyroidSE, knitr, klaR, gtable, scales,
e1071, rmarkdown, IRanges
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), BRAIN,
UniProt.ws (>= 2.1.4)
RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS,
BiocStyle
BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
BiocStyle, knitr, diagram, testthat, scRNAseq
AnnotationHub, GSEABase, KEGG.db, knitr, org.Hs.eg.db,
prettydoc, pathview, ReactomePA, testthat, topGO
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat,
BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Ggallus.UCSC.galGal3
minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph
testthat, knitr, BiocStyle, VanillaICE (>= 1.31.3),
BiocCheck, MASS, oligoClasses, dplyr, tidyr, ggplot2
flowWorkspace (>= 3.9.66), flowCore, ncdfFlow, shiny,
testthat, devtools, Kmisc, flowWorkspaceData
BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>=
2.2.0), genefilter, NOISeq, TCC, samr, NBPSeq (>= 0.3.0)
BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr,
rtracklayer
testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust,
dendsort, HilbertCurve, Cairo, png, jpeg, tiff, fastcluster
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, minfiData, RCurl
knitr, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools,
xtable
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown,
rtracklayer, sangerseqR, testthat, VariantAnnotation
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
RUnit
knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
ncdfFlow, testthat, BiocGenerics, knitr, edgeR, limma,
glmnet, BiocStyle, flowStats
testthat, flowWorkspaceData (>= 2.11.1), knitr, ggcyto
XML, UniProt.ws, BiocStyle, knitr, rmarkdown, testthat
BiocGenerics, Biobase, testthat, BiocStyle, Prostar
mgcv, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr,
RColorBrewer, matrixStats
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL,
rrcov, Rgraphviz, NCIgraph
biomaRt, RUnit, BiocStyle, BiocGenerics, org.Hs.eg.db,
DESeq2, AnnotationDbi, BiocParallel
BiocStyle (>= 2.3.12), biovizBase, devtools (>= 1.6),
derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2,
knitcitations (>= 1.0.1), knitr (>= 1.6), limma, RefManageR,
rmarkdown (>= 0.3.3), testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene
devtools (>= 1.6), knitcitations (>= 1.0.1), knitr (>= 1.6),
BiocStyle (>= 2.3.12), rmarkdown (>= 0.3.3), testthat
biovizBase, bumphunter (>= 1.7.6), derfinderData (>= 0.99.0),
devtools (>= 1.6), knitcitations (>= 1.0.1), knitr (>= 1.6),
BiocStyle (>= 2.3.12), org.Hs.eg.db, rmarkdown (>= 0.3.3),
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, IHW,
tximport, tximportData, readr, pbapply, airway, pasilla (>=
0.2.10)
GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22),
parathyroidSE, BiocStyle, knitr
parallel, statmod, stats, DESeq, RColorBrewer
DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat
lattice, parallel, MASS, RColorBrewer, xtable
knitr, RUnit, BiocGenerics,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC,
RUnit, simulatorZ, proxy
BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat,
UpSetR
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
limma, convert, GEOquery, dyebiasexamples, methods
BiocStyle (>= 1.9.2), BSgenome (>= 1.39.0),
BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl,
GenomicFeatures (>= 1.23.15), knitr, rmarkdown, RnaSeqTutorial
(>= 0.9.0), RUnit (>= 0.4.31)
ecoliLeucine, ecolicdf, graph, multtest, affy
BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth
igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust,
MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db,
org.Hs.eg.db
DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer
parallel, snow, BiocStyle, knitr, R.utils, downloader
minfiData (>= 0.4.1), RPMM, RUnit, BiocGenerics
testthat (>= 0.3), knitr, markdown, circlize (>= 0.3.1)
BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75 (>= 0.99.8),
shiny, testthat, BSgenome.Hsapiens.UCSC.hg19, ggbio (>=
1.24.0), Gviz (>= 1.20.0)
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db
testthat, roxygen2, knitr, Biobase, SummarizedExperiment,
antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle
testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus,
TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown,
BiocStyle, EnsDb.Mmusculus.v79
testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9),
Mus.musculus, Biobase, BiocStyle
rmarkdown, BiocStyle, knitr, GO.db, BiocParallel, png, DT,
doParallel
ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
RGtk2, RCurl, RDAVIDWebService, gage, topGO, KEGGprofile,
GO.db, KEGG.db, reactome.db, RUnit, BiocGenerics,
org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi
testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel
BiocStyle, testthat, knitr, rmarkdown, reutils
Rgraphviz, flowViz, flowStats, testthat, flowWorkspace,
flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra
flowQBData, FlowRepositoryR, xlsx, RUnit, BiocGenerics
knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments,
stats
testthat, flowWorkspaceData, RSVGTipsDevice, knitr, ggcyto,
parallel
oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM,
hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf,
hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData
AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown,
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db,
GSEABase, Rsamtools, GenomicAlignments,
TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
BiocGenerics, KEGG.db, reactome.db, RUnit, GO.db, mgsa
affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db,
org.Hs.eg.db, org.Mm.eg.db, RUnit
edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db,
org.Hs.eg.db, RUnit, BiocGenerics
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
parallel, digest, crayon, RUnit, knitr, BiocGenerics
RUnit, rentrez, knitr, rmarkdown, BiocStyle
RUnit, BiocGenerics, knitr, golubEsets (>= 1.0)
GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi,
org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat
class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla,
BiocStyle, knitr
GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival
RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny,
STRINGdb
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db
CompQuadForm, logistf, survey, SNPRelate, GWASdata, RUnit,
knitr
BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter
(>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr
BiocGenerics, genomationData, knitr, knitrBootstrap,
RColorBrewer, rmarkdown
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
ShortRead, rtracklayer, BSgenome, GenomicFeatures,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19,
DESeq2, edgeR, RUnit, BiocStyle
BiocStyle, knitr, rmarkdown, DT, testthat, listviewer,
ggplot2, GenomicAlignments, Rsamtools
org.Mm.eg.db, org.Hs.eg.db, BSgenome,
BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17),
BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>=
1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1),
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
TxDb.Hsapiens.UCSC.hg38.knownGene,
SNPlocs.Hsapiens.dbSNP141.GRCh38, Rsamtools, pasillaBamSubset
(>= 0.0.5), GenomicAlignments, RUnit, BiocStyle, knitr
BiocStyle, RUnit, genefilter, deepSNV,
RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
Biobase, AnnotationDbi (>= 1.21.1), annotate, Biostrings (>=
2.25.3), Rsamtools (>= 1.13.53), SummarizedExperiment (>=
0.1.5), Matrix, GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,
DESeq2, DEXSeq, edgeR, KEGGgraph, BiocStyle, digest, RUnit,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2,
KEGG.db, hgu95av2.db, org.Hs.eg.db, org.Mm.eg.db,
org.Sc.sgd.db, pasilla, pasillaBamSubset,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene,
RNAseqData.HNRNPC.bam.chr14, hgu95av2probe
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
phastCons100way.UCSC.hg19, VariantAnnotation,
TxDb.Hsapiens.UCSC.hg19.knownGene
RUnit, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome,
Biostrings
BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL,
roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene,
rmarkdown
limma, knitr, rmarkdown, RUnit, BiocGenerics
knitr, shiny, DT, org.Ag.eg.db, org.At.tair.db, org.Bt.eg.db,
org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db,
org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db,
org.Mmu.eg.db, org.Pf.plasmo.db, org.Pt.eg.db, org.Rn.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db
vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens,
TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq,
TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat,
EnsDb.Hsapiens.v75
testthat, flowWorkspaceData, knitr, rmarkdown, flowStats,
openCyto, flowViz
GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37,
multtest, aod, rmeta
Biostrings, colorspace, EBImage, emojifont, knitr, prettydoc,
rmarkdown, scales, testthat
BiocStyle, DESeq2, limma, testthat, knitr, rmarkdown
Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db,
vsn, GSEABase, Rgraphviz
vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS,
boot, rpart
RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
LungCancerLines
BiocStyle, httpuv, knitr, rmarkdown, testthat, ggbio,
ggplot2, BSgenome.Hsapiens.UCSC.hg19, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocInstaller, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, testthat
hgu95av2.db (>= 1.13.0), ALL, GO.db (>= 1.13.0), annotate,
multtest, genefilter, RColorBrewer, Rgraphviz, xtable, SparseM,
GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics
geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, GGtools,
Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack
geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio,
BiocStyle, Homo.sapiens, RUnit, multtest, gwascat
SparseM (>= 0.36), XML, RBGL, RUnit, cluster
BiocStyle, hgu133plus2.db, org.Hs.eg.db, SPIA (>= 2.2),
topologyGSA (>= 1.4.0), clipper, ALL, testthat
BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate,
org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR,
BiocStyle
hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
limma, RColorBrewer, genefilter, mclust, edgeR, snow,
parallel, GSVAdata
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
ComplexHeatmap (>= 1.9.7), Cairo, png, jpeg, tiff
knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
GWASdata, BiocGenerics, RUnit, SNPRelate, snpStats,
VariantAnnotation
knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
h5vcData, SummarizedExperiment (>= 1.5.6), GenomicRanges,
BiocStyle
parallel, knitr, gdsfmt (>= 1.2.2), SNPRelate (>= 1.1.6)
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.13.2),
markdown, RColorBrewer, RCurl, GetoptLong
org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat
KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow
testthat, BiocStyle, airway, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr
RUnit, hgu95av2.db, knitr, GenomicRanges,
SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer,
metagenomeSeq, gplots, vegan, Biobase
BiocStyle, knitr, rmarkdown, gridExtra, testthat,
minionSummaryData
RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
XVector, GenomicRanges, GenomicFeatures, GenomicAlignments,
BSgenome.Celegans.UCSC.ce2, RUnit
MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots,
RColorBrewer, gridExtra, limma, boot, DBI, MASS
knitr, RUnit, org.Mm.eg.db, cluster, clusterProfiler,
BiocStyle
BiocStyle, knitr, testthat, magrittr,
BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset
Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db,
hgu133plus2.db, SPIA
affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db,
gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines,
statmod (>= 1.2.2), vsn
BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments,
testthat
knitr, BiocStyle, Biobase, roxygen2, devtools, xtable,
gridExtra, RColorBrewer, seqLogo, aRxiv
beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
rgl, som
BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit,
BiocGenerics
knitr, rmarkdown, testthat, lme4(>= 1.0), roxygen2(> 4.0.0),
numDeriv, car, gdata, lattice, GGally, GSEABase, NMF,
TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat
BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit,
BiocGenerics
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
MEALData, BiocStyle
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown, similaRpeak
annotate, BiocGenerics, biomformat, knitr, gss, testthat (>=
0.8), vegan, interactiveDisplay
BiocGenerics, GenomicRanges, rtracklayer, Rsamtools,
survcomp, VennDiagram, knitr, zoo, RUnit, BiocInstaller,
BSgenome, RSQLite
knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
testthat, gss
BiocStyle, knitr, MethylAidData, minfiData, RUnit
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit
BiocStyle, doParallel, testthat, knitr, rmarkdown
lumi, lattice, limma, xtable, SQN, MASS, matrixStats,
parallel, rtracklayer, Biostrings, methyAnalysis,
TCGAMethylation450k,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr
breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG,
breastCancerUNT, breastCancerUPP, breastCancerVDX, pbcmc,
MIGSAdata
knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind,
affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1
biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
breastCancerVDX
IlluminaHumanMethylation450kmanifest (>= 0.2.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1),
minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>=
1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown
human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg19, SNPchip, RUnit
seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>=
1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell,
IRanges, GenomicRanges (>= 1.8.3), BSgenome,
beadarrayExampleData
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny
knitr, RUnit, BiocGenerics, AnnotationDbi, org.Hs.eg.db,
GOstats, Category
minfiData, BiocStyle, knitr, rmarkdown, edgeR,
tweeDEseqCountData
class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL,
hgu95av2.db, som, rgl, hu6800.db, lattice, caret (>= 5.07),
golubEsets, ada, keggorthology, kernlab, mboost, party
GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma,
mouse4302.db, reactome.db
knitr, e1071, kernlab, earth, ellipse, fastICA, gam, ipred,
klaR, MASS, mda, mgcv, mlbench, nnet, party, pls, pROC, proxy,
RANN, spls, affy
MMDiffBamSubset, MotifDb, knitr, BiocStyle,
BSgenome.Mmusculus.UCSC.mm9
GOstats, graph, Category, org.Mm.eg.db, microRNA,
targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid,
class, cluster, multtest, RColorBrewer, latticeExtra
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
png
BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608,
SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown,
BSgenome.Drerio.UCSC.danRer7, BiocStyle
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr
testthat, pryr, reshape2, gridExtra, microbenchmark, zoo,
knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1),
msdata (>= 0.12.2), roxygen2, rgl, rpx, AnnotationHub,
BiocStyle, rmarkdown, imputeLCMD, norm, gplots, shiny
BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics
testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData
BiocStyle, testthat, knitr, GenomicFiles, HDF5Array,
RaggedExperiment, rmarkdown
knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase,
GEOquery
MEALData, minfi, minfiData, knitr, rmarkdown, testthat,
methylumi, omicade4, iClusterPlus, GEOquery,
MultiAssayExperiment
BSgenome (>= 1.40.0), BiocStyle (>= 2.0.3), biomaRt (>=
2.28.0), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0),
BSgenome.Hsapiens.1000genomes.hs37d5 (>= 0.99.1),
TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), rtracklayer (>=
1.32.2), testthat
msdata (>= 0.15.1), RUnit, mzID, BiocStyle, knitr, XML
RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
testthat
roxygen2 (>= 4.0.1), testthat, BiocStyle
testthat, knitr, rmarkdown, lintr, lassoshooting
BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0)
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
ALL, genefilter, limma, hgu95av2.db, ReportingTools,
BiocStyle
BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2,
pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr,
pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma,
RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt,
AnnotationDbi, GenomeGraphs, RCurl, ACME, biomaRt,
AnnotationDbi, GenomeGraphs, RCurl
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
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
annotate, genefilter, maSigPro, pamr, pdmclass, ChIPpeakAnno,
chipseq, BSgenome, Rgraphviz, affy ,annaffy, affyPLM, multtest,
ssize, sizepower, RankProd, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, edgeR, metaArray, MergeMaid, biomaRt,
GenomeGraphs,AffyCompatible, rtracklayer, Genominator, EDASeq,
limma, DESeq, DEXSeq, goseq, hugene10sttranscriptcluster.db,
mogene10sttranscriptcluster.db, ragene10sttranscriptcluster.db,
GOstats, AnnotationDbi, preprocessCore, baySeq,
HuExExonProbesetLocation, MoExExonProbesetLocation,
RaExExonProbesetLocation, snow, RmiR, RmiR.Hs.miRNA,
BSgenome.Hsapiens.UCSC.hg19, R.utils, cummeRbund,
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn4,
DESeq2, GenomicAlignments, BiocParallel, KEGG.db, miRNApath,
miRNAtap, miRNAtap.db
flowWorkspaceData, knitr, testthat, utils, tools, parallel
knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat,
knitr, rmarkdown, BiocStyle, ggplot2
Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19,
AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit
BiocStyle, knitr, rmarkdown, testthat, digest
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt,
estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW,
parallel, org.Hs.eg.db
testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr,
rmarkdown, BiocStyle, EnsDb.Hsapiens.v86 (>= 2.0.0)
breastCancerUPP, breastCancerNKI, breastCancerVDX,
breastCancerTRANSBIG, breastCancerMAINZ, breastCancerUNT
Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db,
hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db,
pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9,
pcaGoPromoter.Rn.rn4, serumStimulation, parallel
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle,
knitr, R.utils
GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma
testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet,
dplyr
foreach, doParallel, BiocStyle, knitr, rmarkdown, png,
GGally, gridExtra, ExpressionAtlas, ggforce, fgsea
yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi
org.Hs.eg.db, org.Mm.eg.db, biomaRt, knitr, BiocStyle,
AnnotationDbi, energy
BSgenome.Hsapiens.UCSC.hg38.masked,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
VariantAnnotation, SummarizedExperiment, knitr
BiocStyle, knitr, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat
quantsmooth, qvalue, samr, limma, caTools, affy,
PREDAsampledata
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2,
synapter, xtable, Rtsne, rgl, BiocStyle, hpar (>= 1.15.3),
dplyr, GO.db, AnnotationDbi
RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car
pumadata, affydata, snow, limma, ROCR,annotate
PSCBS, RUnit, BiocStyle, BiocGenerics, knitr, getopt,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
MotifDb, BSgenome.Dmelanogaster.UCSC.dm3,
PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel,
PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background,
BiocStyle, knitr
affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX,
RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf, BiocStyle
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle,
knitr, rmarkdown
readr, org.Hs.eg.db, dplyr, stringr, knitr, fdrtool
QUBICdata, qgraph, fields, knitr, rmarkdown
BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene,
biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny,
ChIPpeakAnno
BSgenome.Mmusculus.UCSC.mm9.masked,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg18.masked,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Rnorvegicus.UCSC.rn5.masked
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37,
BSgenome.Ecoli.NCBI.20080805
h5vcData, testthat, knitr, optparse,
BSgenome.Hsapiens.UCSC.hg19
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL,
igraph
limma, biomaRt, RUnit, BiocGenerics, BiocStyle
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Celegans.UCSC.ce10,
BSgenome.Dmelanogaster.UCSC.dm3, org.Mm.eg.db, org.Ce.eg.db,
org.Dm.eg.db, testthat
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite
BiocGenerics, RUnit, knitr, igraph, RColorBrewer, paxtoolsr,
rmarkdown
BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat
AnnotationDbi, BiocStyle (>= 2.3.20), DESeq2, devtools (>=
1.6), EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr
(>= 1.6), org.Hs.eg.db, regionReport (>= 1.9.4), rmarkdown (>=
0.9.5), testthat
grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown,
zoo, RUnit, BiocInstaller, BSgenome, RSQLite, RMySQL
biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.3.2),
devtools (>= 1.6), DT, DESeq, edgeR, ggbio (>= 1.13.13),
ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap,
RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker
RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla,
org.Sc.sgd.db
RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve
RUnit, BiocStyle, BiocGenerics, xtable, sna
boot, tools, RUnit, BiocGenerics, knitr, xtable
knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0)
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, ontoCAT,
RUnit, enviPat
Category, GEOquery, GOstats, Gviz,
IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS,
RnBeads.hg19, XML, annotate, biomaRt, foreach, doParallel,
ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, sva,
wateRmelon, wordcloud, argparse, glmnet, impute, GLAD,
IlluminaHumanMethylation450kanno.ilmn12.hg19, scales
GO.db, knitr (>= 1.1.0), BiocStyle, testthat, lubridate, DT,
rmarkdown
BiocGenerics, BiocStyle, CAMERA, faahKO, knitr, multtest,
rmarkdown, RUnit, xcms
org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db,
org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db,
hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI
MSnbase, Biostrings, BiocStyle, testthat, knitr, covr
GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, RUnit, BiocStyle
devtools, testthat, pander, Biobase, GenomicRanges, IRanges,
S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations,
RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation,
RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr
HTSanalyzeR, RUnit, BiocGenerics, BiocStyle, ff
BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1),
genefilter, limma, org.Hs.eg.db, hgu133plus2.db,
GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt,
knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked,
org.Hs.eg.db, org.Mm.eg.db, ggplot2
BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
IRanges, GenomicRanges, Matrix, ShortRead, graph, data.table,
RUnit
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
RUnit, BiocGenerics, knitr, knitcitations, formatR,
org.Sc.sgd.db, BioNet, DLBCL, msm
BiocStyle, cowplot, cluster, destiny, knitr, monocle,
mvoutlier, rmarkdown, Rtsne, testthat, magrittr
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
BiocStyle, scRNAseq, knitr, rmarkdown, testthat
testthat, knitr, BiocStyle, limSolve, org.Mm.eg.db, DESeq2,
monocle, S4Vectors, Rtsne, pracma
BiocParallel, digest, crayon, RUnit, Biobase, BiocGenerics,
knitr, Rcpp, SNPRelate
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
testthat, BiocStyle, knitr, rmarkdown, covr
knitr, rmarkdown, testthat, readr, clipr
BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0),
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle
affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5)
testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx
RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments,
rtracklayer, rmarkdown, BiocStyle
BiocGenerics, BiocStyle, testthat, knitr, igraph,
RUnit, BiocStyle, curatedOvarianData, parathyroidSE, superpc
BiocStyle, knitr, biomaRt, stringr, monocle
BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
parallel, RUnit, knitr, MASS, BiocGenerics
testthat, knitr, parallel,
BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations,
ggdendro, fastICA, sva
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
testthat, scran, progress, lme4, pscl, scDD, knitr,
rmarkdown, BiocStyle, covr, S4Vectors, SummarizedExperiment,
cowplot
igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
qgraph, png, grid
RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>=
1.3), roxygen2, doSNOW
RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown,
digest, jsonlite, rhdf5, HDF5Array (>= 1.4.8), airway, RUnit
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr,
scater
synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN,
BiocStyle
ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt,
BiocParallel
png, BiocStyle, rmarkdown, devtools, maftools, parmigene,
c3net, minet, dnet, Biobase, affy, testthat, limma, pathview,
clusterProfiler, igraph, supraHex
testthat, knitr, roxygen2, devtools, rvest, xml2, BiocStyle,
animation, pander
knitr, aroma.light, affxparser, RUnit, BiocGenerics
EBImage, knitr, rmarkdown, testthat, tofsimsData,
BiocParallel, RColorBrewer
RUnit, BiocGenerics, gageData, DEGraph, plotrix, org.Hs.eg.db
ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocGenerics, BiocStyle, knitr, VariantAnnotation
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
Biostrings, ggtree (>= 1.7.5), knitr, prettydoc, testthat
survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg
(>= 1.5.3), logicFS (>= 1.28.1), KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer,
GenomeGraphs
EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT
(>= 0.1.67), rtracklayer, BiocStyle (>= 2.1.23), knitr (>=
1.12), rmarkdown, testthat, covr, pander
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma,
edgeR, DESeq2 (>= 1.11.6), rhdf5, rjson
testthat, knitr, rmarkdown, BiocGenerics, RUnit
edgeR, dendextend, tximport, tximportData, ballgown, DESeq2,
readr, knitr, BiocStyle
RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132,
SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats,
ggplot2, BiocStyle
RUnit, BiocStyle, org.Hs.eg.db,
BSgenome.Hsapiens.1000genomes.hs37d5,
TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37,
MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19,
PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137
RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>=
1.13.4)
affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat
BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData,
pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart22
knitr, rmarkdown, biomaRt, GenomicFeatures, testthat,
ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi,
AnnotationFilter
knitr, DESeq, rmarkdown, BiocStyle, testthat
BiocStyle, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl,
microbenchmark, RUnit
siggenes, genefilter, MASS, RColorBrewer, GeneMeta, RUnit
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr,
rmarkdown
MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk
Rsubread, BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene
rGADEM, seqLogo, genoPlotR, parallel, VennDiagram,
RColorBrewer, vcd, MotifDb, snowfall
iplots, reshape, ggplot2, cairoDevice, OTUbase
doMC, doMPI, doSNOW, doParallel, doRedis
parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
doSNOW, VanillaICE (>= 1.21.24), RColorBrewer