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 (>=
0.23.1), Biobase (>= 1.17.0), IRanges
R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges
(>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.9.14)
R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy,
lumi
methods, grDevices, stats, utils, parallel, edgeR
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 (>= 3.4), Biostrings, GenomicAlignments, caTools,
GenomicRanges, grDevices, graphics, stats, utils
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
methods, utils, graphics, stats, parallel
R (>= 3.4.0), reticulate, methods, SummarizedExperiment, knitr
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 (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment,
GenomicRanges
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 3.3), methods, BiocGenerics, GenomicRanges (>= 1.29.14),
SummarizedExperiment (>= 1.7.8), parallel
R (>= 3.3), IRanges, GenomicRanges, plyr, dplyr, magrittr
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 3.4), 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 (>= 3.4.1),GenomicRanges, Biostrings, BSgenome, RcppRoll
R (>= 3.2), methods, grid, IRanges (>= 2.11.16), Biostrings,
GenomicRanges (>= 1.29.14), 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 (>= 3.4), stats, utils, graphics, infotheo, lattice,
latticeExtra, httr, jsonlite
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 (>= 3.1.0), grid, utils, biomaRt, Gviz, psych, ggbio,
trackViewer
R (>= 3.1.1), methods, topGO, GenomicRanges
R (>= 3.1.2), methods, 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 (>= 3.4.1), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
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 (>= 3.0.1), 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, matrixStats, BiocGenerics, S4Vectors (>=
0.15.3), IRanges (>= 2.11.17)
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 (>= 3.4), GenomicRanges, SummarizedExperiment
R (>= 3.4), GenomicRanges, InteractionSet,
SummarizedExperiment
R (>= 3.4.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges, fdrtool
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 (>= 3.3), Biobase, bsseq, splines, methods
blockmodeling, gplots, testthat, R (>= 3.0.0)
isa2, Biobase (>= 2.17.8), AnnotationDbi, methods
parallel,doParallel,foreach, SummarizedExperiment (>=
1.1.6),minfi (>= 1.22.0)
R (>= 3.1.2), methods, grid, ComplexHeatmap (>= 1.15.2),
GenomicRanges
R(>= 3.4.0), SummarizedExperiment, graph, pathview
BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.23.21),
GenomicFeatures (>= 1.29.10), AnnotationFilter (>= 1.1.9)
R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment
R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase
R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2)
R (>= 3.4), Rsamtools, GenomicRanges, ShortRead
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 (>= 2.9.11)
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, doParallel, stats,
Hmisc, utils
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), 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
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
GO.db, org.Rn.eg.db, rtracklayer, R (>= 3.3.1)
R (>= 3.3), Rsamtools (>= 1.18.2), SummarizedExperiment (>=
1.1.19), GenomicRanges (>= 1.29.14), methods
R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges
(>= 1.29.6), 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 (>= 0.3.18), rhdf5
methods, BiocGenerics, S4Vectors (>= 0.11.6), IRanges (>=
2.11.8), GenomicRanges (>= 1.29.6), 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
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(>= 3.3), methods, stats, graphics, grid, lattice, grDevices,
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 (>= 1.29.6), 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 (>= 0.23.3),
S4Vectors (>= 0.15.5)
R (>= 3.4), DiscriMiner, SummarizedExperiment, TMB (>= 1.7.6),
RcppEigen
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (> 3.0.0),GenomicFeatures, ggplot2, Biobase
R (>= 3.2.2), methods, SummarizedExperiment (>= 0.2.0), Rcpp
(>= 0.11.0), RcppArmadillo (>= 0.3.4.4)
R (>= 3.4), regioneR, GenomicRanges, methods
R (>= 3.3.0), methods, stats, utils, graphics
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 (>= 3.4.0), 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 (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment,
limma
R (>= 3.1), methods, BiocGenerics (>= 0.7.1), Biobase (>=
2.15.2), mzR (>= 2.11.11), BiocParallel, ProtGenerics (>=
1.9.1)
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
R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d
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 (>= 3.4), cn.mops, methods, utils, stats, graphics
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 (>= 2.34.1),
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 (>= 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 (>= 3.4.0), biclust, SummarizedExperiment
R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>=
0.23.3)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 3.4), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 3.4), Biobase, ggplot2, SingleCellExperiment,
SummarizedExperiment
R (>= 2.10), GO.db, RpsiXML, annotate, apComplex
R (>= 3.4), methods, SummarizedExperiment
R (>= 3.4), ggplot2, methods, SingleCellExperiment
R (>= 3.4), BiocParallel, SingleCellExperiment
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
R (>= 3.4), GenomicRanges (>= 1.26.4), VariantAnnotation(>=
1.20.3)
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 (>= 0.23.3), 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 (>= 3.4), scater, SingleCellExperiment
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 (>= 3.4), Biobase, BiocParallel, cluster, matrixStats,
stats, graphics, utils
R (>= 3.2), methods, GenomicRanges (>= 1.29.14), Biobase,
DelayedArray (>= 0.3.20)
R (>= 3.2), mgcv, genefilter, BiocParallel
R (>= 3.4.1), 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
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
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 (>= 3.4), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene,
zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit
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 (>= 2.3.11)
R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 3.3.0), GenomicRanges, ggplot2, grid
R (>= 3.4), methods, SummarizedExperiment,
SingleCellExperiment
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, DBI
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
BiocParallel, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, multtest
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
igraph, Biobase, survival, MASS, stats, RColorBrewer
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, curl,
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
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils
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, 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)
GenomicRanges, GenomicFeatures, BiocGenerics, IRanges,
GenomicAlignments, Gviz, S4Vectors, AnnotationDbi, Rsamtools,
BiocStyle
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
ggplot2
BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges,
GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid,
limma, Rsamtools, randomForest, rtracklayer, stats, motifStack
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
R.utils, utils, graphics, stats, data.table, mixtools,
GSEABase, SummarizedExperiment, 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
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>=
0.11.3), methods, coda, scran, testthat, data.table,
matrixStats, graphics, KernSmooth, grDevices, stats, utils
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
utils, Rhdf5lib, HDF5Array, DelayedArray, Rcpp (>= 0.12.14),
rhdf5, methods
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio
data.table, RCurl, digest, methods, stats, utils, dplyr,
graph, Biobase
DT (>= 0.2), dplyr (>= 0.7.2), shiny (>= 1.0.5), AlgDesign (>=
1.1.7.3), import (>= 1.1.0), methods, shinythemes, Biobase,
geNetClassifier, AnnotationFuncs, org.Hs.eg.db, DOSE,
clusterProfiler, reactome.db, ReactomePA, DiagrammeR(>= 0.7),
visNetwork, htmlwidgets, plyr, tibble
biocViews (>= 1.33.7), BiocInstaller, stringdist, graph, httr,
tools, optparse, codetools, methods, utils
methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, httr
Rgraphviz, geneplotter, graph, BiocGenerics, methods
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, git2r, httr, knitr, rmarkdown, stringr,
tools, utils
utils, XML, RCurl, AnnotationDbi, progress, stringr, httr
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
dplyr, magrittr, ggplot2, superheat, wesanderson, doFuture,
future, stats, Matrix, methods, DBI, limma, BiocParallel,
SummarizedExperiment, biotmleData (>= 1.1.1), SuperLearner,
tmle
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
Rcpp (>= 0.12.12), IRanges, GenomeInfoDb, S4Vectors,
matrixStats, preprocessCore, sva, parallel, EBImage, utils
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, stats,
BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges,
GenomeInfoDb, IRanges, S4Vectors, data.table
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
XVector, GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
rtracklayer
IRanges (>= 2.11.16), GenomeInfoDb, scales, stats, graphics,
Biobase, locfit, gtools, data.table, S4Vectors, R.utils (>=
2.0.0), matrixStats (>= 0.50.0), permute, limma, DelayedArray,
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, stats
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, cluster, impute, limma,
ConsensusClusterPlus, grDevices, survival
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
drc, flowCore, ggplot2, graphics, grDevices, grid, gridExtra,
matrixStats, methods, plotly, RColorBrewer, reshape2, stats,
utils
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCy3
BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots,
grDevices, stats, utils, xlsx
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
methods, scales, gRbase, data.table (>= 1.9.4), WGCNA, grid,
ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler,
fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools,
pracma, intergraph, grDevices, utils, network, matrixStats,
ggdendro, gridExtra, gtable
Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
Biobase, CGHbase, CGHcall, methods, stats, utils
prettydoc,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,
dplyr, BiocStyle, ArgumentCheck
AnnotationDbi, BiocGenerics, chipenrich.data, 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, utils, 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.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 (>= 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
IRanges, GenomeInfoDb, GenomicRanges, ggplot2, nabor,
BiocParallel, BiocGenerics, Biostrings, TFBSTools, Rsamtools,
S4Vectors, methods, Rcpp, grid, plotly, shiny, miniUI, stats,
utils, graphics, DT, Rtsne, Matrix, SummarizedExperiment,
RColorBrewer, BSgenome
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
methods, NMF, RColorBrewer, ape, phylobase, cluster, stats,
limma, dendextend, howmany, locfdr, matrixStats, graphics,
parallel, RSpectra, kernlab, stringr
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, matrixStats, RColorBrewer,
gtools, combinat, GenomeInfoDb (>= 1.11.6), methods,
BiocGenerics, graphics, stats, coda, SummarizedExperiment,
mclust, reshape2, ggplot2, magrittr, purrr, tidyr, dplyr,
tibble
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
affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma,
graphics, stats, utils, STRINGdb, SummarizedExperiment, minet,
rmarkdown
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, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang
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
circlize (>= 0.4.1), GetoptLong, colorspace, RColorBrewer,
GlobalOptions (>= 0.0.10)
Biobase, ALL, graphics, stats, utils, cluster
Biobase, GSVA, gdata, genefu, limma, matrixStats,
randomForest, stats, utils
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
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, SQUAREM, slam, plyr(>= 1.7.1), cowplot, gtools,
flexmix, picante, limma, parallel, reshape2, stats, utils,
graphics, grDevices
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, Rcpp
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
shiny, ConsensusClusterPlus, RColorBrewer, gplots, plyr,
ggplot2, jsonlite, ape, WGCNA
viridis, methods, shiny, graphics, stats, grDevices,
S4Vectors, flowCore, Biobase, Rcpp
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 (>= 1.43.10), flowWorkspace (>= 3.25.16), openCyto
(>= 1.11.3), XML, data.table, flowUtils (>= 1.35.7), jsonlite,
RBGL, ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics,
utils, base64enc, plyr, ggcyto (>= 1.5.4)
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 (>= 0.5),
highcharter, DAPARdata (>= 1.7.1), siggenes, graph, lme4,
readxl, clusterProfiler, dplyr, tidyr,AnnotationDbi
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, RCurl, pathview, shinyBS, googleAuthR
methods, DBI, S4Vectors, IRanges, XVector
GenomicRanges, data.table, stringr, diffr, dplyr, methods,
rjson, utils, R.utils, foreach, withr, rtracklayer,
GenomeInfoDb, settings, filehash
checkmate, data.table, DESeq2, edgeR (>= 3.13.4),
GenomicRanges, methods, stats, SummarizedExperiment
utils, methods, Biobase, BiocGenerics, ConsensusClusterPlus,
S4Vectors, SummarizedExperiment, DESeq2, ggplot2, cowplot,
ggrepel, Nozzle.R1, edgeR, cluster, logging, dplyr, tidyr,
tibble, reshape, ComplexHeatmap, knitr, grDevices, magrittr,
scales, stats, psych, rlang
graphics, grDevices, methods, stats, utils
methods, matrixStats (>= 0.53.1), Matrix, S4Vectors, IRanges
ggplot2, dplyr, purrr, readr, tibble, tidyr, broom, Biobase,
SummarizedExperiment, MSnbase, limma, vsn, fdrtool, ggrepel,
ComplexHeatmap, RColorBrewer, circlize, shiny, shinydashboard,
DT, rmarkdown, assertthat, gridExtra, grid, stats, imputeLCMD
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, 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, Rcpp
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
grDevices, stats, methods, Matrix, MASS, expm, igraph, Rcpp,
RcppArmadillo, RcppParallel, plyr, precrec
Biobase, stats, biwt, gtools, MASS, tools
utils, stats, grDevices, rtracklayer, multcomp, calibrate,
graphics
limma, missMethyl, GenomicRanges, parallel, methods, graphics,
plyr, Gviz, IRanges, stats, utils, S4Vectors
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, 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
methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy,
limma, stringr, ggplot2, graphics, grDevices, calibrate,
corrgram, gridExtra, DT, shiny, shinydashboard, readxl,
d3heatmap, prodlim, matrixStats
AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim
(>= 2.0.0), graphics, grDevices, grid, igraph, methods, qvalue,
reshape2, rvcheck, S4Vectors, scales, stats, stats4, utils
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
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,
htmltools, htmlwidgets, RCurl
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
graphics, stats, utils, methods, locfit, Rcpp
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),
Glimma (>= 1.4.0), htmlwidgets, plotly, DT
GenomicRanges, ggplot2, reshape, grid, grDevices, graphics,
methods, parallel, stats, utils, IRanges, GenomeInfoDb,
S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.5.5), plyr,
Matrix, dplyr, Gviz, ComplexHeatmap, circlize,
MultiAssayExperiment, SummarizedExperiment, biomaRt,
doParallel, downloader, ggrepel, lattice, magrittr, readr,
rvest, xml2, plotly, gridExtra
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
tools, jsonlite, parallel, RCurl, tidyr, data.table, dplyr,
stringr, stringi
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.1), IRanges
AnnotationDbi, BiocFileCache, ComplexHeatmap, DESeq2, EDASeq,
GSEABase, GO.db, KEGGREST, KEGGgraph, MASS, ReportingTools,
Rgraphviz, S4Vectors, SPIA, biocGraph, edgeR, geneplotter,
hwriter, limma, methods, rappdirs, safe, topGO
methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb,
AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors,
AnnotationHub, Rsamtools, IRanges (>= 2.11.16), ProtGenerics,
Biostrings, curl
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
epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson,
methods
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,
qvalue, reshape2, ROCR, scales, stringr
rtracklayer, S4Vectors, BiocGenerics, GenomicRanges,
SummarizedExperiment, ggplot2, Biobase, shiny, foreach,
AnnotationDbi
Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer,
ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph,
rJava, DiagrammeR, magrittr, digest, BSgenome, AnnotationDbi,
GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics,
S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid,
JASPAR2016, TFBSTools, grDevices, graphics, stats, utils,
parallel, corrplot, BiocInstaller
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, sp, rgeos, gplots, RFOC, GEOmap,
flowWorkspace (>= 3.21.5), 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, 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, grDevices, 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, VariantAnnotation
AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb,
openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny,
shinyjs, tidyr, shinythemes
BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings,
BSgenome, GenomicRanges, Rsamtools, GenomicAlignments,
matrixStats, MASS, splines, grDevices, graphics, stats, methods
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
AnnotationDbi, data.table, dplyr, graphics, networkD3,
org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db,
org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db,
org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db, org.Sc.sgd.db,
org.Ss.eg.db, org.Xl.eg.db, RColorBrewer, SnowballC, tm, utils,
wordcloud
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, Rcpp (>= 0.12.14)
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), RMySQL,
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 (>= 1.29.6), 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, Biobase, IRanges (>= 2.3.23), Biostrings,
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
httr, readr, xml2, dplyr, tidyr, magrittr, limma
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 (>= 2.11.16), GenomeInfoDb (>=
1.1.3), GenomicRanges (>= 1.29.14), SummarizedExperiment,
Biostrings, Rsamtools (>= 1.17.28), GenomicAlignments (>=
1.1.16), BSgenome, VariantAnnotation (>= 1.11.4), rtracklayer
(>= 1.25.16), GenomicFeatures (>= 1.29.11), 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 (>= 1.29.6), iterators, Biostrings,
ROCR, biglm, ggplot2, reshape2
ape, grDevices, grid, magrittr, methods, rvcheck, scales,
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, stats,
S4Vectors, utils
methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, DBI,
SparseM
Biostrings, GenomeInfoDb, GenomicRanges, IRanges, httr, rjson,
Rsamtools, S4Vectors (>= 0.9.25), Biobase, methods, utils
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), GO.db (>=
1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz
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, ggbeeswarm
AnnotationDbi, checkmate, graph, httr, rappdirs, stats, utils
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),
geneplotter, shiny, shinythemes
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 (>= 1.29.6), snpStats, Biostrings,
Rsamtools, rtracklayer, gQTLstats, Gviz, VariantAnnotation,
AnnotationHub, AnnotationDbi, GenomicFeatures, graph, ggbio,
ggplot2, SummarizedExperiment
graphics, stats, utils, methods, 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
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq,
KernSmooth, methods, utils, graphics, pheatmap, gtools
methods, utils, HilbertVis, png, grDevices, circlize (>=
0.3.3)
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
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 (>= 2.0.0), 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
utils, methods, data.table, httr, Rlabkey (>= 2.1.136),
Biobase, pheatmap, ggplot2, scales, stats, gtools, gplots,
reshape2, plotly, heatmaply (>= 0.7.0), rjson, rmarkdown,
preprocessCore, parallel
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, Rcpp
interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer,
ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi
seqLogo, Biostrings, GenomicFeatures, IRanges, seqinr,
graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL,
GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2
Biostrings, RCurl, XML, xml2, RJSONIO, sqldf, igraph, httr,
S4Vectors, IRanges, GenomicRanges, SummarizedExperiment,
methods
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2,
methods, BiocGenerics, XVector, tibble, stats, BiocParallel,
bit64, stringr, utils
Rcpp (>= 0.12.7), SpatialTools, gplots, spatstat, tiff,
RColorBrewer, methods, grDevices, graphics, stats, utils,
data.table, ggplot2, dplyr, magrittr, tibble
methods, BSgenome, plyr, reshape2, gridExtra, Biostrings,
IRanges, GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer,
ggplot2, VennDiagram, DBI, grDevices, graphics, stats, utils,
GenomeInfoDb, grid, tximport, edgeR
Rcpp, tkrplot, multtest, relimp, geneplotter, RColorBrewer,
Iso, IsoGene, ORCME, ORIClust, orQA, goric, ff, Biobase, jpeg
BiocGenerics (>= 0.7.5), IRanges, S4Vectors, GenomicRanges,
Biobase, DESeq2, reshape, tidyr, readr, dplyr, RColorBrewer,
gplots, methods, ggplot2, gtools, gridExtra, grid, grDevices,
graphics, stats, GGally, gamlss, lme4, gamlss.dist
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
shiny, survival, survminer, hwriter, plotly, ggplot2,
S4Vectors, graphics, stats, utils, UpSetR
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, IRanges, 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 (>= 1.13.6)
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 (>= 0.8.100.1.0), 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,
reshape2, utils, stats
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
ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel,
foreach, doParallel, matrixcalc
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,
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, 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, WGCNA
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), permute, Gviz, missMethyl, isva,
SummarizedExperiment, SmartSVA, graphics, stats, utils,
matrixStats
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, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75,
stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi,
MWASTools, mygene
flowCore (>= 1.4),tidyr (>=
0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices,
graphics, stats, utils
rtracklayer, gplots, tools, GenomicAlignments, GenomeInfoDb,
GenomicFeatures, IRanges, ggplot2, muStat, Rsamtools, DBChIP,
matrixStats, purrr, data.table, magrittr, methods, utils,
ensembldb, EnsDb.Hsapiens.v86, stringr
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
Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats,
GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm
methylKit, GenomicRanges, GenomeInfoDb, parallel,
BiocGenerics, S4Vectors, methods, stats, IRanges, msm
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 (>= 1.22.0),
methods, RColorBrewer, shiny, stats, SummarizedExperiment,
utils
methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors,
methods, parallel, ggplot2, gridExtra, rebus
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
stats, cluster, methods, ggplot2, gridExtra, superheat,
wesanderson, magrittr, dplyr, gtools, tmle, future, doFuture,
BiocParallel, BiocGenerics, SummarizedExperiment, GenomeInfoDb,
bumphunter, IRanges, limma, minfi
methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack,
MCMCglmm, coda, magrittr, tibble, Biobase
dplyr, reshape2, stats, tidyr, utils, vegan
AnnotationDbi, Biobase, BiocParallel, data.table, edgeR,
futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph,
graphics, grDevices, grid, GSEABase, limma, matrixStats, mGSZ,
org.Hs.eg.db, RBGL, reshape2, Rgraphviz, RJSONIO, stats, utils,
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,
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
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
ggplot2, Biobase, stats, bsseq, methods
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
corpcor, parallel, igraph, ProNet, clusterProfiler,
ReactomePA, DOSE, survival, grDevices, graphics, stats,
varhandle, utils
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
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 (>= 0.3), Rtsne, MASS,
reshape2, limma, tibble, dplyr, qlcMatrix, pheatmap, stringr,
proxy, slam, viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>=
0.12.0)
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
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, GenomeInfoDb
XML, scales, htmlwidgets,grDevices, stats, utils
graphics, grid, methods, S4Vectors, IRanges (>= 1.13.5),
Biostrings (>= 1.24.0), lattice, rGADEM, utils
S4Vectors, scales, stats, graphics, statmod
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, MALDIquant (>= 1.16), mzID (>= 1.5.2),
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, DBI, RSQLite
Rcpp, lme4, marray, limma, gplots, ggplot2, methods, grid,
ggrepel, preprocessCore, MSnbase, reshape2, survival,
minpack.lm, utils, grDevices, graphics, stats, doSNOW, snow,
foreach, data.table, MASS, dplyr, tidyr, purrr, stringr, broom
methods, GenomicRanges (>= 1.25.93), BiocGenerics,
SummarizedExperiment (>= 1.3.81), S4Vectors, IRanges, Biobase,
reshape2, shinydashboard, shiny, stats, tidyr, utils
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
BiocGenerics, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman,
limma
stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, parallel, doParallel, foreach, grDevices, graphics,
utils, SummarizedExperiment, stats
stats, parallel, S4Vectors, 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 (>= 1.12.0), Biostrings (>= 2.40.0), ggdendro (>=
0.1-20), cowplot (>= 0.9.2)
gProfileR, stringr, topGO, GOstats, annotate, AnnotationDbi,
graph
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST,
ComplexHeatmap, 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 (>= 1.9.1)
graphics, methods, baseline, signal, GenomicAlignments,
GenomeInfoDb, rtracklayer, SummarizedExperiment, limma,
trackViewer, stats, utils
BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
fda, CSAR, ICSNP
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, DBI
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
stats, utils, grDevices, graphics, methods, rexposome, limma,
sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet,
SmartSVA, isva, parallel, SummarizedExperiment, stringr
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
smatr, ggplot2, ggrepel, nem
Rtsne, plotly, gplots, grDevices, graphics, stats, utils,
methods, flowCore
Biobase, S4Vectors, methods, AnnotationDbi, stats, utils,
shiny
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, DBI, dbplyr
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
GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb,
grDevices
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
goseq, Biobase, DOSE, reshape2, igraph, org.Hs.eg.db,
org.Mm.eg.db, BiocGenerics, AnnotationDbi, JunctionSeq,
BiasedUrn, GO.db,gdata, geneLenDataBase, grDevices, graphics,
stats, utils, VennDiagram, RColorBrewer, ensembldb,
AnnotationHub, S4Vectors, dplyr, plotly, webshot, htmlwidgets ,
mgcv ,gridExtra, grid ,gplots, tibble
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
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
survival, limma, Hmisc, gplots, Category, AnnotationDbi,
hopach, biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
SNPchip, hgu133a.db, HTSanalyzeR, ellipse
SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf,
knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4,
graphics, grDevices, utils, stats
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, Biobase,
minpack.lm, BiocParallel, missForest, ropls
Biobase, mclust (>= 4.3), caret, e1071, sampling, class,
kernlab, Rtsne (>= 0.13), 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
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.9.15), DAPARdata (>= 1.7.1), rhandsontable,
data.table, shinyjs, DT, shiny, shinyAce, highcharter,
htmlwidgets, webshot
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, cluster, colourpicker, data.table, digest,
dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2,
ggrepel, grDevices, highcharter (>= 0.5.0), htmltools, httr,
jsonlite, limma, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14),
R.utils, shinyjs, stringr, stats, survival, tools, utils, XML,
xtable, methods
stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel,
biomaRt, BgeeDB, topGO, BiocInstaller, Biobase, labeling, GO.db
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, GenomicFeatures, Rsamtools,
Biostrings, BiocGenerics, rtracklayer, ggplot2, futile.logger,
VGAM, edgeR, tools, 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, 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 (>= 1.12.0),
Biostrings, rtracklayer, org.Hs.eg.db, GenomicFeatures,
rmarkdown (>= 0.9.5), genomation (>= 1.5.5), knitr (>= 1.12.3),
BiocGenerics, S4Vectors, stats, plotrix, pbapply, RSQLite,
proxy, DBI, pheatmap, ggplot2, cowplot, ggseqlogo, methods,
utils
stringr, gplots, ggplot2, methods, stats, utils, shiny
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)
graphics, grDevices, methods, stats, MASS, rgl
assertive.base (>= 0.0-7), assertive.files (>= 0.0-2),
assertive.numbers (>= 0.0-2), assertive.properties (>= 0.0-4),
assertive.sets (>= 0.0-3), assertive.types (>= 0.0-3), Biobase
(>= 2.34.0), data.table (>= 1.10.4), dplyr (>= 0.5.0), magrittr
(>= 1.5), openxlsx (>= 4.0.17), pathological (>= 0.1-2),
reshape2 (>= 1.4.2), stats, stringi (>= 1.1.5),
SummarizedExperiment (>= 1.4.0), testthat (>= 1.0.2), tidyr (>=
0.6.2), 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, methods, GenomeInfoDb, IRanges,
S4Vectors
BiocStyle (>= 2.5.19), 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
utils, stats, methods, S4Vectors, DelayedArray, reshape2,
AnnotationDbi, DBI, GO.db, rhdf5client, dplyr (>= 0.7.1),
magrittr, bigrquery, ExperimentHub, AnnotationHub
methods, utils, stats, lsr, FactoMineR, stringr, circlize,
corrplot, ggplot2, reshape2, pryr, S4Vectors, imputeLCMD,
scatterplot3d, glmnet, gridExtra, grid, Hmisc, gplots, gtools,
scales, lme4, grDevices, graphics, ggrepel, psygenet2r, mice
Biostrings, IRanges, methods, graphics, seqLogo
rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats
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
graphics, stats, utils, grid, gridExtra, reshape2, gplots,
ggplot2, plotrix, RColorBrewer, STRINGdb, MCL, linkcomm,
dynamicTreeCut, sqldf, gsubfn, hash, png, sqldf, igraph,
BgeeDB, 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
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), IRanges(>=
2.10.5), Rsamtools(>= 1.16.1), rtracklayer(>= 1.24.2),
GenomicAlignments(>= 1.5.12), S4Vectors(>= 0.14.7), graphics,
stats, utils
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 (>=
0.23.1)
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
Biobase, BiocGenerics, data.table (>= 1.9.4), GenomicRanges,
GenomeInfoDb, httr, IRanges, limma (>= 3.18), methods, plyr,
RaggedExperiment, RCircos, RCurl, RJSONIO, S4Vectors,
SummarizedExperiment, survival, XML
RedeR, minet, snow, limma, data.table, car, IRanges, igraph,
S4Vectors
survival, RColorBrewer, grDevices, graphics, stats, RTNduals,
png, utils
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
gRain, snpStats, kinship2, methods, stats, utils
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),
SummarizedExperiment, SingleCellExperiment, BiocGenerics,
S4Vectors
biomaRt, BiocGenerics, data.table, dplyr, edgeR, ggbeeswarm,
grid, limma, Matrix, matrixStats, methods, parallel, plyr,
reshape2, rhdf5, rjson, S4Vectors, shiny, shinydashboard,
stats, tximport, utils, viridis, Rcpp
fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm,
SingleCellExperiment, 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
SingleCellExperiment, SummarizedExperiment, methods, stats,
bit, dplyr, hash, reshape2, Rcpp(>= 0.12.12)
AnnotationDbi, GO.db, RpsiXML, annotate, methods,
org.Sc.sgd.db, utils
Biobase, SingleCellExperiment, SummarizedExperiment,
BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy,
utils, googleVis, ggplot2, methods, stats, e1071, randomForest,
Rcpp (>= 0.12.12)
stats, methods, graphics, grDevices, parallel, quantreg,
cluster, moments, data.table, BiocParallel,
SummarizedExperiment, S4Vectors, ggplot2, forcats
graphics, stats, utils, aroma.light, BiocParallel, class,
cluster, compositions, diptest, edgeR, fpc, gplots, grDevices,
hexbin, limma, matrixStats, mixtools, RColorBrewer, boot,
rhdf5, RUVSeq, rARPACK
Biostrings, methods, snpStats, VariantAnnotation,
GenomicRanges, BiocParallel, graphics, SummarizedExperiment
Rhtslib, biomaRt, GGally, MASS, mclust, Rcpp (>= 0.11.3),
reshape, BiocGenerics, robustbase, scales, utils, stats,
S4Vectors, SummarizedExperiment
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp (>=
0.12.14), stats, methods, utils, graphics, grDevices, Matrix,
scater, edgeR, limma, dynamicTreeCut, FNN, igraph, shiny, zoo,
statmod, ggplot2, 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, IRanges, GenomicRanges, GenomeInfoDb,
Biostrings, S4Vectors
Biostrings, cowplot, dplyr, ggplot2, grid, igraph, magrittr,
methods, rvcheck, utils
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
e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges,
methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors,
stats, utils
grDevices, graphics, stats, methods, gdsfmt, GenomicRanges,
IRanges, S4Vectors, GWASExactHW, Biobase, logistf, dplyr, tidyr
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 (>= 1.37.2),
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
Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase,
methods, rsvd, SingleCellExperiment, SummarizedExperiment,
stats
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
akima, BiocGenerics, BiocParallel, checkmate, edgeR,
fitdistrplus, ggplot2, locfit, matrixStats, methods, scales,
stats, SummarizedExperiment, utils
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
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
bigmemory, MASS, expm, gRbase, glmnet, igraph, iterators,
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 (>= 2.11.17), GenomeInfoDb (>=
1.13.1)
ape, MASS, grDevices, graphics, stats, utils
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
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
SummarizedExperiment, dplyr, ggplot2, methods, stats
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, dplyr, 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,
GenomeInfoDb, GenomicFeatures, parallel, tools, sva, limma,
xml2, httr (>= 1.2.1), matlab, circlize, ggrepel (>= 0.6.3)
ELMER (>= 2.0.0), pathview, parallel, maftools, shiny (>=
0.14.1), downloader (>= 0.4), grid, DT, plotly, readr, stringr
(>= 1.1.0), SummarizedExperiment, ggrepel, data.table,
shinyFiles (>= 0.6.2), ggplot2 (>= 2.1.0), clusterProfiler,
TCGAbiolinks (>= 2.5.5), 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, ontoProc (>= 0.99.7), SummarizedExperiment,
AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils
arules, fields, GenomicRanges, graphics, grDevices, stringr,
methods, stats
GenomicRanges, S4Vectors, grDevices, graphics, stats, utils,
IRanges
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
gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel,
flexclust, grDevices, graphics, Biobase, SPEM
methods, stats, utils, grDevices, htmlwidgets, jsonlite,
data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr
Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth,
graphics, grDevices, stats
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, htmlwidgets
biomaRt, data.table, doSNOW, foreach, graphics, grDevices,
igraph, limma, parallel, progress, RedeR, snow, stats, topGO
BiocGenerics, caret, chipseq, e1071, GenomicAlignments,
GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2,
graphics, grDevices, IRanges (>= 2.11.15), 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
RSQLite, lassopv, randomForest, flare, vbsr, foreach,
doParallel, RPostgreSQL, methods, DBI, GenomicRanges
RSQLite, lassopv, randomForest, flare, vbsr, BiocParallel,
RPostgreSQL, methods, RMySQL, DBI, BSgenome, stringr,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, Biostrings,
SNPlocs.Hsapiens.dbSNP144.GRCh38, GenomicRanges, biomaRt,
AnnotationDbi
bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel,
iterators, RColorBrewer, circlize, cgdsr, igraph, grid,
gridExtra, xtable, gtable, scales, R.matlab, 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
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, 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 (>= 1.0.0)
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
wordcloud, csaw, gplots, stats, utils, caTools, graphics,
DESeq, Biobase
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
BiocGenerics, genefilter, graphics, grDevices, gtools,
MergeMaid, methods, stats, utils, mvtnorm, RColorBrewer,
GeneMeta, siggenes
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
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
copula, glmnet, BiocParallel, softImpute, stats, genefilter,
edgeR
Rcpp, BH(>= 1.62.0-1), RProtoBufLib, cytolib(>= 0.99.6)
IRanges, XVector, Biostrings, Rcpp, S4Vectors
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
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
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, gdsfmt
RUnit, knitr, BiocStyle, grasp2db, BiocInstaller
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
DESeq2, airway, BiocStyle, knitr, rmarkdown, 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
utils, BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
MotifDb, trackViewer, testthat
Biobase, GEOquery, devtools, zoo, DT, NMF, plotly, BiocStyle,
knitr, rmarkdown, testthat
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, knitr, 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
reactome.db, org.Hs.eg.db, WGCNA, GOSemSim, GSEABase,
testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot,
targetscan.Hs.eg.db, Hmisc,
BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,
Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,
BiocStyle, knitr
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
testthat, knitr, rmarkdown, lattice, latticeExtra,
rbenchmark, gplots, gridExtra, hgu133plus2.db, ineq
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, knitr
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
RUnit, bsseqData, BiocStyle, rmarkdown, knitr,
testthat, RUnit, doParallel, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocGenerics, RUnit, knitr, RTCGA.mRNA, RTCGA.clinical
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, testthat, trackViewer,
motifStack, OrganismDbi
clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle,
rmarkdown, testthat
knitr, BiocStyle, testthat, biomaRt, ggbio
BiocStyle, devtools (>= 1.13.3), knitr, rmarkdown, testthat
JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat,
knitr, rmarkdown, pheatmap, motifmatchr
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, testthat, scRNAseq, MAST
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
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, rmarkdown, BiocCheck, MASS
flowWorkspace (>= 3.9.66), flowCore, ncdfFlow, shiny,
testthat, devtools, 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,
dendextend (>= 1.0.1)
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, minfiData, RCurl
knitr, kableExtra, 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
knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle
ncdfFlow, testthat, BiocGenerics, knitr, edgeR, limma,
glmnet, BiocStyle, flowStats
testthat, flowWorkspaceData (>= 2.11.1), knitr
XML, UniProt.ws, BiocStyle, knitr, rmarkdown, testthat
BiocGenerics, Biobase, testthat, BiocStyle, Prostar
BiocStyle, knitr, rmarkdown, DESeq2, pcaExplorer, testthat,
ggplot2
mgcv, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr,
RColorBrewer, matrixStats
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
Matrix, HDF5Array, genefilter, SummarizedExperiment, airway,
pryr, knitr, BiocStyle
testthat, HDF5Array, knitr, rmarkdown, covr, BiocStyle,
microbenchmark, profmem
BiocStyle (>= 2.5.19), 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 (>= 2.5.19), 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 (>= 2.5.19), org.Hs.eg.db, rmarkdown (>= 0.3.3),
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, IHW,
apeglm, ashr, 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
testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata,
BiocStyle, reshape2
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)
BiocStyle, digest, knitr, rmarkdown, shiny
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
BiocStyle, knitr, testthat, DT, GenomicInteractions, webshot,
rtracklayer, covr
minfiData (>= 0.4.1), RPMM, RUnit, BiocGenerics
testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer
ALL, BiocStyle, airway, hgu95av2.db, knitr
BiocStyle, knitr, rmarkdown, EnsDb.Hsapiens.v75 (>= 0.99.8),
shiny, testthat, BSgenome.Hsapiens.UCSC.hg19, ggbio (>=
1.24.0), Gviz (>= 1.20.0), magrittr
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
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, knitr, Biobase, GenomicRanges, S4Vectors,
IRanges, SummarizedExperiment, antiProfilesData,
hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens
testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus,
TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown,
BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer,
utils, RMySQL, DBI
testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9),
Mus.musculus, Biobase, BiocStyle
rmarkdown, BiocStyle, knitr, GO.db, BiocParallel, png, DT,
doParallel
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, DiagrammeRsvg,
testthat, webshot
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
BiocStyle, org.Hs.eg.db, knitr, 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
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 (>= 1.2.1), knitr, rmarkdown, BiocStyle
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
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods
BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter
(>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr
BiocGenerics, genomationData, knitr, 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, ensembldb, 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, MafDb.1Kgenomes.phase1.hs37d5,
SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation,
TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer
RUnit, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome,
Biostrings
BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL,
roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene,
rmarkdown
knitr, rmarkdown, BiocGenerics, testthat, covr
vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens,
TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq,
TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat,
EnsDb.Hsapiens.v75, tinytex
testthat, flowWorkspaceData, knitr, rmarkdown, flowStats,
openCyto, flowViz, ggjoy
GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37,
multtest, aod, rmeta
Biostrings, colorspace, EBImage, emojifont, knitr, prettydoc,
rmarkdown, 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
BiocStyle, RProtoBuf, 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, multtest, genefilter,
RColorBrewer, 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
a4Preproc, ALL, BiocStyle, clipper, codetools,
hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db,
parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat,
topologyGSA (>= 1.4.0)
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,
testthat
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
ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
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),
ggplot2
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, Gviz, knitr, rmarkdown, GeneAnswers, GO.db,
org.Hs.eg.db
RDAVIDWebService, gProfileR, topGO, KEGGprofile,
org.Dm.eg.db, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gridExtra, testthat,
minionSummaryData
RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit
MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots,
RColorBrewer, gridExtra, limma, boot, DBI, MASS
knitr, RUnit, org.Mm.eg.db, cluster, clusterProfiler,
pheatmap, BiocStyle, testthat
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
knitr, parallel, testthat, BiocStyle, rmarkdown
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,
BiocStyle
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit,
BiocGenerics
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
BiocStyle, rmarkdown
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
RUnit, BiocGenerics, similaRpeak, knitr, BiocStyle, rmarkdown
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, rmarkdown, RUnit, methylInheritance
BiocStyle, knitr, MethylAidData, minfiData, RUnit
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit,
methInheritSim
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
testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth,
nnet, gam, arm, snow, parallel, BatchJobs, minfiData,
methyvimData
BiocGenerics, BiocStyle, Cairo, knitcitations, knitr,
rmarkdown, testthat
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
BiocGenerics, RUnit, knitr, rtracklayer, utils
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny
knitr, RUnit, BiocGenerics, AnnotationDbi, org.Hs.eg.db,
GOstats, Category
BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db
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
destiny, Hmisc, knitr, Seurat, scater, testthat
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, gridExtra, microbenchmark, zoo, knitr (>=
1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>=
0.12.2), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>=
2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny
BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics
testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData
BiocStyle, testthat, knitr, R.rsp, GenomicFiles, HDF5Array,
RaggedExperiment, rmarkdown, UpSetR, survival, survminer
knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase,
GEOquery
MEALData, minfi, minfiData, knitr, rmarkdown, testthat,
methylumi, omicade4, iClusterPlus, GEOquery,
MultiAssayExperiment
BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2)
BSgenome (>= 1.40.0), BSgenome.Hsapiens.1000genomes.hs37d5
(>= 0.99.1), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle
(>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2),
biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>=
1.32.2), testthat
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML
RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
testthat
roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, lintr, lassoshooting
BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0)
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
ALL, genefilter, limma, hgu95av2.db, ReportingTools,
BiocStyle
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit
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, rmarkdown, snpStats, brgedata
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
flowWorkspaceData, knitr, testthat, utils, tools, parallel,
ggcyto
knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2,
gridExtra, knitr, Matrix, rmarkdown, scales, testthat
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
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
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 (>= 2.30.0), 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
airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr,
readr, readxl
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2,
synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3),
dplyr, GO.db, AnnotationDbi
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown
RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car
pumadata, affydata, snow, limma, ROCR,annotate
PSCBS, RUnit, BiocStyle, knitr, optparse,
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
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.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
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, covr
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, d3heatmap, glmnet, foreach, doSNOW,
parallel
BiocGenerics, RUnit, knitr, igraph, RColorBrewer, paxtoolsr,
rmarkdown
BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat
AnnotationDbi, BiocStyle (>= 2.5.19), 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
knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle
mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown
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, 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, qvalue, sva,
wateRmelon, wordcloud, argparse, glmnet, GLAD,
IlluminaHumanMethylation450kanno.ilmn12.hg19, scales,
missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit
GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), 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
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
BiocStyle, Homo.sapiens, knitr, MultiAssayExperiment, readr,
rmarkdown
HTSanalyzeR, RUnit, BiocGenerics, ff, BiocStyle, knitr,
rmarkdown
Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit,
BiocGenerics
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
knitr, rmarkdown, GEOquery, affy, airway, QUBIC
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, beachmat, cowplot, cluster, destiny, knitr,
monocle, mvoutlier, rmarkdown, Rtsne, testthat, magrittr
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2,
rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork
testthat, BiocStyle, knitr, beachmat, HDF5Array, limSolve,
org.Mm.eg.db, DESeq2, monocle, Rtsne, pracma, Biobase, irlba,
aroma.light
digest, crayon, RUnit, knitr, Rcpp, SNPRelate, Biobase,
BiocParallel, BiocGenerics, VariantAnnotation
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
testthat, BiocStyle, knitr, scRNAseq, magrittr, Rtsne
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
BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress,
pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa,
phenopath, zinbwave, BASiCS
igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel,
gridExtra, digest, doParallel
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq
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 (>= 1.5.8), airway, RUnit
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
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, pathview,
clusterProfiler, igraph, supraHex
testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2,
BiocStyle, animation, pander
knitr, aroma.light, affxparser, RUnit, BiocGenerics
EBImage, knitr, rmarkdown, testthat, tofsimsData,
BiocParallel, RColorBrewer
topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle
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, RUnit, BiocGenerics
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
Biostrings, ggtree (>= 1.7.5), knitr, prettydoc, testthat
RUnit, limma, plyr, knitr, BiocGenerics, rmarkdown
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
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, pander
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr,
rmarkdown
MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk
knitr, limma, edgeR, GEOquery, stringr, printr
knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq,
ggplot2, biomaRt, BiocStyle, Rtsne
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
Mozilla Public License 2.0 + file LICENSE