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 (>= 3.6), adductData, ExperimentHub, AnnotationHub
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 (>= 1.31.8),
SummarizedExperiment (>= 0.2.0), GenomicAlignments (>= 1.15.6)
R (>= 2.7), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.9.25), Biobase (>= 2.15.1), affy, makecdfenv, Biostrings,
hypergraph
R (>= 3.6), impute, doParallel, grDevices, dplyr, methods,
ComplexHeatmap
R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData
R (>= 2.5.0), methods, Biobase, GO.db, KEGG.db
R (>= 2.7.0), methods, utils, stats4, BiocGenerics (>=
0.29.2), Biobase (>= 1.17.0), IRanges
BiocGenerics (>= 0.15.10), BiocFileCache (>= 1.5.1)
R (>= 3.2.2), methods, utils, S4Vectors (>= 0.7.21), IRanges
(>= 2.3.23), GenomicRanges, AnnotationHub (>= 2.15.15)
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 (>= 3.5), vegan, ellipse, ggplot2, ape, SummarizedExperiment
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase
R (>= 2.14.0), rsbml, hyperdraw, LIM,stringr
R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4),
methods, minfi (>= 1.21.0), Biobase, methylumi
R (>= 3.6.0), methods, utils, graphics, stats, parallel
R (>= 3.5.0), reticulate, methods, SummarizedExperiment, knitr
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
R (>= 3.5), shiny, igraph, shinyBS, pathview
R (>= 3.5.0), methods, BiocGenerics, S4Vectors (>= 0.21.13),
IRanges, XVector (>= 0.23.2)
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 (>= 3.5), GenomicRanges, cowplot, breakpointRdata
R (>= 3.5), methods, BiocGenerics, GenomicRanges (>= 1.29.14),
SummarizedExperiment (>= 1.9.18)
R (>= 3.5), IRanges, GenomicRanges, plyr, dplyr, magrittr
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23),
GenomeInfoDb, GenomicRanges, foreach, iterators, methods,
parallel, locfit
R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio
R (>= 3.5), GenomicRanges (>= 1.30.1), rtracklayer (>=
1.38.2), SummarizedExperiment (>= 1.8.1)
R (>= 2.14.0), Biobase, binom, methods, stats
BiocGenerics, BiocParallel, EBImage, graphics, methods,
S4Vectors, 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 (>= 3.6), SingleCellExperiment, magrittr, methods, stats,
tibble, utils
R (>= 2.10), RColorBrewer, Biobase, methods, genefilter,
splots, vsn, hwriter, locfit, grid
R (>= 2.15.0), RBGL, graph, methods, hash, RCurl, Rgraphviz,
XML, ggplot2
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
R (>= 3.6), ggplot2, SingleCellExperiment
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, data.table
R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll,
parallel
R (>= 3.2), methods, grid, IRanges (>= 2.13.12), Biostrings
(>= 2.47.6), GenomicRanges (>= 1.31.8), S4Vectors (>= 0.17.25),
VennDiagram
R (>= 3.0.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19)
R (>= 2.10), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8),
ShortRead
R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25)
R (>= 3.2.0), GenomicRanges, IRanges, 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 (>= 3.6.0), methods, S4Vectors, MultiAssayExperiment,
BiocParallel
R (>= 2.15), BiocGenerics (>= 0.1.0), methods, stats
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.5.0), SingleCellExperiment, SummarizedExperiment,
BiocGenerics
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 (>= 3.6.0), grid, utils, biomaRt, Gviz, psych
R (>= 3.5.0), minfi, Homo.sapiens, mixOmics
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 (>= 3.4.0), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer
R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0)
R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
R (>= 3.3.0), shiny, shinyjs, CRISPRseek
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
R (>= 3.0.1), IRanges, AnnotationDbi, biomaRt(>= 2.17.1)
R (>= 3.0.1), methods, biomaRt, grImport2, grid, motifStack
R (>= 3.4), SummarizedExperiment, ggplot2
R (>= 3.6), foreach, parallel, doParallel
R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1),
stats, parallel
R (>= 3.5.0), AnnotationDbi, BiocParallel,
SummarizedExperiment, limma
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, stats4, matrixStats, BiocGenerics (>=
0.27.1), S4Vectors (>= 0.21.7), IRanges (>= 2.17.3),
BiocParallel
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
R (>= 3.6), parallel, SummarizedExperiment, knitr, KernSmooth
BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice
R (>= 3.5.0), 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 (>= 3.5), GenomicRanges, SummarizedExperiment
R (>= 3.5), GenomicRanges, InteractionSet,
SummarizedExperiment
R (>= 3.5.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges, fdrtool
R (>= 3.5), GenomicRanges, IRanges, S4Vectors
R (>= 3.0.0), BSgenome.Mmusculus.UCSC.mm10, GenomicRanges,
VariantAnnotation
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
R (>= 3.3), Biobase, bsseq, splines, methods
blockmodeling, gplots, testthat, R (>= 3.0.0)
isa2, Biobase (>= 2.17.8), AnnotationDbi, methods
R (>= 3.1.2), methods, grid, ComplexHeatmap (>= 1.99.0),
GenomicRanges
BiocGenerics (>= 0.15.10), GenomicRanges (>= 1.31.18),
GenomicFeatures (>= 1.29.10), AnnotationFilter (>= 1.5.2)
R (>= 3.2.0), methods, Biobase, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment
R(>= 3.6), GenomicRanges, IRanges, S4Vectors, ggplot2,
foreach, Rtsne, igraph
R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase
R (>= 3.1), methods, Homo.sapiens, GenomicFiles (>= 1.5.2)
R (>= 3.5), Rsamtools, GenomicRanges, ShortRead
R (>= 3.6), SummarizedExperiment, MultiAssayExperiment
R (>= 3.4), SGSeq, Matrix, SummarizedExperiment
Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools
Rsamtools, GenomicFeatures (>= 1.14.5), rtracklayer,
GenomicAlignments
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 2.15.9),
BiocFileCache (>= 1.5.1)
utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData
(>= 1.13.11)
R (>= 3.2.0), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2
caTools, bitops, methods, isa2, eisa, GO.db, KEGG.db,
AnnotationDbi
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, 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
Biobase, gCMAP (>= 1.3.0), methods, R (>= 3.4), Rook
R (>= 2.6.0), affy (>= 1.23.2), graphics, methods, stats,
utils
R (>= 3.5), gdsfmt, methods, BiocGenerics, DelayedArray (>=
0.5.32)
R (>= 3.0.0), igraph, RCurl, annotate, Biobase (>= 1.12.0),
methods, XML, RSQLite, MASS, Heatplus, RColorBrewer
R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges
survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10)
R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter
R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods
R (>= 3.1.0), methods, BiocGenerics (>= 0.11.2), GenomicRanges
(>= 1.31.16), 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 (>= 3.5.0), Rcpp (>= 0.12.17), methods, stats, graphics
methods, BiocGenerics, ggplot2 (>= 1.0.0)
R (>= 2.14), GGBase (>= 3.19.7), data.table, parallel,
Homo.sapiens
R (>= 3.5), Matrix, MASS, locfdr, stats, utils
R (>= 3.5), Matrix, MultiAssayExperiment, glmnet
R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0)
Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr
R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2)
R (>= 3.5.0), methods, utils, GenomicRanges, Biostrings,
BSgenome, data.table
R (>= 3.5.0), grid, Homo.sapiens,
TxDb.Hsapiens.UCSC.hg38.knownGene,
R (>= 3.0.2), MASS, parallel, S4Vectors (>= 0.17.25), IRanges
(>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8),
GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7)
R (>= 3.2), penalized, Iso, survival, methods,
graph,stats,glmnet,mvtnorm
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
GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges,
magrittr, ggplot2, methods, stats,utils ,knitr,dplyr
methods, BiocGenerics, S4Vectors (>= 0.17.39), IRanges (>=
2.13.12), GenomicRanges (>= 1.31.10), Biostrings (>= 2.41.3),
BSgenome, GenomicFeatures (>= 1.31.5), VariantAnnotation (>=
1.19.3), Rsamtools, GenomicAlignments (>= 1.15.7), rtracklayer
(>= 1.33.8), GenomeInfoDb, SummarizedExperiment
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
R (>= 3.5), utils, curl, rhdf5, R6, grid
R (>= 3.5), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5),
MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
Biostrings, GenomicAlignments, BiocParallel, hiAnnotator, R
(>= 3.0)
R (>= 2.15.0), methods, IRanges, GenomicRanges
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.12.2), methods, BiocGenerics (>= 0.1.0), Biobase,
S4Vectors, IRanges, methods, MASS, BSgenome, GenomeInfoDb (>=
1.1.3), GenomicRanges (>= 1.17.11)
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
Biobase, IRanges, GenomicRanges, RColorBrewer,
rtracklayer,graphics,GenomeInfoDb
R (>= 2.10), methods, Biobase, annotate, plotrix
R (>= 3.5.0), GenomicRanges, VariantAnnotation,
GenomicAlignments, rtracklayer, BrowserViz (>= 2.5.14)
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 (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges,
MultiAssayExperiment, SummarizedExperiment,stats
R (>= 2.14.0), plyr, ggbio, GenomicRanges
R (>= 2.10), methods, BiocGenerics, grid
R (>= 3.4), GenomicRanges, Rsamtools, SummarizedExperiment,
edgeR, S4Vectors
R(>= 2.15),gdata, scatterplot3d, Biostrings, multtest
R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1),
AnnotationHub
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 (>= 0.25.3),
S4Vectors (>= 0.21.9)
R (>= 3.5), DiscriMiner, SummarizedExperiment
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 (>= 3.5.0), S4Vectors, SingleCellExperiment,
SummarizedExperiment, methods, rhdf5, rtracklayer
R (>= 3.5), ggplot2, stats, grDevices, utils, gridExtra
R (>= 2.10), convert, graph, limma, marray, methods
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
SingleCellExperiment (>= 1.2.0), R(>= 3.5)
R (>= 3.5), BiocParallel, methods, stats, biglm
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 (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R (>= 3.6), R6 (>= 2.0), GenomicRanges, BiocParallel
R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
R (>= 2.13.0), EDASeq, DESeq, limma, qvalue
R (>= 3.4), 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 (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata,
KernSmooth
R (>= 3.5), methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools
R (>= 2.13.0), methods, Biobase, xtable, limma, statmod,
lattice, vsn
R (>= 3.5.1), 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, grImport2, grid, MotIV, ade4,
Biostrings
R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment,
limma
viridis, S4Vectors, GenomeInfoDb, GenomicAlignments,
VariantAnnotation
R (>= 3.6.0), SummarizedExperiment (>= 1.3.81)
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors,
SummarizedExperiment
R (>= 3.6), SummarizedExperiment, S4Vectors
R (>= 2.14.0), flowCore(>= 1.45.11), RcppArmadillo, methods,
BH
R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2
BiocGenerics, ggplot2, tibble (>= 1.3.1)
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 (>= 3.4), BiocParallel, GenomicFeatures,
SummarizedExperiment, data.table, methods
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 3.0.0), methods, Biobase, BiocGenerics,
R (>= 3.4), cn.mops, methods, utils, stats, graphics
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.3.0), methods, ggplot2, gridExtra
R (>= 2.10), methods, BiocGenerics, Rcpp, Gviz
stats, ggplot2, ggrepel, reshape2, lattice, grDevices, cowplot
R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats,
ppiData, annotate (>= 1.17.4)
R (>= 3.5.0), 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 (>= 3.5), methods, BiocGenerics, IRanges (>= 2.12.0),
GenomicRanges (>= 1.28.4)
R (>= 3.2.0), methods, Rsamtools (>= 1.99.1), GenomicRanges
R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph,
graph, graphite
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 (>= 3.6), BiocGenerics, SummarizedExperiment
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,
testthat
R (>= 3.5), Biostrings, BiocGenerics,methods
R (>= 3.6), parallel, GenomicRanges (>= 1.13.3), Rbowtie
GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11),
Biostrings (>= 2.47.6), 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 (>= 2.13.0), GenomicRanges, GenomicAlignments, ggplot2,
ComplexHeatmap
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
R (>= 3.0.0), methods, BiocGenerics (>= 0.8.0)
Rsamtools, GenomicRanges, IRanges, data.table, methods,
parallel
R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
R (>= 2.6.0), methods, utils, graph, grid
R (>= 3.1.2), GenomicRanges, IRanges, methods
R (>= 3.0.2), methods, GenomicRanges, abind
methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix,
grid, lattice
R (>= 2.15), methods, S4Vectors (>= 0.9.25), IRanges,
GenomicRanges, SummarizedExperiment, Rsamtools,
GenomicAlignments, rtracklayer
R (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice
R (>= 2.11.0), methods, Biobase, Rsamtools, GenomicAlignments
R(>= 3.5.0), ggplot2, pathview, edgeR, methods
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 (>= 3.6.0), 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
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 (>= 1.31.8),
Biostrings (>= 2.47.6)
R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
R (>= 3.3), methods, GenomicRanges (>= 1.31.8)
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 (>= 3.6), SingleCellExperiment, ggplot2
R (>= 2.10), GO.db, RpsiXML, annotate, apComplex
R (>= 3.4), methods, SummarizedExperiment
R (>= 3.4), ggplot2, methods, 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 (>= 3.0.2), GenomicRanges (>= 0.1.0), Biostrings (>=
2.15.0), methods
R (>= 3.6), GenomicRanges (>= 1.26.4), VariantAnnotation(>=
1.20.3)
IRanges (>= 2.13.15), GenomicRanges (>= 1.31.10), Rsamtools
(>= 1.31.2), 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 (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
R (>= 2.0.0), methods, utils, grDevices, graphics, stats,
BiocGenerics (>= 0.1.12), Biobase, affy (>= 1.33.6),
genefilter, gcrma
R (>= 3.5), Biobase, SummarizedExperiment, survival, CoxBoost,
BiocGenerics
R (>= 3.5), SummarizedExperiment, SingleCellExperiment,
DelayedArray, Biobase
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
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 (>= 3.6),SummarizedExperiment, methods, Rcpp
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 (>= 3.6), S4Vectors, IRanges, Biostrings
GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R
(>= 3.6.0)
R (>= 3.5), tidyr, SummarizedExperiment, S4Vectors,
BiocGenerics, methods, UpSetR, rlang, stringr, utils,
BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo,
crayon, tibble
R (>= 3.2), methods, GenomicRanges (>= 1.33.6), Biobase,
DelayedArray (>= 0.3.20)
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
R (>= 3.5.0), Rsamtools (>= 1.31.2), Biostrings, ShortRead (>=
1.37.1), methods
R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2),
ggplot2, plyr, openxlsx
R (>= 3.0), methods, DESeq, DESeq2, edgeR, baySeq, ROC
R (>= 3.3.1), shinydashboard (>= 0.5.3), TCGAbiolinksGUI.data
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.6.0), e1071, quadprog, SummarizedExperiment
R (>= 3.3.0), methods, utils, ProtGenerics
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R (>= 3.1.0), grDevices, methods, GenomicRanges, grid
R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq,
edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus,
gplots, plotrix, Biobase
R (>= 3.5), GenomicRanges, Structstrings
R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA
R (>= 3.5), RaggedExperiment (>= 1.3.11), mongolite
R (>= 2.15.2), methods, BiocGenerics, Biobase
methods, utils, RSQLite, RCurl, BiocGenerics (>= 0.13.8)
R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
R (>= 3.5.0), ggplot2, limma, foreach, scales, Biobase,
methods
R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb
(>= 1.15.2), GenomicRanges (>= 1.31.8), SummarizedExperiment
(>= 1.9.9), Rsamtools (>= 1.99.0)
R (>= 3.0.0), methods, BiocGenerics (>= 0.25.1),
VariantAnnotation (>= 1.13.29)
S4Vectors (>= 0.17.33), IRanges (>= 2.13.12), GenomicRanges
(>= 1.31.8), VariantAnnotation (>= 1.11.16), methods
R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28)
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 (>= 1.31.8), 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 (>= 2.9.3)
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
ggplot2, RColorBrewer, circlize, reshape2, VennDiagram, plyr,
flexdashboard, BiocParallel (>= 1.1.25), png, grid, gridExtra,
rmarkdown, knitr, vegan, ggcorrplot, ggdendro, plotly,
BiocStyle, stringr, utils, methods, grDevices, stats, tools,
graphics
Biobase, QDNAseq, ggplot2, grid, stats, utils, methods,
grDevices, GenomicRanges
Biobase, cluster, grDevices, graphics, methods, multtest,
stats, survival, splines, utils
bit, ffbase, DNAcopy, tilingArray, waveslim, cluster, aCGH,
snapCGH
origami (>= 1.0.0), tmle, calibrate, methods, graphics, stats,
utils, SummarizedExperiment
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), BiocManager, 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, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, BiocManager,
R2HTML, xtable
affy, affyPLM, Biobase, genefilter, graphics, grDevices,
lattice, RColorBrewer, simpleaffy, stats, utils, xtable
BiocParallel, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, multtest
rmarkdown, tools, methods, ggplot2, GGally, dplyr, rjson,
shiny, shinydashboard, DT, stats, utils, tximport (>= 1.11.5),
cowplot
methods, BiocGenerics, AnnotationDbi, BSgenome (>= 1.47.3),
VariantAnnotation (>= 1.25.11), Biostrings (>= 2.47.6),
S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), Rsamtools (>=
1.99.3), GenomicFeatures (>= 1.31.3), Gviz, lattice,
latticeExtra, gridExtra, seqinr, GenomeInfoDb, nlme
Biostrings, IRanges, GenomicRanges, GenomicAlignments,
Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm,
splines, graph, RBGL, stringr, stats, methods, graphics,
GenomeInfoDb, S4Vectors
callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT,
MultiAssayExperiment, circlize, curatedTCGAData, foreach,
glmnet, httr, limma, matrixStats, readr, reshape2, tibble,
rmarkdown, graphics, grid, parallel, stats, utils
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, S4Vectors, GenomeInfoDb, IRanges, Rsamtools,
bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments,
reshape2, ggdendro, ggrepel, ReorderCluster, mclust
igraph, Biobase, survival, MASS, stats, RColorBrewer
assertthat, shiny, shinyjs, DESeq2, caret, plotly, ggplot2,
rentrez, reshape2, covr, ape, vegan, dplyr, magrittr,
MultiAssayExperiment, SummarizedExperiment, S4Vectors, XML,
forcats, scales, lattice, glmnet, tsne, DMwR, plotROC, DT,
utils, limma, methods, stats, tibble, httr
DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice,
Rsamtools, genefilter, IRanges, BiocGenerics
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), RCurl
utils, methods, grDevices, RSQLite, BiocManager, curl,
rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors,
interactiveDisplayBase, httr, yaml, dplyr
GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics,
jsonlite, BiocManager, biocViews, AnnotationDbi, Biobase,
Biostrings, DBI, GenomeInfoDb (>= 1.15.4), OrganismDbi,
RSQLite, rBiopaxParser, AnnotationForge, futile.logger (>=
1.3.0), XML, RCurl
AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures,
GenomicRanges, GenomeInfoDb (>= 1.10.3), ggplot2, IRanges,
methods, readr, regioneR, reshape2, rtracklayer, S4Vectors (>=
0.17.5), stats, utils
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
shiny, shinyjs, DT, VariantAnnotation, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, rsnps, Biostrings,
MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.hs37d5,
MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.gnomADex.r2.1.hs37d5,
COSMIC.67, rentrez, PolyPhen.Hsapiens.dbSNP131,
SIFT.Hsapiens.dbSNP137, seqinr, openxlsx, Rsamtools, stringr,
utils, stats, GenomicRanges, S4Vectors, GenomicFeatures,
IRanges, GenomicScores, SummarizedExperiment
Biobase, BiocGenerics, Biostrings, DESeq, GenomicRanges,
Hmisc, IRanges (>= 2.13.11), R2HTML, RColorBrewer, Rsamtools,
ShortRead, XML, biomaRt, edgeR, grDevices, graphics, methods,
rJava, stats, svMisc, utils, sendmailR, bitops
graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter,
graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter,
lattice, latticeExtra, limma, methods, RColorBrewer, setRNG,
stats, utils, vsn (>= 3.23.3), XML, svglite
affy, Biobase, graphics, grDevices, limma, methods, stats,
utils, xtable
methods, foreach, S4Vectors (>= 0.9.25), IRanges (>= 2.13.24),
DNAcopy, oligoClasses (>= 1.21.3)
AnnotationDbi, biomaRt, bit64, circlize, cluster,
ComplexHeatmap, corrplot, data.table, dplyr, factoextra,
FactoMineR, getopt, ggdendro, ggplot2, gplots, ggrepel,
gProfileR, graphics, grDevices, grid, limma, MSstats, openxlsx,
org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics, pheatmap,
plotly, plyr, RColorBrewer, scales, seqinr, stats, stringr,
tidyr, UpSetR, utils, VennDiagram, yaml
BiocParallel, ggplot2, grDevices, gridExtra, methods, PepsNMR,
plyr, quadprog, ropls, stats, SummarizedExperiment, TSdist,
utils, Matrix, zoo
GenomicRanges, GenomicFeatures, BiocGenerics, IRanges,
GenomicAlignments, Gviz, S4Vectors, AnnotationDbi, Rsamtools,
BiocStyle
Biostrings, GenomicRanges, IRanges, graphics, grDevices,
methods, stats, utils
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
ggplot2, yaml
BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges,
GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid,
limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats,
motifStack, preseqR, utils, KernSmooth, edgeR
Rcpp, data.table, BiocParallel, BiocFileCache, rappdirs,
BSgenome, motifStack, grDevices, graphics, stats, utils, grid
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
data.table, graphics, grDevices, GSEABase, methods, mixtools,
R.utils, shiny, stats, SummarizedExperiment, utils
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
Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach,
methods, stats, graphics, ggplot2, DRIMSeq, BiocParallel
ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
magrittr, DT, lazyeval, ShortRead
Biobase, BiocGenerics, coda, cowplot, data.table, ggExtra,
ggplot2, graphics, grDevices, KernSmooth, MASS, matrixStats,
methods, Rcpp (>= 0.11.3), S4Vectors, scran, stats, stats4,
SummarizedExperiment, viridis, utils
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, BiocNeighbors, BiocSingular, Matrix, DelayedArray,
DelayedMatrixStats, scater, BiocParallel
utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva,
corpcor, moments, matrixStats, ggvis, d3heatmap, reshape2,
limma, grDevices, graphics, stats, methods, Matrix
Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, parallel,
MASS, locfit, fitdistrplus, stats, methods, graphics,
grDevices, SingleCellExperiment, SummarizedExperiment,
BiocParallel, utils
SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices,
GenomicRanges, IRanges, Biostrings
Rcpp (>= 0.12.12), RcppArmadillo, RcppEigen, stats
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio, methods, ggplot2
ggplot2, SingleCellExperiment, data.table, stats, utils,
graphics, compiler
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
stats, graphics, utils, methods
data.table, RCurl, digest, methods, stats, utils, dplyr,
graph, Biobase
stats, utils, GEOquery, graphics, BiocGenerics
DT (>= 0.3), 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), BiocManager, stringdist, graph, httr,
tools, optparse, codetools, methods, utils, knitr
methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, curl,
httr
methods, utils, graphics, stats, parallel
Rgraphviz, geneplotter, graph, BiocGenerics, methods
Rcpp, BiocGenerics, S4Vectors, BiocParallel, stats, methods
ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr,
rjson, dplyr, magrittr, grid, utils, DT, GenomicRanges,
IRanges, ggplot2, SummarizedExperiment, DBI, GenomicFeatures
stats, utils, futile.logger, parallel, snow
BiocManager, biocViews, tibble, stringr, rvest, rex, dplyr,
xml2, readr, httr, htmltools, DT, tools, utils, igraph, tidyr,
jsonlite, gh, RBGL, graph, magrittr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, irlba, rsvd, Rcpp
bookdown, knitr (>= 1.12), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit, BiocManager
BiocStyle, bookdown, devtools, git2r, httr, knitr, rmarkdown,
rstudioapi, stringr, tools, utils, usethis
utils, XML, RCurl, AnnotationDbi, progress, stringr, httr
stats, utils, grDevices, lattice, BiocParallel, glmnet, rms,
nsprcomp, ranger, e1071, variancePartition, ggplot2
igraph (>= 1.0.1), AnnotationDbi, Biobase
BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr,
utils, stats, RColorBrewer, Hmisc, psych, knitr
Biostrings, ipred, e1071, klaR, randomForest, class, tree,
nnet, rpart, party, foreign, Biobase, utils, stats, grDevices
BiocGenerics, Biobase, methods, grid, graphics, NMF
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, future, doFuture, S4Vectors, BiocGenerics,
BiocParallel, SummarizedExperiment, limma, 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), rlang
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, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc,
magrittr, kernlab, ggplot2, cowplot, BiocStyle
BiocGenerics, ExperimentHub, ggplot2, grDevices, grid,
gridExtra, methods, randomForest, RColorBrewer, stats, testthat
plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt,
Biostrings, parallel, utils, stats,
BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges,
GenomeInfoDb, IRanges, S4Vectors, data.table
methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>=
1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2,
BiocGenerics, gtools, doParallel, foreach
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 (>= 1.11.8), S4Vectors,
R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2), permute,
limma, DelayedArray (>= 0.9.8), Rcpp, BiocParallel, BSgenome,
Biostrings, utils, HDF5Array (>= 1.11.9), rhdf5
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
gplots, methods, grDevices, stats, SummarizedExperiment
affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase
beanplot, BiocGenerics, BiocParallel, BSgenome, data.table,
DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments,
GenomicRanges (>= 1.23.16), ggplot2 (>= 2.2.0), gtools, IRanges
(>= 2.5.27), KernSmooth, memoise, MultiAssayExperiment, plyr,
Rsamtools, reshape, rtracklayer, S4Vectors, som, stringdist,
stringi, SummarizedExperiment, utils, vegan, VGAM
methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph
methods, rJava, BiocParallel, stats, Biobase,
SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR,
pcaPP, apcluster, graphics
GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart,
survival, Biobase, phenoTest, circlize, plyr, graphics, stats,
utils, grDevices
SNFtool, iCluster, cluster, impute, limma,
ConsensusClusterPlus, grDevices, survival
Biobase, dplyr, grid, irlba, lattice, Matrix, matter,
magrittr, mclust, nlme, parallel, signal, sp, stats4, utils,
viridisLite
BiocGenerics, coda, EBarrays, gaga, gtools, GenomeInfoDb,
GenomicFeatures, limma, mgcv, Rsamtools, rtracklayer, S4Vectors
(>= 0.9.25), sqldf, survival, VGAM
Biobase, circlize, ComplexHeatmap, ConsensusClusterPlus,
data.table, dplyr, drc, DT, flowCore, FlowSOM, ggplot2,
ggrepel, ggridges, graphics, grDevices, grid, gridExtra,
htmltools, limma, magrittr, matrixStats, methods, nnls, plotly,
purrr, RColorBrewer, reshape2, Rtsne, S4Vectors, scales,
scater, shiny, shinydashboard, shinyBS, shinyjs,
SingleCellExperiment, stats, SummarizedExperiment, utils
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29),
methods, grDevices, utils
BiocFileCache, RColorBrewer, cgdsr, genefilter, gplots,
grDevices, stats, utils, xlsx
stats, S4Vectors, utils, methods, Matrix,
SummarizedExperiment, SingleCellExperiment, Rtsne, graphics,
grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp
MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang,
BiocGenerics, S4Vectors, readr, tibble, DelayedArray
stats, plyr, foreach, ggplot2, RColorBrewer, grid, scales,
gtable, grDevices, graphics, matrixStats, doParallel, digest,
gridExtra, methods, reshape2, MAST, S4Vectors, data.table,
Rcpp, RcppEigen, umap, enrichR, stringi, SummarizedExperiment,
MCMCprecision, ggrepel, Rtsne, withr
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
BiocFileCache, BiocParallel, dplyr, rlang, glue, memoise,
purrr (>= 0.3.0), rappdirs, tidyr, lubridate
prada, GSEABase, Category, stats4, BiocGenerics
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
BiocNeighbors, ggplot2, scater, viridis, cowplot,
SummarizedExperiment, SingleCellExperiment, tidyr, magrittr,
dplyr, ggridges, stats, purrr, listarrays, methods,
BiocParallel
BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats,
ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv,
reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
topicmodels, slam, maptpx, igraph, xtable, gplots
methods, scales, gRbase, dplyr, 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, GeneOverlap, limma,
tidyr, plyr, ff, ffbase, RColorBrewer
Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
Biobase, CGHbase, CGHcall, methods, stats, utils
prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
limma,RPMM, DNAcopy, preprocessCore,impute, marray, wateRmelon,
plyr,goseq,missMethyl,kpmt,
GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly
(>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat
SummarizedExperiment, FactoMineR, factoextra, IRanges,
graphics, modes, parallel, plyr, cluster, diptest, stats,
matrixStats
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, png,base64enc,DT,rsvg
gplots, shiny, plotly, pheatmap, bioDist, dendextend, cowplot,
corrplot, grDevices, stats, graphics, reshape2, S4Vectors,
SummarizedExperiment
ChIC.data (>= 1.3.3), caTools, methods,GenomicRanges, IRanges,
parallel, progress, caret, grDevices, stats, utils, graphics,
S4Vectors, BiocGenerics
matrixStats, MASS, Hmisc, Delaporte, methods, grDevices,
graphics, stats, utils
methods, grid, Rsamtools, GenomeInfoDb, GenomicAlignments,
RColorBrewer, graphics, AnnotationDbi, RCircos, org.Hs.eg.db,
org.Mm.eg.db, rmarkdown, graph, Rgraphviz, DT, plyr, dplyr,
BiocStyle, ArgumentCheck, gtools
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, BiocManager, stats, regioneR,
DBI, ensembldb, Biobase, seqinr, idr, GenomicAlignments,
DelayedArray, SummarizedExperiment, rtracklayer, 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, enrichplot, IRanges (>=
2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8),
GenomicFeatures (>= 1.31.3), ggplot2 (>= 2.2.0), gplots,
graphics, grDevices, grid, gridBase, gtools, methods, plotrix,
dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors
(>= 0.17.25), 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
tools, stringr, Rsamtools, GenomicRanges, IRanges, seqplots,
ggplot2, LSD, corrplot, methods, stats, grDevices, graphics,
utils, BiocGenerics, S4Vectors
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
Biobase, GEOquery, frma, affy, bigmemory, biganalytics
graphics, stats, utils, methods, survival
cluster, DPpackage, ICSNP, ellipse, vegan
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,
igraph, circlize, graph, stats, utils, grDevices, graphics,
methods, biomaRt
bitops,gplots,grDevices,som,
dplyr,gridExtra,png,stringr,S4Vectors, IRanges,
GenomeInfoDb,graphics, stats, utils
BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges,
utils, BSgenome.Drerio.UCSC.danRer7
methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor, RBGL
mzR, S4Vectors, dbscan, RColorBrewer, ape, network, GGally,
ggplot2, plotly, methods, utils, stats, sna, grDevices,
graphics, Biobase, gplots, MSnbase
methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats,
limma, howmany, locfdr, matrixStats, graphics, parallel,
RSpectra, kernlab, stringr, S4Vectors, grDevices, DelayedArray
(>= 0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR,
scales, zinbwave, phylobase, pracma
AnnotationDbi, DOSE (>= 3.5.1), enrichplot (>= 0.99.7),
ggplot2, GO.db, GOSemSim, magrittr, methods, plyr, qvalue,
rvcheck, stats, tidyr, utils
methods, pracma, princurve (>= 2.0.5), 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, scales, data.table, RcppArmadillo
S4Vectors, grDevices, stats, utils, NOISeq, IRanges,
Rsamtools, exomeCopy, foreach, ggplot2, plyr, GenomeInfoDb,
gplots, reshape2, stringr, testthat, graphics, methods, shiny,
shinyFiles, shinyjs, grid, openxlsx
BiocParallel, GDSArray, GenomeInfoDb, Gviz, IRanges,
S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR,
gdsfmt, grDevices, lattice, limma, methods, plyr, qqman,
rappdirs, reshape2, stats, utils
methods, seqinr, yaml, rtfbs, gplots, mclust, gmp,
BiocGenerics (>= 0.13.8), IRanges, Biostrings, BSgenome,
biomaRt
BiocGenerics, S4Vectors, IRanges, data.table, ggplot2,
Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid,
grDevices
affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma,
graphics, stats, utils, STRINGdb, SummarizedExperiment, minet,
rmarkdown
BiocParallel, cluster, data.table, methods, gplots, graphics,
grDevices, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
stats, SummarizedExperiment, tools, utils, rhdf5
methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, dplyr, devtools
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.0.0), matrixStats, GetoptLong, circlize (>= 0.4.7),
GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer,
cluster, skmeans, png, mclust, crayon, methods, xml2,
microbenchmark, httr, knitr, markdown, digest, impute, brew,
Rcpp (>= 0.11.0), BiocGenerics, eulerr
colortools, hash,grDevices, gridExtra, rtracklayer, IRanges,
S4Vectors, GenomicRanges, stats, corrplot
methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown
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 (>= 0.4.5), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), parallel, png
matrixStats, gplots, grDevices, methods, graphics, stats,
utils
Biobase, ALL, graphics, stats, utils, cluster
airway, AnnotationDbi, BiocParallel, Biobase, Biostrings,
data.table, dendextend, DESeq2 (>= 1.20.0), EDASeq, ensembldb,
edgeR, EnsDb.Hsapiens.v86, GenomicAlignments, GenomicFeatures,
limma, org.Hs.eg.db, pcaMethods, RColorBrewer, Rsamtools,
RUVSeq, S4Vectors, stats, SummarizedExperiment,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, utils
Biobase, GSVA, gdata, genefu, limma, matrixStats,
randomForest, stats, utils
GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods
data.table, 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
regioneR, IRanges, Rsamtools, SummarizedExperiment,
VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges,
cn.mops, utils
matrixStats, gtools, data.table, S4Vectors, chipseq, IRanges,
Rsamtools, DNAcopy, GenomicAlignments, GenomicRanges,
CopyhelpeR, GenomeInfoDb, futile.logger
methods, stats, utils, Biostrings, Biobase, dplyr, stringr,
purrr, ggplot2, data.table
edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2
(>= 2.1.0), scales, HTSFilter, corrplot, HTSCluster (>= 2.0.8),
grDevices, graphics, stats, methods, compositions, mvtnorm
SQUAREM, slam, maptpx, plyr(>= 1.7.1), cowplot, gtools,
flexmix, picante, limma, parallel, reshape2, stats, utils,
graphics, grDevices
rmarkdown (>= 0.9.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr,
ggplot2, grDevices, tools, SummarizedExperiment, genefilter,
DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods
S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges,
GenomicAlignments, parallel, tools
parallel, genefilter, grDevices, stats, graphics
methods, corpcor, BiocParallel, ggplot2, plyr
parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges,
BSgenome, BiocParallel, hash
DT, utils, GUIDEseq, GenomicRanges, GenomicFeatures,
BiocManager, 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
Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures,
AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb,
stats, BiocParallel, utils
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache, rappdirs
data.table, limma, stats, fgsea, pbapply, plyr, cowplot,
ggplot2, rhdf5, R.utils, httr, methods, piano, readr, utils,
graphics
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
S4Vectors (>= 0.9.25), DBI, GenomeInfoDb, GenomicRanges,
Rsamtools (>= 1.10.2), GenomicAlignments, Biostrings (>=
2.26.3), GenomicFeatures (>= 1.32.0), stringr, RCurl, plyr,
VariantAnnotation (>= 1.13.44), rtracklayer, RSQLite,
AhoCorasickTrie, methods
shiny, ConsensusClusterPlus, RColorBrewer, gplots, jsonlite,
ape, WGCNA
viridis, methods, shiny, graphics, stats, grDevices, utils,
BiocGenerics, S4Vectors, flowCore, Biobase, Rcpp,
BiocNeighbors, SummarizedExperiment
doParallel, dplyr, glmnet, rpart, rpart.plot, stats,
flowCore,grDevices, graphics, utils
flowCore, ggplot2, ggridges, RColorBrewer, reshape2, stats,
grDevices, Rdpack, methods, grid, FlowSOM
flowCore (>= 1.43.10), flowWorkspace (>= 3.31.17), openCyto
(>= 1.11.3), XML, data.table, flowUtils (>= 1.35.7), jsonlite,
RBGL, ncdfFlow, Rgraphviz, Biobase, methods, graph, graphics,
utils, base64enc, plyr, dplyr, grDevices, methods, ggcyto (>=
1.11.4), yaml, lattice
pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils
DESeq2, limma, EDASeq, RColorBrewer, sva, Hmisc, pheatmap,
FactoMineR, corrplot, randomForest, e1071, caret, MASS,
lubridate, plsVarSel, kknn, FSelector, methods, stats, utils,
graphics, grDevices, reshape2, ineq, arm, pls, RSNNS, edgeR
MSnbase, RColorBrewer,stats,preprocessCore,Cairo,png,
lattice,reshape2,gplots,pcaMethods,ggplot2,
limma,knitr,tmvtnorm,norm,impute, stringr, grDevices, graphics,
openxlsx, utils, cp4p (>= 0.3.5), scales, Matrix, vioplot,
imp4p (>= 0.8), highcharter (>= 0.5.0), DAPARdata (>= 1.11.2),
siggenes, graph, lme4, readxl, clusterProfiler, dplyr,
tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
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
plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore,
flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks
shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT,
ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE,
igraph, grDevices, graphics, stats, utils, GenomicRanges,
IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2,
d3heatmap, org.Hs.eg.db, org.Mm.eg.db, limma, edgeR,
clusterProfiler, methods, sva, RCurl, enrichplot, colourpicker,
plotly, heatmaply, Harman, pathview
methods, DBI, S4Vectors, IRanges, XVector
stats, methods, ggplot2, foreign, graphics, BiocStyle,
Biobase, cluster, gplots, RColorBrewer, locfit, made4, ade4,
sfsmisc, scatterplot3d, gdata, grDevices, utils, reshape2,
gridExtra
Rcpp (>= 0.12.7), DESeq2, edgeR, SummarizedExperiment,
ComplexHeatmap, grid, parallel, BiocParallel, grDevices,
graphics, stats, methods, utils
methods, Matrix, quadprog(>= 1.5-5), vcfR, GenomicRanges,
stats, GenomicFeatures, Biostrings, BiocGenerics, S4Vectors,
plyr, utils, graphics, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
SummarizedExperiment, ggseqlogo, gridExtra, data.table
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, S4Vectors, stats, SummarizedExperiment
utils, methods, Biobase, BiocGenerics, broom, circlize,
ComplexHeatmap, cowplot, ConsensusClusterPlus, cluster, DESeq2,
dplyr, edgeR, ggplot2, ggdendro, grid, ggrepel, grDevices,
knitr, logging, lasso2, magrittr, Nozzle.R1, psych,
RColorBrewer, reshape, rlang, scales, stats, stringr,
S4Vectors, SummarizedExperiment, tidyr, tibble
graphics, grDevices, methods, stats, utils
methods, matrixStats (>= 0.55.0), Matrix, S4Vectors (>=
0.17.5), IRanges, HDF5Array (>= 1.7.10), BiocParallel
ggplot2, dplyr, purrr, readr, tibble, tidyr,
SummarizedExperiment (>= 1.11.5), MSnbase, limma, vsn, fdrtool,
ggrepel, ComplexHeatmap, RColorBrewer, circlize, shiny,
shinydashboard, DT, rmarkdown, assertthat, gridExtra, grid,
stats, imputeLCMD, cluster
BiocGenerics (>= 0.25.1), AnnotationDbi (>= 1.27.9),
BiocParallel (>= 1.15.15), 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), stats
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, RefManageR, reshape2,
S4Vectors (>= 0.9.38), scales, utils
BiocParallel, BiocGenerics, ChIPpeakAnno, data.table,
DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges,
plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors,
SummarizedExperiment, tools, 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,
SummarizedExperiment, ggplot2, ggthemes, VIM, proxy, igraph,
smoother, scales, scatterplot3d
graph, igraph, RBGL, circlize, limma, edgeR, 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, lattice,
systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel,
parallel, S4Vectors, Rsamtools (>= 1.99.1), DESeq2, methods,
graphics, ggrepel
stats, DiffCorr, psych, igraph, BiocGenerics
flowCore, FlowSOM, SummarizedExperiment, S4Vectors, limma,
edgeR, lme4, multcomp, dplyr, tidyr, reshape2, magrittr, stats,
methods, utils, grDevices, graphics, ComplexHeatmap, circlize,
grid
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,
rtracklayer
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
matrixTests, matrixStats, MetaCycle (>= 1.2.0), data.table,
ggplot2, ggExtra, dplyr, broom, shiny, shinyBS,
shinycssloaders, shinydashboard, shinyjs, BiocStyle, rmarkdown,
knitr, kableExtra, magick, VennDiagram, UpSetR, heatmaply,
viridis, plotly, DT, gridExtra, methods, stats,
SummarizedExperiment, BiocGenerics, S4Vectors
utils, stats, grDevices, rtracklayer, multcomp, calibrate,
graphics
parallel, Rcpp, RcppRoll, betareg, grDevices, graphics,
methods, stats, utils
limma, missMethyl, GenomicRanges, parallel, methods, graphics,
plyr, Gviz, IRanges, stats, utils, S4Vectors
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb,
methods, mvtnorm, stats, parallel
GenomicRanges, nlme, ggplot2, S4Vectors, RColorBrewer,
bumphunter, DelayedMatrixStats (>= 1.1.13), matrixStats,
BiocParallel, outliers, methods, locfit, IRanges, grDevices,
graphics, stats, utils, annotatr, AnnotationHub, rtracklayer,
GenomeInfoDb, splines
dplyr, tidyr, numbers, purrr, stringr, DNABarcodes, stats,
utils, methods
biomaRt, data.table, utils, stats, Biostrings,
SummarizedExperiment, VariantAnnotation, AnnotationDbi,
GenomeInfoDb, IRanges, GenomicRanges
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, SummarizedExperiment, 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), methods, qvalue, reshape2, S4Vectors, stats, utils
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
ggplot2, httr, dplyr, readr, stringr, tidyr
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
S4Vectors, BiocParallel, Rcpp, Matrix, methods, utils, stats,
edgeR, rhdf5, HDF5Array, R.utils, dqrng
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
stats, Rcpp (>= 0.11.3), ggplot2, reshape2, GO.db,
org.Hs.eg.db, AnnotationDbi, graphics
Biobase (>= 2.41.2), BiocFileCache (>= 1.7.10), BiocGenerics
(>= 0.27.1), BiocParallel (>= 1.15.15), biomaRt (>= 2.37.9),
Biostrings (>= 2.49.2), DESeq (>= 1.33.0), edgeR (>= 3.23.6),
GenomeInfoDb (>= 1.17.4), genomeIntervals (>= 1.37.0),
GenomicAlignments (>= 1.17.3), GenomicRanges (>= 1.33.14),
SummarizedExperiment (>= 1.11.6), graphics, IRanges (>=
2.15.18), LSD (>= 4.0), locfit, methods, parallel, rappdirs (>=
0.3.1), Rsamtools (>= 1.33.7), S4Vectors (>= 0.19.23),
ShortRead (>= 1.39.0), utils
Biobase, cluster, graphics, grDevices, lattice, methods, stats
BiocGenerics (>= 0.7.1), 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, BiocManager
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
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, gespeR,RcppAnnoy (>= 0.0.9)
GenomicRanges, ggplot2, reshape, grid, grDevices, graphics,
methods, parallel, stats, utils, IRanges, GenomeInfoDb,
S4Vectors, GenomicFeatures, TCGAbiolinks (>= 2.9.2), plyr,
Matrix, dplyr, Gviz, ComplexHeatmap, circlize,
MultiAssayExperiment, SummarizedExperiment, biomaRt,
doParallel, downloader, ggrepel, lattice, magrittr, readr,
scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr,
tibble, tidyr, progress, purrr, ggpubr, rtracklayer,
DelayedArray
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
tools, jsonlite, RCurl, tidyr, data.table, dplyr, stringr,
stringi, utils, AnnotationHub
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap,
DESeq2, EDASeq, GSEABase, GO.db, KEGGREST, KEGGgraph, MASS,
ReportingTools, Rgraphviz, S4Vectors, SPIA, biocGraph, edgeR,
geneplotter, graphite, hwriter, limma, methods, pathview,
rappdirs, safe, topGO
AnnotationDbi, cowplot, DOSE (>= 3.5.1), europepmc, ggplot2,
ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices,
grid, gridExtra, igraph, methods, purrr, RColorBrewer,
reshape2, stats, UpSetR, utils
BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils,
methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, utils, parallel, stats
methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb,
AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors, Rsamtools,
IRanges (>= 2.13.24), ProtGenerics, Biostrings (>= 2.47.9),
curl
S4Vectors (>= 0.9.25), Biostrings, SummarizedExperiment,
GenomeInfoDb, stats
MASS, e1071, quadprog, parallel, stats, matrixStats, stringr
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
data.table, doParallel, EntropyExplorer, graphics, stats,
grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA
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, BiocGenerics
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 (>= 1.38.1), S4Vectors, BiocGenerics,
GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb,
Biobase, shiny, BiocParallel, IRanges, 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, BiocManager, motifmatchr
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
cluster (>= 2.0.7-1), corrplot (>= 0.84), grDevices, graphics,
stats, Rdpack
GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls,
limma, matrixStats, RBGL, prodlim, graph, methods, utils,
stats, doParallel, foreach, affxparser, GenomicRanges,
S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome,
BSgenome.Hsapiens.UCSC.hg38, Biostrings
stats, methods, grDevices, graphics, utils
utils, S4Vectors, BiocManager, curl, rappdirs
methods, ExperimentHub, BiocManager, DBI, BiocCheck, httr,
curl, biocViews, graph
methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi
methods, graphics, grDevices, stats, utils
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
affy, MASS, Biobase (>= 1.13.41), methods, graphics
methods, shiny, stats, IRanges, Biostrings, ShortRead, DT,
methods, S4Vectors, graphics, htmltools, shinyBS, Rcpp (>=
0.12.12)
methods, graphics, stats, BiocGenerics, S4Vectors, IRanges
ggplot2, gridExtra, pbapply, parallel, SummarizedExperiment,
stats, mclust
fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap,
grDevices, stats, utils
tcltk, graphics, grDevices, stats, utils
methods, igraph, Matrix, KEGGREST, plyr, stats, graphics,
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, Matrix, utils
methods, BiocGenerics, Biobase, tools, dplyr, IRanges,
Biostrings, S4Vectors, kebabs, igraph, Matrix, digest,
filehash, Rcpp, ggplot2, gtable, grid, reshape2, ggdendro,
BiocParallel, utils, stats
graphics, stats, utils, methods, abind, gtools, qvalue,
S4Vectors, SummarizedExperiment, matrixStats, svMisc
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,
rmarkdown
colorRamps, abind, BiocParallel, graphics, stats, utils,
plotly, shiny
methods, flowCore, EBImage, vegan, hexbin, ggplot2, grid
BiocGenerics, methods, Biobase, graph, ellipse, flowViz,
flowCore, clue, corpcor, mnormt, parallel
Biobase, BiocGenerics (>= 0.29.2), graph, grDevices, graphics,
methods, rrcov, stats, utils, stats4, corpcor, Rcpp,
matrixStats, MASS
flowCore, graphics, car, sp, rgeos, gplots, RFOC,
flowWorkspace (>= 3.20.5), methods, stats, 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, fda (>= 2.2.6), Biobase, methods,
grDevices, graphics, stats, utils, KernSmooth, lattice,ks,
RColorBrewer
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, tools, gridExtra,
Rgraphviz, data.table, dplyr, latticeExtra, Rcpp, RColorBrewer,
stringr, scales, flowViz, matrixStats, digest, RcppParallel
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
stats, utils, methods, Matrix, fastmatch, plyr, dplyr,
magrittr, data.table, igraph, graph, RBGL, GO.db, org.Hs.eg.db,
org.Mm.eg.db, GOSemSim, GEOquery, AnnotationDbi, Biobase,
BiocFileCache, matrixStats
DaMiRseq, MLSeq, stats, methods, SummarizedExperiment
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings,
BSgenome, GenomicRanges, Rsamtools, GenomicAlignments,
matrixStats, MASS, splines, grDevices, graphics, stats, methods
Biobase, methods, GSEAlm, Category, Matrix (>= 1.0.9),
parallel, annotate, genefilter, AnnotationDbi, DESeq,
grDevices, graphics, stats, utils, bigmemory, bigmemoryExtras
(>= 1.1.2)
brew, BiocGenerics, annotate, AnnotationDbi, graphics,
grDevices, GSEABase, hwriter, parallel, stats, utils, yaml
Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db,
rmarkdown, grDevices, graphics, stats, utils, parallel
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2,
clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival,
survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons,
BiocParallel
tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray
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 (>= 2.13.15), GenomicRanges (>=
1.31.10), GenomicFeatures (>= 1.31.5), Biostrings,
VariantAnnotation, rtracklayer, S4Vectors (>= 0.17.28),
GenomeInfoDb, Biobase
biomaRt, caTools, dplyr, ggplot2, graphics, grDevices, gtools,
ggpubr, magrittr, maxLik, RColorBrewer, reshape2, stats,
tibble, utils
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,grDevices, graphics,stats, utils, methods
plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods,
grDevices, stats, graphics
igraph, snow, ape, grDevices, graphics, stats, utils
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,
IRanges, S4Vectors, SeqArray, SeqVarTools, SNPRelate,
data.table, dplyr, foreach, graphics, grDevices, igraph,
Matrix, methods, reshape2, stats, utils
gmodels, graphics, gtools (>= 2.4.0), mvtnorm, stats
data.table, dplyr, graphics, networkD3, RColorBrewer,
SnowballC, tm, utils, wordcloud, AnnotationDbi, BiocStyle,
org.Rn.eg.db
Biostrings (>= 2.47.6), BSgenome (>= 1.47.3), data.table,
GenomeInfoDb, GenomicRanges (>= 1.31.8), GenomicAlignments (>=
1.15.6), S4Vectors (>= 0.17.25), ggplot2, gridBase, impute,
IRanges (>= 2.13.12), matrixStats, methods, parallel, plotrix,
plyr, readr, reshape2, Rsamtools (>= 1.31.2), seqPattern,
rtracklayer (>= 1.39.7), 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, rlang, readr,
GenomicRanges, IRanges, dplyr, rappdirs, SummarizedExperiment,
S4Vectors, tibble
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
XVector (>= 0.19.7), Biostrings (>= 2.47.6), rtracklayer (>=
1.39.7), biomaRt (>= 2.17.1), Biobase (>= 2.15.1)
GenomicAlignments (>= 1.7.7), IRanges, S4Vectors (>= 0.9.25),
VariantAnnotation (>= 1.27.9), 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,
grDevices
utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings,
BSgenome, GenomeInfoDb, AnnotationHub
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.13.13), data.table, stats4
S4Vectors (>= 0.13.13), GenomeInfoDb (>= 1.1.3), IRanges (>=
2.5.12), methods, graphics
ggplot2, rtracklayer, BiocGenerics, GenomicRanges,
GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats
rstan (>= 2.17.3), ranger, parallel, foreach, doParallel,
e1071, Biostrings, rPref
AnnotationDbi, biomaRt, BiocGenerics, Biostrings, DBI, FField,
GenomicFeatures, GenomicRanges (>= 1.25.4), ggplot2 (>= 2.1.0),
grid, gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5),
plyr (>= 1.8.3), reshape2, Rsamtools, scales, stats, utils,
viridis, data.table, BSgenome, grDevices, GenomeInfoDb,
VariantAnnotation
httr, readr (>= 1.3.1), xml2, dplyr, tidyr, magrittr, limma
repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods,
Biobase, XML, rhdf5, digest, iterators
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 (>= 1.29.2), 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, rlang
plyr, scales, data.table, RColorBrewer, gridExtra, rlang
methods, utils, stats, BiocGenerics (>= 0.25.1), 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, dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods,
purrr, rlang, rvcheck (>= 0.1.0), tidyr, tidytree (>= 0.2.4),
treeio (>= 1.7.3), utils
methods, Biobase, Biostrings (>= 2.47.6), graphics, grDevices,
stats, utils, IRanges (>= 2.13.12)
Biobase, changepoint, data.table, genefilter, graphics,
GSEABase, HH, lattice, latticeExtra, plyr, scatterplot3d, stats
DBI, RMySQL, RSQLite, numDeriv, RColorBrewer, parallel, stats,
methods, graphics, grDevices, xtable, tools, brew, stringr,
RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML
edgeR, grDevices, jsonlite, methods, stats, S4Vectors, utils
SummarizedExperiment, STRINGdb, biomaRt, futile.logger,
sparsebn, sparsebnUtils, forcats, dplyr, readr, ggplot2,
survminer, reshape2, stats, stringr, rlang, parallel, methods,
loose.rock (>= 1.0.12)
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>=
0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3),
Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase,
BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel
Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0),
GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils,
grDevices, graphics, stats,
methods, Biobase, graph, Rgraphviz, GO.db, AnnotationDbi, DBI,
SparseM
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, BiocManager
igraph, biomaRt, Rcpp, data.table, OrganismDbi, AnnotationDbi,
grDevices, stats, utils, GenomicRanges, IRanges
Deriv, DescTools, digest, pryr, stringr, BiocGenerics
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, plotly,
erma, ggbeeswarm
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, checkmate, graph, httr, rappdirs, stats, utils
graphics, grDevices, reshape2, stats, utils
GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS,
parallel, GenomeInfoDb, SummarizedExperiment, stats, utils
AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel,
edgeR, EnrichmentBrowser, ExperimentHub, GEOquery, grDevices,
graphics, KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO,
methods, rappdirs, S4Vectors, stats, utils
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4),
geneplotter, shiny, shinythemes
circlize (>= 0.4.8), 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), GenomicFeatures,
Biostrings, Rsamtools, rtracklayer, AnnotationDbi
graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth
GWASTools, survival, VariantAnnotation, parallel, matrixStats,
SummarizedExperiment, stats, utils, SNPRelate
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
1.99.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
BiocFileCache, S4Vectors, googleAuthR, httr, jsonlite,
methods, plyr, readr, rlang, stringr, tibble, tidygraph, tidyr,
utils
utils, tools, BiocGenerics (>= 0.25.1), S4Vectors, IRanges
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, GenomeInfoDb
foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2,
scales, methods
ggplot2, viridis, RColorBrewer, scales, reshape2, stringr,
data.table, GenomeInfoDb, GenomicRanges, stats, IRanges,
grDevices, S4Vectors, digest
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), IRanges, GenomicRanges, polylabelr
coin, stats, limma, grDevices, utils, graphics,
preprocessCore, servr, DelayedArray, matrixStats, methods,
S4Vectors
sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl,
methods
Biostrings, graphics, grDevices, rtracklayer, RColorBrewer,
Matrix, parallel, GenomeInfoDb
graphics, grDevices, stats, utils, BiocGenerics
dplyr, openxlsx, ggplot2, readr, tibble, xml2, tidyr, stats,
utils, hpar, gridExtra
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
shiny, ssrch, S4Vectors, SummarizedExperiment, utils
plotly, DT, magrittr, dplyr, openxlsx, msigdbr,
methods, grid, graph, hypergraph, Rgraphviz, stats4
irlba, stats, cluster, graphics, SummarizedExperiment,
BiocParallel
stats, utils, methods, graphics, grDevices, ggplot2,
GenomicFeatures, ShortRead, BiocParallel, Biostrings,
S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments,
GenomicRanges, rtracklayer, SummarizedExperiment,
VariantAnnotation, limma, edgeR, csaw, DESeq2,
TxDb.Dmelanogaster.UCSC.dm6.ensGene
stats, graphics, preprocessCore, grDevices, randomForest,
affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest,
scatterplot3d, utils
fields, ggplot2, truncnorm, tidyr, data.table, dplyr,
grDevices, graphics, stats, utils, rlang
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, dplyr, limma,
GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0),
shinydashboard, shinyBS, DT, rentrez, rintrojs, ggrepel, knitr,
rmarkdown, shinyAce, BiocParallel, grDevices, base64enc,
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
STRINGdb, Biostrings, igraph, graphics, utils, seqinr
utils, R6, data.table, curl, httr, Rlabkey (>= 2.1.136),
Biobase, pheatmap, ggplot2 (>= 3.2.0), scales, stats, gplots,
plotly, heatmaply (>= 0.7.0), jsonlite, rmarkdown,
preprocessCore, flowCore, flowWorkspace, digest
Biobase, BiocParallel, ComplexHeatmap, circlize, compiler,
cowplot, DESeq2, ggplot2, grDevices, knitr, Matrix, methods,
S4Vectors, stats, SummarizedExperiment, utils
graphics, grDevices, RColorBrewer, gplots, futile.logger,
stats, utils, methods, ape, Matrix, fastcluster, dplyr,
HiddenMarkov, ggplot2, edgeR, coin, caTools, reshape, rjags,
fitdistrplus, future, foreach, doParallel, BiocGenerics,
SummarizedExperiment, SingleCellExperiment, tidyr, parallel,
coda, gridExtra, argparse
AnnotationDbi, BSgenome, cleanUpdTSeq, Gviz, seqinr,
preprocessCore, IRanges, GenomeInfoDb, depmixS4, limma,
BiocParallel
pROC, deSolve, rootSolve, compiler, preprocessCore,
GenomicFeatures, GenomicRanges, IRanges, BiocGenerics,
GenomicAlignments, Rsamtools, S4Vectors, DESeq2, plgem,
SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny
IRanges, S4Vectors, 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
Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats,
assertthat
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2,
colourpicker, igraph, vipor, mgcv, reshape2, rentrez,
AnnotationDbi, graphics, grDevices, viridisLite, cowplot,
scales, dplyr
dplyr, magrittr, methods, quadprog, readr, readxl, stringr,
tibble, tools, utils, pracma, WriteXLS
IsoCorrectoR, readxl, tcltk2, tcltk, utils
methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>=
2.50.0), IRanges, GenomicRanges, DRIMSeq, RColorBrewer,
rtracklayer, VennDiagram, DBI, grDevices, graphics, stats,
utils, GenomeInfoDb, grid, tximport (>= 1.7.1), edgeR,
futile.logger, stringr, dplyr, magrittr, readr, XVector
Rcpp, tkrplot, multtest, relimp, geneplotter, RColorBrewer,
Iso, IsoGene, ORCME, ORIClust, orQA, goric, ff, Biobase, jpeg
AnnotationDbi, assertive.sets, BiocGenerics, Biobase, broom,
cluster, cowplot, DEGreport, DESeq2, IRanges, dplyr,
GenomicRanges, gplots, ggplot2, gtools, gridExtra, grid,
grDevices, graphics, GGally, limma, methods, RColorBrewer,
readr, reshape, rlang, stats, stringr, S4Vectors, tidyr, tibble
affxparser, DBI, GLAD, oligo, oligoClasses, stats
graphics, grDevices, stats, survival, utils
magrittr, graphics, utils, GenomicRanges, SummarizedExperiment
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, GenomicFeatures, bamsignals, AnnotationDbi,
grDevices
methods, stats, Rcpp (>= 0.11.2), Matrix, XVector (>= 0.7.3),
S4Vectors (>= 0.5.11), e1071, LiblineaR, graphics, grDevices,
utils, apcluster
methods, XML (>= 2.3-0), graph, utils, RCurl
AnnotationDbi,graph,DBI, graph, grDevices, methods, stats,
tools, utils
data.table, BiocParallel, sqldf, stats, grid, grDevices
aod, Biobase, DESeq2, DSS, ggplot2, gplots, graphics,
grDevices, matrixStats, stats, utils, foreach, doParallel,
parallel
Biobase, graphics, grDevices, methods, stats, tools, utils
Matrix, snpStats, VariantAnnotation, GenomeInfoDb, Rsamtools,
GO.db, GenomicFiles (>= 1.13.6), BiocGenerics (>= 0.25.1),
EnsDb.Hsapiens.v75, ensembldb, httr
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
grDevices, graphics, stats, utils, methods
methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot,
xtable, utils
Rcpp (>= 0.11.0), DOSE, ggtree, gridExtra, ape, grid, png,
Biobase, sva, reshape2, utils, grDevices, org.Hs.eg.db,
clusterProfiler, ggplot2, ReactomePA
BiocParallel, circlize, compiler, ComplexHeatmap, ggplot2,
gplots, grDevices, grid, knitr, Matrix, methods, RColorBrewer,
SingleCellExperiment, splines, stats, SummarizedExperiment,
utils
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
methods, stats, utils, S4Vectors, rlang, dplyr, tidyr,
forcats, ggplot2, limma, fgsea, ropls, magrittr
Biobase, graphics, grDevices, methods, stats
pheatmap, wordcloud, RColorBrewer, data.table, methods,
grDevices, stats, graphics, GenomicRanges, BiocParallel,
S4Vectors
grid, SQUAREM, LaplacesDemon, stats, graphics, utils, ggplot2,
gridBase, Biostrings
Matrix, penalized, graphics, grDevices, stats
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
reshape2, utils, stats, methods
DelayedArray, GenomicRanges, HDF5Array, stats, utils
cgdsr, parallel, stringr, reshape2, data.table, RColorBrewer,
methods, LowMACAAnnotation, BiocParallel, motifStack,
Biostrings, httr, grid, gridBase
methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase
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, dendextend, sigclust, Rtsne,
survival, corpcor, umap
parallel, Rcpp, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment, BiSeq
RColorBrewer, gplots, bbmle, statmod, grDevices, graphics,
stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods
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, vcfR
data.table, cometExactTest, RColorBrewer, NMF, methods,
wordcloud, grDevices, survival
ggExtra, ggsci, ggrepel, clusterProfiler, png, data.table,
pheatmap, sva, DOSE, biomaRt, grid, pathview
Biobase, affy, methods, stats, utils, zlibbioc
multtest, clusterSim, apcluster, limma, e1071, AnnotationDbi,
methods, parmigene,igraph,reactome.db
dplyr, rtracklayer, reshape2, Gviz, DT, GenomeInfoDb, stats,
utils, IRanges, methods, BiocGenerics, parallel, data.table
Biobase, graphics, grDevices, venn, mclust, stats, MASS
Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr,
stringr, abind, methods, parallel, reshape2, stats, stats4,
graphics, utils, blme, SummarizedExperiment(>= 1.5.3), progress
methods, TFBSTools, IRanges, XVector, Biostrings
methods, DelayedArray, Rcpp, SingleCellExperiment,
SummarizedExperiment, ClusterR, benchmarkme, Matrix
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
biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2,
graphics, grDevices, Gviz, IRanges, limma, parallel, S4Vectors,
stats, SummarizedExperiment, utils
AnnotationDbi, DBI, GO.db, KEGG.db, cluster, Matrix
GenomicAlignments, GenomicRanges, IRanges, Biostrings,
DNAcopy, Rsamtools, parallel, stringr
GenomicRanges, Biostrings, graphics, gtools, IRanges, methods,
stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer,
preprocessCore
data.table, parallel, ROCR, matrixcalc, clues, ggplot2,
doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm,
truncnorm, assertthat, BiocStyle, stats, utils
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, GOSemSim (>=
1.99.3), MeSH.db, methods, rvcheck, utils
methods, stats, utils, fdrtool, 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, cummeRbund, org.Hs.eg.db,
Category, S4Vectors, BiocGenerics, RSQLite
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
rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges,
ggplot2, Rsamtools, DBChIP, purrr, data.table, methods, dplyr,
magrittr
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench, IHW
beanplot (>= 1.2), GenomicRanges (>= 1.34.0), gplots (>=
3.0.1), Matrix (>= 1.2), matrixStats (>= 0.54), Rcpp,
RColorBrewer (>= 1.1), stats (>= 3.4), SummarizedExperiment (>=
1.12), utils (>= 3.4)
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,
data.table
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
RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler,
missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db,
AnnotationDbi, IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
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, mgcv, 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, ggsci, gridExtra, superheat,
dplyr, gtools, tmle, future, doFuture, S4Vectors, BiocGenerics,
BiocParallel, SummarizedExperiment, GenomeInfoDb, bumphunter,
IRanges, limma, minfi
methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack,
MCMCglmm, coda, magrittr, tibble, Biobase
dplyr, reshape2, Rtsne, scales, stats, tidyr, utils, vegan
AnnotationDbi, Biobase, BiocParallel, compiler, data.table,
edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph,
graphics, grDevices, grid, GSEABase, ismev, limma, matrixStats,
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 (>= 0.23.2), DelayedMatrixStats (>=
1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog,
data.table, GEOquery, stats, grDevices, graphics, utils,
DelayedArray (>= 0.9.8), HDF5Array, BiocParallel
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
methods, stats, utils, RCurl, httr, stringr, Hmisc, energy,
entropy, Roleswitch, gplots, glmnet, impute, limma,
pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc,
heatmap.plus, InvariantCausalPrediction, Category, GOstats,
org.Hs.eg.db
DBI, RSQLite, stringr, sqldf, plyr, methods
WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL,
NMF, biclust, runibic, iBBiG, fabia, BicARE, isa2, s4vd,
BiBitR, rqubic, Biobase, PMA, stats, dbscan, subspace, mclust,
SOMbrero, ppclust, miRspongeR, Rcpp, utils,
SummarizedExperiment, GSEABase, org.Hs.eg.db
corpcor, parallel, igraph, MCL, clusterProfiler, ReactomePA,
DOSE, survival, grDevices, graphics, stats, varhandle,
linkcomm, utils, Rcpp, org.Hs.eg.db
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.ilm10b4.hg19
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, utils
gdata, pls, sfsmisc, MASS, rpart, rda, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats
rstan (>= 2.17.3),rstantools (>=
1.5.0),MASS,Matrix,stats4,ggplot2
methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment,
plyr, foreach, utils, sSeq, xtable
GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
cluster, nem, epiNEM, graph, Rgraphviz, flexclust, lattice,
naturalsort, snowfall, stats4, tsne, methods, graphics, stats,
utils, Linnorm, data.table, Rcpp, RcppEigen, matrixStats,
grDevices
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, assertive, BiocGenerics, GenomicRanges, S4Vectors,
IRanges, XVector, stringi, stringr
rhdf5, dplyr, reshape2, pheatmap, corrplot, ggplot2,
ggbeeswarm, methods, scales, GGally, RColorBrewer, cowplot,
ggrepel, MultiAssayExperiment, Biobase, doParallel, foreach,
reticulate, grDevices, stats, utils
methods, graphite, genefilter, BiocGenerics, gplots, GSEABase,
Biobase, parallel, corpcor, svd, cluster, grDevices, graphics,
stats, utils
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,
SummarizedExperiment
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, GenomeInfoDb
XML, scales, htmlwidgets,grDevices, stats, stats4, graphics,
utils
graphics, grid, methods, S4Vectors, IRanges (>= 1.13.5),
Biostrings (>= 1.24.0), lattice, rGADEM, utils
S4Vectors, scales, stats, graphics, statmod
BiocParallel, methods, progress, stats, SummarizedExperiment
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
BiocParallel, IRanges (>= 2.13.28), plyr, preprocessCore, vsn,
grid, stats4, affy, impute, pcaMethods, MALDIquant (>= 1.16),
mzID (>= 1.5.2), digest, lattice, ggplot2, XML, scales, MASS,
Rcpp
MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach,
doParallel, parallel, methods, iterators, data.table, Biobase,
ProtGenerics, reshape2, dplyr, mzR
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite,
uuid, jsonlite, KEGGREST
lme4, marray, limma, gplots, ggplot2, methods, grid, ggrepel,
preprocessCore, reshape2, survival, statmod, minpack.lm, utils,
grDevices, graphics, stats, doSNOW, snow, foreach, data.table,
MASS, dplyr, tidyr, broom, purrr, stringr, randomForest
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr,
RecordLinkage, grid
limma, lme4, dplyr, tidyr, nlme, statmod, reshape2,
data.table, matrixStats, stats, utils, ggplot2, grDevices,
graphics, MSstats
xml2, utils, gmapR, methods, IRanges, Biobase, circlize,
jsonlite, graphics, Rsamtools, grDevices, Biostrings,
rtracklayer, VariantTools, Homo.sapiens, BiocGenerics,
GenomicRanges, GenomicFeatures, SummarizedExperiment
graphics, grDevices, stats, methods, fields
methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors
(>= 0.17.5), IRanges, Biobase, stats, tidyr, utils
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
BiocGenerics, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman,
limma
data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman,
pheatmap, methods, metap, GenomicRanges, graphics, stats,
utils, pbapply, GenomeInfoDbData, BLMA, GenomeInfoDb
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)
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),
ncdf4
graphics, methods, baseline, signal, GenomicAlignments,
GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils,
Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot,
csaw
hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats,
grDevices, graphics, stringr, knitr, testthat, utils,
AnnotationDbi, httr, org.Hs.eg.db, rtracklayer
BiocGenerics, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb,
fda, CSAR, ICSNP
DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods,
stats,
edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2
boot, e1071, graph, graphics, grDevices, methods, RBGL (>=
1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod,
plotrix, limma
Rcpp (>= 0.11.0), minet, GENIE3, c3net, PCIT, GeneNet, tools,
pracma, Matrix, corpcor, fdrtool
Rcpp, RcppParallel, parallel, grDevices, graphics, stats,
utils, dynamicTreeCut, WGCNA, impute, colorspace, methods,
R.utils
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
entropy, SummarizedExperiment, SingleCellExperiment, Matrix,
cluster, data.table, stats, methods, DelayedArray, HDF5Array
methods, parallel, Xmisc (>= 0.2.1), rbamtools (>= 2.6.0),
changepoint (>= 2.1.1)
Biostrings, checkmate, dplyr (>= 0.8.0), ggdendro, grDevices,
grid, kableExtra, lubridate, methods, pander, parallel, plotly,
readr, reshape2, rmarkdown, Rsamtools, scales, ShortRead,
stats, stringr, tidyr, tidyselect (>= 0.2.3), truncnorm, utils,
viridisLite, XVector, zoo
graphics, grDevices, marray, methods, nnet, stats
limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0)
vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods,
Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment,
matrixStats, ggforce
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
Biobase, BiocGenerics, Biostrings, GenomeInfoDb,
GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr,
ggplot2, magrittr, parallel, stats, utils
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 (>= 0.27.1), Biobase (>= 2.17.8), methods,
graphics, IRanges (>= 2.5.17), GenomicRanges (>= 1.23.7),
SummarizedExperiment, Biostrings (>= 2.23.6), affyio (>=
1.23.2), ff, foreach, BiocManager, utils, S4Vectors (>=
0.9.25), RSQLite, DBI
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
utils, ape, Biostrings, GenomicRanges, IRanges, methods,
topGO, jsonlite
ALDEx2 (>= 1.8.0), compositions, grDevices, knitr,
matrixStats, rmarkdown, shiny, stats, vegan, zCompositions
stats, utils, grDevices, graphics, methods, rexposome, limma,
sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet,
SmartSVA, isva, parallel, SummarizedExperiment, stringr
SummarizedExperiment, gss, plyr, zoo, pracma, ggplot2,
BiocParallel, parallel, grDevices, graphics, stats, utils,
methods, BiocGenerics
HelloRanges, fpc, stats, MultiAssayExperiment, pdftools,
methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown,
kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2,
ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR,
PerformanceAnalytics, tidyr, data.table, cluster, magick
methods, matrixStats, graphics, stats, SummarizedExperiment,
MultiAssayExperiment, RaggedExperiment
GEOmetadb, RSQLite, data.table, methods, tools, utils,
AnnotationDbi, RCurl, stats, DT, data.table, knitr
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
biomaRt, grDevices, graphics, utils, methods,
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, graph, Rgraphviz, ontologyPlot, dplyr, magrittr
methods,Biobase,BiocGenerics,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
fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt,
Biobase, RcppParallel, Rcpp
Biobase, graphics, methods, stats, twilight
RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges,
GenomicFeatures, AnnotationDbi, methods, tools, utils,
BiocFileCache, DBI, dbplyr
Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph,
IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats
BBmisc, Biobase, BiocGenerics, compiler, DESeq2 (>= 1.16.1),
GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap, gplots,
graphics, IRanges, matrixStats, plotly, plyr, pcaMethods,
PRROC, RColorBrewer, Rcpp, S4Vectors, scales, splines, stats,
utils
stats, utils, methods, BiocParallel, SummarizedExperiment,
limma, fdrtool, Rcpp
e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR,
sva
limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db,
hgu133a.db, KEGG.db, nlme
SummarizedExperiment, S4Vectors, stats, methods, abind,
BiocParallel
matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit,
hexbin
GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb,
grDevices
graphics, grDevices, MASS, methods, pvclust, stats, utils,
RedeR
shiny, tools, jsonlite, pcaMethods, FindMyFriends, igraph,
stats, utils
stats, utils, dplyr, rlang, iterators, parallel, foreach,
doParallel, qvalue, rtracklayer, ggplot2
limma, corpcor,matrixStats, reshape2, scales, ggplot2,
rentrez, DT, tidyr, plyr, dplyr, phyloseq, shiny, stats,
methods, XML, graphics, utils, BiocStyle, edgeR, DESeq2,
ComplexHeatmap, plotly, webshot, vegan, shinyjs, glmnet,
gmodels, ROCR, RColorBrewer, knitr, devtools, ape
EMT, mclust, Matching, data.table, stats, grDevices, graphics,
utils
KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,
KEGGREST, methods, utils
lars, methods, parallel, stats, survival, 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 , EnrichmentBrowser,
annotate , KEGGREST
utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr
cleaver (>= 1.3.6), Biobase, Biostrings (>= 2.47.5), IRanges
(>= 2.13.11), S4Vectors (>= 0.17.24), mzID, mzR (>= 1.99.1),
MSnbase (>= 1.15.5), Pviz, biomaRt, GenomicRanges (>= 1.31.7),
rtracklayer (>= 1.39.6), ensembldb (>= 1.99.13), BiocParallel,
AnnotationFilter
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, base64enc, 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
Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2,
methods, graphics, stats
limma, fields, GenomicRanges, ggplot2, plyr, tools, methods,
data.table
dplyr, ggplot2, tidyr, assertthat, lme4, splines, igraph,
foreach, parallel, doParallel, diffusr, lazyeval, tibble, grid,
utils, graphics, scales, magrittr, formula.tools, rlang
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 (>= 1.21.5), pheatmap
ggplot2, protolite, Biobase, GEOquery, Rook, htmltools,
httpuv, jsonlite, limma, opencpu, assertthat, methods, httr,
rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4), svglite,
gtable, stats, Matrix, Matrix.utils, pheatmap, scales, ccaPP,
grid, grDevices, AnnotationDbi
Biobase, piano, magicaxis, RColorBrewer, parallel, caTools,
methods, downloader, stats, utils, graphics, grDevices, lsa,
reshape2
SingleCellExperiment, RColorBrewer, igraph, transport, pracma,
cluster, Rtsne, destiny, Seurat, RANN, ggplot2, maptree,
pheatmap, scatterplot3d, VGAM, methods, grDevices, graphics,
stats, utils, cowplot, S4Vectors, BiocGenerics,
SummarizedExperiment, Biobase
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, ggbio, GenomicRanges, GenomeInfoDb, supraHex, scales,
grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz, lattice,
caret, plot3D, stats
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods
methods, stats4, IRanges, GenomicRanges, graphics, grDevices,
stats, Rsamtools, GenomicAlignments, S4Vectors
bnlearn (>= 4.4.1), C50 (>= 0.1.2), 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
BSgenome, digest, visNetwork, magrittr, methods, Biostrings,
GenomeInfoDb, parallel, stats, utils
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
dplyr, rlang (>= 0.2.0), magrittr, tidyselect, rtracklayer,
GenomicAlignments, GenomeInfoDb, Rsamtools, S4Vectors (>=
0.17.41), utils
Rcpp (>= 0.11.1), parallel, stats, graphics, grDevices, utils,
Biobase, BiocGenerics, Matrix, GenomeInfoDb, IRanges,
Biostrings, BSgenome (>= 1.32.0)
methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics
Biostrings (>= 2.32.0), IRanges, S4Vectors, logspline, limma,
zlibbioc
stats, CompQuadForm, Matrix, survival, Biobase, GSEABase
DESeq2, ROTS, vsn, stats, utils, methods, gridExtra, MASS,
data.table, ggplot2, Biobase, S4Vectors, BiocParallel
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, tcR, truncdist, vegan, VGAM
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
methods, BiocParallel, tools, utils, data.table (>= 1.11.8),
GenomicAlignments (>= 1.16.0), rtracklayer (>= 1.40.6),
BiocGenerics (>= 0.26.0), GenomeInfoDb (>= 1.16.0),
GenomicRanges (>= 1.32.0), IRanges (>= 2.14.12), Rsamtools (>=
1.32.3), S4Vectors (>= 0.18.3)
parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges,
Biobase, GenomeInfoDb, S4Vectors
graphics, grDevices, stats, utils, methods, cgdsr, parallel,
stringr, reshape2, data.table, RColorBrewer, BiocParallel,
magrittr, biomaRt, XML, httr, jsonlite, ggplot2, ggrepel, grid,
S4Vectors, IRanges, GenomicRanges, LowMACAAnnotation,
googleVis, shiny, shinyBS, DT, brglm, matrixStats
diagram, stringr, ggplot2, reshape2, grDevices, matrixcalc,
stats, gplots, methods, utils, graphics
Biobase, corrplot, dplyr, data.table, ggfortify, ggplot2,
grDevices, lazyeval, lubridate, magrittr, pheatmap,
preprocessCore, purrr, pvca, RColorBrewer, readr, reshape2,
rlang, scales, viridis, stats, sva, tidyr, tibble, utils,
wesanderson, WGCNA
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, graphics, utils, grDevices, methods, pracma, Biobase,
minpack.lm, BiocParallel, missForest, ropls
GenomicRanges, stats, soGGi, methods, utils, S4Vectors,
R.utils, dplyr, magrittr, tidyr, IRanges, rjson,
ChIPseeker,GenomicFeatures,TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,org.Hs.eg.db,org.Mm.eg.db,rGREAT,
pheatmap, EnrichedHeatmap, ComplexHeatmap, grid, circlize,
BiocParallel, rtracklayer, GenomeInfoDb
methods, cluster, stats, limma, CoGAPS, NMF, ROCR
Biobase, mclust (>= 4.3), caret, e1071, sampling, class,
kernlab, lattice, nnet, randomForest, proxy, FNN, hexbin,
BiocGenerics, stats, dendextend, RColorBrewer, scales, MASS,
knitr, mvtnorm, LaplacesDemon, coda, mixtools, 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 (>= 1.16.11), DAPARdata (>= 1.14.0), rhandsontable,
data.table, shinyjs, DT, shiny, shinyBS, shinyAce, highcharter,
htmlwidgets, webshot, R.utils, shinythemes, XML,later,
shinycssloaders, future, promises, colourpicker, BiocManager,
shinyjqui,shinyTree, shinyWidgets
mzR (>= 2.3.2), MSnbase, Biostrings, GenomeInfoDb, utils,
Biobase, BiocManager, RCurl
gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats,
graphics
rTANDEM, plyr, seqinr, Nozzle.R1, ggplot2, reshape2, parallel,
rpx, tidyr, dplyr, plotly, rmarkdown,
AnnotationDbi, AnnotationHub, cluster, colourpicker,
data.table, digest, dplyr, DT (>= 0.2), edgeR, fastICA,
fastmatch, ggplot2, ggrepel, graphics, grDevices, highcharter
(>= 0.5.0), htmltools, httr, jsonlite, limma, miscTools,
pairsD3, plyr, Rcpp (>= 0.12.14), recount, R.utils, reshape2,
shinyjs, stringr, stats, SummarizedExperiment, survival, tools,
utils, XML, xtable, methods, org.Hs.eg.db
stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel,
biomaRt, BgeeDB, topGO, BiocManager, 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, gridExtra,
futile.logger, VGAM, tools, methods, rhdf5, Matrix
biovizBase, Biostrings, GenomicRanges, IRanges, data.table,
methods
data.table, rBiopaxParser, igraph, STRINGdb, graphics, gplots,
Biobase, BiocGenerics, AnnotationDbi, biomaRt, AnnotationHub,
GenomicRanges, graph, grDevices, stats, utils
magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table,
reshape2, grDevices, graphics, stats, utils, Rcpp, rlang,
RSeqAn
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
tidyr, preprocessCore, limma, ggplot2, RColorBrewer, stats,
utils, Biostrings, GenomicRanges, IRanges, graphics,
BiocGenerics, stringr, purrr, tibble, ggdendro, grDevices,
dplyr, magrittr, assertthat
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
SummarizedExperiment, utils, sva, stats, methods, graphics
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
methods, grDevices, graphics, utils, BiocGenerics, S4Vectors
(>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings,
BSgenome, Rsamtools (>= 1.99.1), GenomicFeatures (>= 1.17.13),
ShortRead (>= 1.19.1), GenomicAlignments, BiocParallel,
GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi
methods, parallel, clues, ggplot2, pheatmap, clValid, igraph,
data.table, reshape2, Hmisc, RCurl, BiocGenerics, S4Vectors,
IRanges (>= 2.13.12), GenomeInfoDb, GenomicRanges (>= 1.31.8),
ggbio
methods, GenomeInfoDb, IRanges, Biostrings, data.table, sqldf,
RColorBrewer
utils, grDevices, graphics, stats, tools, xtable, R2HTML,
TeachingDemos, BiocGenerics, S4Vectors (>= 0.17.25), IRanges
(>= 2.13.12), XVector, GenomicRanges (>= 1.31.8),
SummarizedExperiment, biomaRt, BSgenome (>= 1.47.3), Rsamtools,
ShortRead (>= 1.37.1)
BiocGenerics, GenomeInfoDb, 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, BiocGenerics, 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)
AUCell (>= 1.1.6), BiocGenerics, data.table, feather,
graphics, GSEABase, methods, R.utils, stats,
SummarizedExperiment, utils
RColorBrewer, alabama, edgeR, reshape2, tseries, vegan, VGAM,
ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS,
stats, grDevices, graphics, methods
stats, utils, methods, RCurl, rjson, foreach, doParallel,
Biostrings, GOSemSim, ChemmineR, fmcsR, rcdk (>= 3.3.8)
utils, stats, BiocParallel, batchtools, DiagrammeR, shiny,
R.utils, codetools
httr, methods, RJSONIO, XML, utils, BiocGenerics, igraph,
stats, graph, R.utils
methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils
graphics, grDevices, methods, stats, MASS, rgl
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2, ggraph,
reactome.db, igraph, graphite
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, IRanges, BSgenome, Biostrings,
rtracklayer, parallel, graphics, stats, utils, methods,
GenomeInfoDb, 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
readr, rtracklayer, graphics, stats, utils, methods, settings,
BiocGenerics, S4Vectors, Biostrings, GenomicRanges, IRanges,
GenomeInfoDb, BiocParallel, doParallel, parallel, foreach,
caret, kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db,
impute, iterators
parallel, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb, GenomicRanges, Biostrings, Rsamtools,
GenomicAlignments, rtracklayer, BSgenome (>= 1.47.3), 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, Biobase,reshape2,
AnnotationDbi, DBI, GO.db, rhdf5client, dplyr (>= 0.7.1),
magrittr, bigrquery, ExperimentHub, AnnotationHub, rlang
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, mice
Biostrings, IRanges, methods, graphics, seqLogo
httr, rJava, GenomicRanges, rtracklayer, data.table, utils,
plyr, xml2, methods, S4Vectors, dplyr, stats, glue,
BiocGenerics
rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats
gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment,
hash, AnnotationDbi
GenomicFeatures, SGSeq, GenomicRanges, methods, utils
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
stats, methods, BiocGenerics, IRanges, Biobase, affxparser,
stats4
Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges,
SummarizedExperiment, devtools, TBX20BamSubset,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2,
BiocStyle
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr
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
Rsamtools, tools, reticulate, ballgown, gridExtra, rafalib,
FactoMineR, factoextra, corrplot, PerformanceAnalytics,
reshape2, DESeq2, systemPipeR, systemPipeRdata,
clusterProfiler, org.Hs.eg.db, org.Sc.sgd.db, stringr,
pheatmap, grDevices, graphics, stats, utils, DOSE, Biostrings,
parallel
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 (>= 0.25.1), Biostrings, IRanges, methods,
S4Vectors, knitr (>= 1.7), BiocStyle, plyr, markdown, grid,
reshape2, Rcpp (>= 0.11.6), biovizBase, shiny, Rsamtools,
GenomicAlignments, GenomicFiles
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops,
BiocParallel
methods, stats, igraph, stringr, grDevices, Biobase,
S4Vectors, SummarizedExperiment, BiocGenerics
XML, assertthat, stringi, rvest, data.table, xml2, dplyr,
purrr, survival, survminer, ggplot2, ggthemes, viridis, knitr,
scales
BiocGenerics, data.table, DelayedArray, GenomicRanges,
GenomeInfoDb, IRanges, limma, methods, RaggedExperiment,
RCircos, RCurl, RJSONIO, S4Vectors, stringr,
SummarizedExperiment, survival, TCGAutils, XML
RedeR, minet, viper, mixtools, snow, limma, data.table,
IRanges, igraph, S4Vectors, SummarizedExperiment
survival, RColorBrewer, grDevices, graphics, stats, utils,
scales, data.table, egg, ggplot2, pheatmap, dunn.test
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
GENLIB, 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
SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4), tensorflow,
purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
BiocGenerics, SummarizedExperiment, Matrix, dplyr, ggbeeswarm,
grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors,
stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular,
BiocParallel
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
Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment,
xgboost, methods, stats
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)
BiocParallel, cluster, distr, doSNOW, foreach, igraph, irlba,
iterators, matrixStats, M3Drop (>= 1.9.4), parallel, pdist,
proxy, Rcpp (>= 0.12.18), RcppEigen (>= 0.3.3.4.0), ruv, rsvd,
S4Vectors, SingleCellExperiment, SummarizedExperiment
knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges,
reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15),
annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb,
Biostrings, DT, HDF5Array (>= 1.7.5)
stats, methods, graphics, grDevices, parallel, quantreg,
cluster, moments, data.table, BiocParallel,
SingleCellExperiment, 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
tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils,
stats, readr
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, AnnotationDbi, org.Hs.eg.db,
org.Mm.eg.db, stringr, rtracklayer, hashmap, dplyr,
GenomicRanges, magrittr, glue
SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel,
Rcpp (>= 0.12.14), stats, methods, utils, Matrix, scater,
edgeR, limma, dynamicTreeCut, BiocNeighbors, igraph, statmod,
DelayedArray, DelayedMatrixStats, BiocSingular, dqrng
stats, utils, methods, graphics, doParallel, foreach,
parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS
(>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>=
4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), Rmagic (>=
1.3.0), BiocParallel (>= 1.12.0)
data.table, GenomicAlignments, GenomicFeatures, GenomicRanges,
Rsamtools, ShortRead, parallel, plyr, BiocGenerics,
BiocParallel, S4Vectors, AnnotationDbi, Biostrings, methods,
ggplot2, ggthemes, scales, GenomeInfoDb, stringdist, ggbio,
rtracklayer, SingleCellExperiment, SummarizedExperiment
sqldf, hash, ggplot2, graphics,grDevices, RColorBrewer
methods, RSQLite, igraph, S4Vectors, plotly, reactome.db,
AnnotationDbi, SummarizedExperiment, SingleCellExperiment,
nnTensor, rTensor, abind, plotrix, heatmaply, tagcloud,
rmarkdown, BiocStyle, knitr, AnnotationHub, MeSHDbi, grDevices,
graphics, stats, utils, outliers, Category, meshr, GOstats,
ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork
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, BiocManager
data.table, eulerr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, grDevices, grid, IRanges, limma, methods,
parallel, pbapply, png, RColorBrewer, Rsamtools, rtracklayer,
S4Vectors, stats
e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges,
methods, rbokeh, RColorBrewer, reshape2, rmarkdown, S4Vectors,
stats, utils
grDevices, graphics, stats, methods, Biobase, gdsfmt,
GenomicRanges, IRanges, S4Vectors, GWASExactHW, logistf,
Matrix, dplyr, rlang, tidyr
BiocParallel, R6, grDevices, utils, illuminaio, MASS,
GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors,
randomForest, wheatmap, ggplot2, parallel, matrixStats, DNAcopy
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, dplyr
AnnotationDbi, BiocGenerics, Biostrings (>= 2.47.6),
GenomicAlignments (>= 1.15.7), GenomicFeatures (>= 1.31.5),
GenomeInfoDb, RUnit, S4Vectors (>= 0.17.28), grDevices,
graphics, igraph, parallel, rtracklayer (>= 1.39.7), stats
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), hwriter,
methods, zlibbioc, lattice, latticeExtra,
beanplot, glmnet, graphics, grDevices, grid, gridBase,
gridExtra, LiblineaR, matrixStats, methods, ParamHelpers, pROC,
PRROC, RColorBrewer, scales, stats, stringr, utils, infotheo,
progress, corrplot
corpcor (>= 1.6.2), graphics, igraph, limma, marray, MASS,
penalized, quadprog, snowfall, stats
biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer,
Matrix, SparseM, graphics, stats, utils, SummarizedExperiment,
BiocParallel, methods
stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
BiocGenerics, Biostrings, class, graphics, grDevices,
GenomicRanges, nloptr, methods, stats, utils, PMCMR
graph, igraph, RBGL, graphics, utils, stats, methods
mzR, ggplot2, grid, reshape2, grDevices, stats, utils
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, utils, grDevices, graphics, stats, BiocGenerics,
Biobase, affy, genefilter, gcrma
graphics, stats, gbm, Hmisc, GenomicRanges, methods
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
S4Vectors, methods, BiocGenerics, utils, stats
ape, colourpicker, cluster, ComplexHeatmap, data.table,
DESeq2, DT, ggplot2, ggtree, gridExtra, GSVA (>= 1.26.0),
GSVAdata, limma, MAST, matrixStats, methods, multtest, plotly,
RColorBrewer, Rtsne, S4Vectors, shiny, shinyjs, sva, reshape2,
AnnotationDbi, shinyalert, circlize, enrichR, shinycssloaders,
shinythemes, umap
methods, stats, graphics, ggplot2, grDevices, ggrepel, plotly,
tidyr, plyr, magrittr, reshape, edgeR, RColorBrewer, Biobase,
BiocParallel, SummarizedExperiment, matrixStats, reshape2,
S4Vectors
ape, seqinr, Rcpp, methods, graphics, utils, stats
minfi, S4Vectors (>= 0.19.1), RColorBrewer
Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase,
methods, rsvd, SingleCellExperiment, SummarizedExperiment,
stats
AnnotationDbi, Biobase, GO.db, ScISI, graphics, lattice,
methods, stats, BiocGenerics
ape, clusterExperiment, graphics, grDevices, igraph,
matrixStats, methods, rgl, SingleCellExperiment,
SummarizedExperiment
SummarizedExperiment, curl, dplyr, foreach, httr, stats,
utils, methods, readr, rhdf5, jsonlite, tidyr
magrittr (>= 1.5), matrixStats, dplyr, stats, tidyr, utils,
Rcpp (>= 1.0.0)
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
methods, glmnet, parcor, huge, stats, graphics, utils
nnlasso, nnls, parallel, data.table, Biostrings,
GenomicRanges, IRanges, BSgenome,
BSgenome.Hsapiens.1000genomes.hs37d5, GenomeInfoDb, ggplot2,
gridExtra
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges
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,
scater (>= 1.7.4), stats, SummarizedExperiment, utils, crayon
annotate, Biobase, graphics, grDevices, grid, methods, utils,
XML
methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>=
0.17.5), BiocParallel, 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,stringr, methods,
BSgenome.Mmusculus.UCSC.mm9, googleVis
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
MASS, expm, gRbase, glmnet, igraph, iterators,
graphics, grDevices, methods, RColorBrewer, stats, utils
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils
Rcpp (>= 0.12.8), methods, utils, devtools, BiocStyle,
S4Vectors, GenomeInfoDb, rtracklayer, SummarizedExperiment,
IRanges, GenomicRanges, DESeq2, Rsamtools, GenomicFeatures,
GenomicAlignments, ggplot2, BiocParallel
GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb,
Gviz, Rsolnp
SpidermiR, graphite, AnnotationDbi, e1071, ROCR, MLmetrics,
grDevices, igraph, reshape2, ggplot2
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
dplyr, magrittr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, IRanges, Rsamtools, S4Vectors, grid,
BiocGenerics, ggplot2, reshape2, stats, gridExtra,
TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr
methods, graph, RBGL, parallel, BiocGenerics
png, sqldf, plyr, igraph, RCurl, methods, RColorBrewer,
gplots, hash, plotrix
methods, assertive, BiocGenerics, XVector, stringr, stringi
assertthat, Biostrings, stringr, dplyr, methods, rlang
Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra,
networkD3, ggrepel, graphics, stats
data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99),
digest, Biobase
utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3),
S4Vectors (>= 0.17.25), IRanges (>= 2.13.16), GenomeInfoDb (>=
1.13.1)
ape, MASS, grDevices, graphics, stats, utils
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma,
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, biomaRt
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
seqinr, methods, Biostrings, stringr, BiocGenerics
BiocGenerics, GenomicRanges, GenomicFeatures (>= 1.31.3),
SummarizedExperiment, VariantAnnotation (>= 1.25.11), rjson,
ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate,
pheatmap, batchtools, yaml
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, tidyr, sva,
limma, purrr, xml2, httr (>= 1.2.1), matlab, circlize, ggrepel
(>= 0.6.3)
shiny (>= 0.14.1), downloader (>= 0.4), grid, DT, plotly,
readr, maftools, stringr (>= 1.1.0), SummarizedExperiment,
ggrepel, data.table, caret, shinyFiles (>= 0.6.2), ggplot2 (>=
2.1.0), pathview, ELMER (>= 2.0.0), clusterProfiler, parallel,
TCGAbiolinks (>= 2.5.5), shinyjs (>= 0.7), colourpicker,
sesame, shinyBS (>= 0.61)
AnnotationDbi, BiocGenerics, GenomeInfoDb, GenomicFeatures,
GenomicRanges, GenomicDataCommons, IRanges, methods,
MultiAssayExperiment, RaggedExperiment (>= 1.5.7), rvest,
S4Vectors, stats, stringr, SummarizedExperiment, utils, xml2
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, IRanges, biomaRt, GenomicFeatures, grDevices,
dplyr, stats, utils, R.utils, methods, org.Hs.eg.db
GenomicRanges, S4Vectors, grDevices, graphics, stats, utils,
IRanges, methods
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
dynamicTreeCut, dplyr, edgeR, DESeq2, ggplot2 (>= 3.0.0),
graphics, Hmisc, limma, methods, magrittr, proxy, stats,
tibble, tidyr, vegan, viridis, utils
gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel,
flexclust, grDevices, graphics, Biobase, SPEM
GSVA (>= 1.26.0), pheatmap, grDevices, RColorBrewer, pracma,
GGally, R.utils, forestplot, ggplot2, ggpubr, survival, grid,
stats, methods
methods, stats, utils, grDevices, htmlwidgets, jsonlite,
data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr
Rcpp (>= 0.11.2), ALS, ChemometricsWithR, signal, KernSmooth,
graphics, grDevices, stats
Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment,
gRbase, limma, corpcor
methods, utils, stats, assertthat, ggplot2
grDevices, stats, tools, utils, Biobase, Matrix (>= 1.2.10),
MSnbase (>= 2.3.10), ggplot2 (>= 2.2.1), mzR (>= 2.11.4)
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
ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl,
parallel
IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base,
stringr, RColorBrewer, methods
GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz,
Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools,
IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix,
Rgraphviz, InteractionSet, graph, utils
biomaRt, data.table, doSNOW, foreach, ggplot2, graphics,
grDevices, igraph, limma, parallel, progress, RedeR, snow,
stats, tidyr, topGO
BiocGenerics, caret, chipseq, e1071, GenomicAlignments,
GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2,
graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2,
Rsamtools, rtracklayer, S4Vectors, stats, utils
BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>=
0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0),
ggseqlogo (>= 0.1), gridExtra (>= 2.3), methods, parallel, Rcpp
(>= 0.12.18), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8),
utils
BiocGenerics, S4Vectors (>= 0.9.25), IRanges, zlibbioc, gplots
ape, dplyr, jsonlite, magrittr, methods, rlang, tibble,
tidytree (>= 0.2.3), utils
methods, utils, ape, dplyr, SummarizedExperiment
RSQLite, RMySQL, lassopv, randomForest, flare, vbsr,
BiocParallel, RPostgreSQL, methods, DBI, BSgenome,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10, SNPlocs.Hsapiens.dbSNP150.GRCh38,
org.Hs.eg.db, Biostrings, GenomicRanges, biomaRt, AnnotationDbi
stats, utils, graphics, grDevices, segmented, gplots,
parallel, magrittr, BiocParallel, DT, S4Vectors,
SummarizedExperiment, methods, shiny, shinyFiles
grDevices, graphics, methods, stats, survival, utils,
siggenes, LogicReg (>= 1.5.3)
stringr, S4Vectors, methods, assertive, BiocGenerics, IRanges,
XVector, Biostrings, Modstrings, ggplot2, scales
Biostrings, BiocGenerics, stringr, xml2, S4Vectors, assertive,
methods, httr, IRanges, utils
methods, assertive, stringr, BiocGenerics, Biostrings,
Structstrings, S4Vectors, GenomeInfoDb, rtracklayer
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, dplyr,
GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools,
IRanges, methods, readxl, Rsamtools (>= 1.14.3), rtracklayer,
S4Vectors, SummarizedExperiment, tools, utils
methods, BiocGenerics (>= 0.3.2), S4Vectors, Hmisc, minqa,
stats, Biobase (>= 0.3.2), plyr, IRanges
AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel,
Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges,
GGally, ggplot2, Gviz, limma, IRanges (>= 2.7.1), reshape2,
Rsamtools, S4Vectors (>= 0.11.11), SummarizedExperiment,
VariantAnnotation (>= 1.19.9)
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
SummarizedExperiment, tximport, jsonlite, S4Vectors,
GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb,
Biostrings, BiocFileCache, tibble, GenomeInfoDb, rappdirs,
utils, methods
methods, rjson, GenomicRanges, IRanges, BiocParallel,
GenomeInfoDb, S4Vectors, SummarizedExperiment, utils
AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings,
BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures,
GenomeInfoDb, GenomeInfoDbData, GenomicAlignments,
GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, S4Vectors,
shiny, shinyFiles, Sushi, yaml
stringr, R.utils, WriteXLS, stats, doParallel, foreach,
GenomicRanges, IRanges, VariantAnnotation
methods, stats, utils, ggplot2, ape, ggtree, ggseqlogo,
gtools, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics,
processx, S4Vectors, yaml
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), lmerTest, iterators, splines,
colorRamps, BiocParallel, gplots, progress, reshape2, lme4 (>=
1.1-10), doParallel, grDevices, graphics, utils, stats
utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.17.24), IRanges
(>= 2.13.13), XVector (>= 0.19.7), Biostrings (>= 2.47.6),
AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.39.7), BSgenome
(>= 1.47.3), GenomicFeatures (>= 1.31.3)
utils, stats, 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, GenomicScores (>= 1.0.0), Gviz, shiny,
shinythemes, shinyjs, DT, shinyTree
Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel,
GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7),
BiocParallel, GenomeInfoDb, BSgenome, Biobase
tools, GenomicRanges, VariantAnnotation (>= 1.29.3),
GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools
utils, grDevices, stats, methods, dplyr, purrr, tibble,
magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger
Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr,
RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment,
tidyr, utils
mixtools, stats, parallel, e1071, KernSmooth
wordcloud, csaw, gplots, stats, utils, caTools, graphics,
DESeq, Biobase
methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>=
2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>=
1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7),
seqinr, stringr, wmtsa
methods, affy, preprocessCore, GenomicRanges, waveslim,
IRanges
multtest, qvalue, stats, utils, BiocManager
dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer,
cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb
limma, matrixStats, locfit, stats, graphics
pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr,
magrittr, roar
mzR (>= 2.13.3), BiocGenerics, ProtGenerics, lattice,
RColorBrewer, plyr, RANN, multtest, MassSpecWavelet (>= 1.5.2),
S4Vectors, robustbase
BiocGenerics, genefilter, graphics, grDevices, gtools,
MergeMaid, methods, stats, utils, mvtnorm, RColorBrewer,
GeneMeta, siggenes
methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
methods, utils, 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, Matrix
Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.3.7), cytolib(>=
1.3.3), RcppParallel
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 1.16.3), S4Vectors, IRanges, XVector, Biostrings
S4Vectors (>= 0.13.8), IRanges, XVector, Biostrings
Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
testthat, Matrix, SuperLearner, earth, gam, nnls, airway,
rmarkdown, knitr, BiocStyle
R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools
affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl,
rmarkdown
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
BiocStyle, knitr, rmarkdown, testthat, usethis
hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,
rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,
org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit,
hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db,
RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db,
org.Hs.eg.db, reactome.db, AnnotationForge, graph,
EnsDb.Hsapiens.v75, BiocStyle, knitr
BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db
biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy,
hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens,
hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager
IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation,
Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge,
rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR,
Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt
RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData
BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db,
org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2,
testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Ggallus.UCSC.galGal5.refGene,
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
DESeq2, airway, 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
knitr, rmarkdown, BiocStyle, testthat, ASICSdata
testthat, BiocStyle, lintr, knitr, rmarkdown
BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
MotifDb, trackViewer, testthat
Biobase, BiocStyle, devtools, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat,
zoo
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
testthat, BiocStyle, knitr, beachmat, scRNAseq
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, Matrix, devtools
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
aCGH, affy, limma, snapCGH, beadarray, DNAcopy
testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF
testthat, BiocStyle, knitr, rmarkdown, pander
BiocGenerics, BiocStyle, minfiData, parallel,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter
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, devtools
(>= 1.4.1), usethis, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,
AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,
DESeq2, MSnbase, annotate, RUnit
testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy,
RcppHNSW
knitr, dbplyr, DBI, org.Hs.eg.db, MultiAssayExperiment,
BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb,
restfulSE (>= 1.3.7), BiocFileCache,
TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase,
TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat,
AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75
reactome.db, org.Hs.eg.db, WGCNA, methods, GOSemSim,
testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot,
targetscan.Hs.eg.db, Hmisc, spelling
BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel,
Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit,
BiocStyle, knitr, batchtools, data.table
BiocStyle, knitr, rmarkdown, testthat, tm, SnowballC,
pdftools, visNetwork, clipr
testthat, BiocStyle, knitr, rmarkdown, beachmat
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, BiocGenerics, BiocStyle, golubEsets, hu6800.db,
knitr, rmarkdown, testthat
BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>=
1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11),
BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe,
hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy
(>= 1.41.3), affydata (>= 1.11.5), RUnit
testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix,
DBI, biotmleData (>= 1.1.1)
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,
EnsDb.Hsapiens.v75, RUnit
xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db,
lumi, knitr
BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg38.masked,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5,
BSgenome.Scerevisiae.UCSC.sacCer1,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix,
doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat
(>= 1.5.2), BatchJobs
testthat, RUnit, doParallel, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, BiocStyle, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm9.knownGene
BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE,
BiocStyle, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl
BiocGenerics, RUnit, knitr, RTCGA.mRNA, RTCGA.clinical
BiocStyle, knitr, rmarkdown, testthat, diffcyt, umap
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, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db,
limma, affy, genefilter
crossmeta, knitr, rmarkdown, testthat, lydata
limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
testthat, knitr, roxygen2, rmarkdown, corrplot, Matrix,
biomaRt, covr, M3DExampleData, BiocManager, BiocStyle
BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation
BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
BiocStyle, knitr, rmarkdown, testthat, limma
data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics,
AnnotationDbi, destiny, RUnit, scater, scran, knitr,
org.Mm.eg.db, rmarkdown
BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db,
Biobase, tools
ChemmineR, BiocStyle, knitr, knitcitations, knitrBootstrap,
BiocManager
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB (>=
1.16.1), ChemmineDrugs, png,rmarkdown, BiocManager
knitr, rmarkdown, Matrix, testthat, vdiffr
argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat,
Rsamtools, GenomicInteractions, GenomicRanges, IRanges,
AnnotationHub
testthat, roxygen2, devtools, knitr, lintr
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
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, knitr,
rmarkdown, testthat, trackViewer, motifStack, OrganismDbi
clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle,
rmarkdown, testthat
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3),
GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3),
testthat
JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat,
knitr, rmarkdown, pheatmap, motifmatchr
AnnotationDbi (>= 1.38.2), knitr, rmarkdown, rtracklayer (>=
1.36.6), testthat, vdiffr (>= 0.2.3), covr
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, genefilter, edgeR, car, Rmixmod, ggplot2, gridExtra,
cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr,
htmltools, gtable, scales, e1071, rmarkdown, IRanges,
randomForest, robustbase, glmnet, class
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown,
BRAIN, UniProt.ws (>= 2.1.4)
RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS,
BiocStyle
BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan
knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr,
CluMSIDdata, metaMS, metaMSdata, xcms
BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran,
igraph
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, dplyr, KEGG.db, knitr, org.Hs.eg.db,
prettydoc, ReactomePA, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
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,
VanillaICE, tidyverse
AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked,
BiocStyle, MultiAssayExperiment, TCGAutils, curatedTCGAData,
ensembldb, knitr, regioneR, rmarkdown
knitr, parallel, testthat, BiocStyle, rmarkdown,
AnnotationHub, LOLA
genefilter, mvtnorm, testthat (>= 0.3), data.tree,
dendextend, samr, pamr, kohonen, NMF, WGCNA, Rtsne, umap,
clusterProfiler, AnnotationDbi, gplots
flowWorkspace (>= 3.9.66), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2
BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>=
2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0)
BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr,
rtracklayer
testthat (>= 1.0.0), knitr, markdown, dendsort, Cairo, jpeg,
tiff, fastcluster, dendextend (>= 1.0.1), grImport, grImport2,
glue, GenomicRanges
testthat, knitr, rmarkdown, BiocStyle, Matrix, Seurat,
monocle, HSMMSingleCell
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, minfiData, RCurl
BiocStyle, knitr, panelcn.mops,
BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy
glpkAPI, testthat, knitr, rmarkdown, digest, R.cache,
ggplot2, plyr, igraph, methods, latex2exp,
rBayesianOptimization
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
org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat,
GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle
ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle,
flowStats
testthat, flowWorkspaceData (>= 2.11.1), knitr, parallel
XML, BiocStyle, knitr, rmarkdown, testthat
EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust,
minqa, SummarizedExperiment, Biobase, knitr, rmarkdown,
BiocStyle, edgeR
mgcv, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr,
RColorBrewer, matrixStats
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown,
statmod, testthat
Matrix, HDF5Array, genefilter, SummarizedExperiment, airway,
pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit
testthat, knitr, rmarkdown, SeqArray, GDSArray
testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark,
profmem
Rtsne, testthat, knitr, rmarkdown, BiocStyle
BiocStyle (>= 2.5.19), biovizBase, sessioninfo, derfinderData
(>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>=
1.0.1), knitr (>= 1.6), limma, RefManageR, rmarkdown (>=
0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene
sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6),
BiocStyle (>= 2.5.19), rmarkdown (>= 0.3.3), testthat
biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData
(>= 0.99.0), sessioninfo, 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
BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq,
RUVSeq, RColorBrewer, statmod
testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW,
apeglm, ashr, tximport, tximportData, readr, pbapply, airway,
pasilla (>= 0.2.10)
nbconvertR, testthat, FNN, tidyr, SingleCellExperiment
GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22),
parathyroidSE, BiocStyle, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
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.ilm10b4.hg19
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC,
RUnit, simulatorZ, proxy
prettydoc, clusterProfiler, knitr, org.Hs.eg.db, testthat
covr, testthat, knitr, rmarkdown, BiocStyle
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
testthat, beachmat, knitr, BiocStyle, rmarkdown
limma, convert, GEOquery, dyebiasexamples, methods
BiocStyle (>= 2.9.6), BSgenome (>= 1.49.5),
BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr,
rmarkdown, RUnit (>= 0.4.32)
BiocStyle, digest, knitr, rmarkdown, shiny
ecoliLeucine, ecolicdf, graph, multtest, affy
BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR,
KernSmooth, testthat
AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines
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,
hgu133plus2cdf, hgu133plus2probe
BiocStyle, knitr, testthat, data.table, DT,
GenomicInteractions, webshot, R.utils, covr
RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway,
gridExtra, magrittr
testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer
ALL, BiocStyle, airway, hgu95av2.db, knitr
clusterProfiler, dplyr, knitr, org.Hs.eg.db, prettydoc
BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat,
BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>=
1.20.0), magrittr, AnnotationHub
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
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, shiny,
minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr,
AnnotationHub
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, 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
BiocStyle, knitr, rmarkdown, kableExtra, magrittr
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
kableExtra
caret, mlbench, SingleCellExperiment, knitr, rmarkdown,
testthat, BiocManager
shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown,
testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi,
GOSemSim
RCurl, RDAVIDWebService, gage, topGO, GO.db, KEGG.db,
reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr,
rmarkdown, AnnotationDbi, RGtk2, BiocManager
testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel, org.Mm.eg.db, limma, GEOquery
BiocStyle, testthat, knitr, rmarkdown, reutils
testthat, knitr, rmarkdown, macrophage, tximeta,
org.Hs.eg.db, samr, DESeq2, apeglm
testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown,
openCyto
Rgraphviz, flowViz, flowStats, testthat, flowWorkspace,
flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra
flowQBData, FlowRepositoryR, xlsx, RUnit, BiocGenerics
knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments,
stats
testthat, flowWorkspaceData, knitr, ggcyto, parallel, CytoML
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
org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Dr.eg.db,
org.Ce.eg.db, org.At.tair.db, org.EcK12.eg.db, org.Bt.eg.db,
org.Cf.eg.db, org.Ag.eg.db, org.EcSakai.eg.db, org.Gg.eg.db,
org.Pt.eg.db, org.Pf.plasmo.db, org.Mmu.eg.db, org.Ss.eg.db,
org.Xl.eg.db, testthat, pryr, knitr, rmarkdown, prettydoc,
ggplot2, kableExtra, profvis, reshape2
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
BiocGenerics, KEGG.db, reactome.db, RUnit, GO.db, mgsa
affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db,
org.Hs.eg.db, org.Mm.eg.db, RUnit
edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db,
org.Hs.eg.db, RUnit, BiocGenerics
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
parallel, digest, crayon, RUnit, knitr, BiocGenerics
RUnit, rentrez, knitr, rmarkdown, BiocStyle
assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat
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,
RColorBrewer, BiocStyle, knitr
GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival
RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny,
STRINGdb
RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown,
Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db
CompQuadForm, poibin, survey, testthat, BiocStyle, knitr,
rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, testthat, 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.Pt.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer
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, rmarkdown
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
RMariaDB, 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 (>= 3.4.7),
TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts,
TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.4.6),
SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset
(>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit,
BiocStyle, knitr
BiocStyle, RUnit, genefilter, deepSNV,
RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=
1.13.53), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub,
DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14,
pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
BiocStyle
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
testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats,
BSgenome, Biostrings
testthat, ggplot2, gridExtra, ape, ggrepel, knitr, reshape,
xtable
BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL,
roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene,
rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Hsapiens.UCSC.hg38
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, ggridges, vdiffr
GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37,
multtest, aod, rmeta
emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc,
rmarkdown, scales, testthat, tibble
roxygen2, knitr, rmarkdown, testthat, BiocStyle
BiocStyle, IRanges, GenomicRanges, SummarizedExperiment,
DESeq2, limma, testthat, knitr, rmarkdown, pryr
testthat, knitr, rmarkdown, survival, survcomp, pROC,
VennDiagram, BiocStyle, curatedTCGAData, TCGAutils
GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz
vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS,
boot, rpart, mstate
RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
LungCancerLines
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, 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, RUnit, multtest, gwascat, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, ldblock
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, BiocStyle, knitr
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
SummarizedExperiment, knitr, plotly, RANKS, WGCNA
limma, RColorBrewer, genefilter, mclust, edgeR, snow,
parallel, GSVAdata
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff
knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr, kableExtra,
rmarkdown, testthat
DO.db, DT, utils, knitr, RBGL, RUnit, snpStats, Gviz,
VariantAnnotation, AnnotationHub, gQTLstats, graph, ggbio,
ggplot2, DelayedArray
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 (>= 1.9.6), GenomicRanges,
ExperimentHub, TENxBrainData, BiocParallel, GenomicFeatures,
BiocStyle
parallel, knitr, gdsfmt (>= 1.2.2), SNPRelate (>= 1.1.6),
ggplot2, reshape2
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
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
knitr, BiocStyle, beeswarm, tximportData, DT, tximport,
dplyr, magrittr, BiocFileCache, testthat, BiocManager
knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot,
DescTools, RColorBrewer
knitr, rmarkdown, Rsubread (>= 1.29.0), testthat
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, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater,
DelayedArray (>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis,
org.Mm.eg.db, htmltools
MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots,
RColorBrewer, gridExtra, limma, boot, DBI, MASS
knitr, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap,
BiocStyle, testthat
knitr, png, limma, grid, DT, randomForest, digest, testthat
BiocStyle, knitr, testthat, magrittr,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Hs.eg.db, org.Mm.eg.db,
pasillaBamSubset
Rgraphviz, RBGL, testthat, 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, rmarkdown, BiocStyle, ggrepel, plotly, covr, spelling
knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable,
gridExtra, RColorBrewer, seqLogo, ggseqlogo
parallel, testthat, knitr, BiocStyle, rmarkdown
beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
ROCR, knitr, M3DExampleData, scater, SingleCellExperiment,
monocle, Seurat, Biobase
knitr, rmarkdown, BSgenome, Biostrings, mclust, rjson
amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
rgl, som
BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit,
BiocGenerics
biomaRt (>= 2.34.1), httr (>= 1.2.1), IRanges (>= 2.8.2),
knitr, testthat, tidyverse, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, AnnotationHub
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, scater
beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData,
scater, DelayedMatrixStats, knitr, testthat
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k,
knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit,
BiocGenerics
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle,
rmarkdown, similaRpeak
BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown
annotate, BiocGenerics, biomformat, knitr, gss, testthat (>=
0.8), vegan, interactiveDisplay
BiocGenerics, GenomicRanges, rtracklayer, Rsamtools,
survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager,
BSgenome, RSQLite
knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
testthat, gss, curatedMetagenomicData
BiocStyle, knitr, rmarkdown, RUnit, methylInheritance
BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC,
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, mGSZ,
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, tools
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
minfiData, BiocStyle, knitr, rmarkdown, edgeR,
tweeDEseqCountData
BiocStyle, knitr, rmarkdown, testthat, rgl
class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL,
hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07),
golubEsets, ada, keggorthology, kernlab, mboost, party
testthat, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0)
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, testthat, BiocStyle, VennDiagram, pamr
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
knitr, devtools, rmarkdown, BiocGenerics, RUnit
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 (>=
0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>=
2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr,
SummarizedExperiment
BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics
testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData,
CAMERA
MTseekerData, BiocStyle, rmarkdown, ggthemes, ggplot2,
pkgdown, knitr, rsvg
BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array,
RaggedExperiment, UpSetR, survival, survminer
knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase,
GEOquery
brgedata, minfi, minfiData, knitr, rmarkdown, testthat,
omicade4, iClusterPlus, GEOquery, MultiAssayExperiment,
BiocStyle, RaggedExperiment
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, BiocManager
roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
testthat, knitr, rmarkdown, BiocStyle, lintr, lassoshooting
knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI,
pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel
knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics
(>= 0.8.0)
knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
ALL, genefilter, limma, hgu95av2.db, ReportingTools,
BiocStyle
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit
Starr, BiocStyle, knitr, rmarkdown, testthat
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
knitr, rmarkdown, testthat, devtools, BiocManager
BiocStyle, knitr, rmarkdown, testthat, GEOquery,
VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges,
FDb.InfiniumMethylation.hg19, snpStats
BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots,
GenomicRanges, kableExtra
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle
flowWorkspaceData, knitr, testthat, utils, tools, parallel,
ggcyto, CytoML
knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2,
gridExtra, knitr, Matrix, rmarkdown, scales, testthat
testthat, rmarkdown, knitr, BiocStyle, BSgenome,
BSgenome.Hsapiens.UCSC.hg19
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,
RMariaDB
testthat, knitr, rmarkdown, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB,
AnnotationDbi, beeswarm, covr
knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra,
grid, reshape2, scales
BiocStyle, knitr, rmarkdown, testthat, digest
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gQTLBase, gQTLstats, geuvStore2, gwascat, BiocStyle
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
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)
testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
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
RUnit, BiocGenerics, knitr, Biobase, GEOquery, biomaRt,
ggplotify
knitr, markdown, rmarkdown, BiocStyle, PepsNMRData
testthat, lintr, knitr, rmarkdown, BiocStyle
RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics,
BiocStyle, knitr, R.utils
GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma
testthat, BiocStyle, knitr, rmarkdown, data.table
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet,
dplyr
foreach, doParallel, BiocStyle, knitr, rmarkdown, png,
GGally, gridExtra, ExpressionAtlas, ggforce, fgsea, pathview,
tidyr, dplyr
yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown,
BiocStyle
org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>=
2.30.0), knitr, BiocStyle, AnnotationDbi, energy
knitr, htmltools, BiocStyle, rmarkdown, testthat
knitr, BiocStyle, rmarkdown, testthat, ggplot2, HelloRanges,
HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset,
covr
BSgenome.Hsapiens.UCSC.hg38.masked,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
VariantAnnotation, SummarizedExperiment, knitr
BiocStyle, knitr, rmarkdown, colr, metap, repmis
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
BiocStyle, knitr, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
knitr, rmarkdown, devtools, roxygen2, testthat
BiocStyle, testthat, knitr, rmarkdown, png, Rsamtools,
ggplot2
airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr,
readr, readxl
BiocStyle, gridExtra, grid, testthat, devtools, knitr,
rmarkdown, ComplexHeatmap, viridis, ggplot2
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2,
synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3),
dplyr, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals, reshape
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown
RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi
pumadata, affydata, snow, limma, ROCR,annotate
PSCBS, copynumber, BiocStyle, BiocParallel, knitr, optparse,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, covr, testthat
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, BiocManager
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
Gviz, BiocStyle, knitr, rmarkdown, covr, testthat
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.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
Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach,
igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp,
rmarkdown, testthat, visNetwork
RUnit, BiocStyle, RefNet, knitr, rmarkdown
BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc,
testthat
AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2,
sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures,
knitcitations, knitr (>= 1.6), org.Hs.eg.db, RefManageR,
regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat (>=
2.1.0)
grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown,
zoo, RUnit, BiocManager, BSgenome, RSQLite, RMySQL
BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot
(>= 1.3.2), sessioninfo, DT, DESeq, edgeR, ggbio (>= 1.13.13),
ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap,
RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, minfiDataEPIC
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, restfulSEData
mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown
RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve
RUnit, BiocStyle, BiocGenerics, xtable, sna
testthat (>= 0.3), knitr, circlize (>= 0.4.8), rmarkdown
boot, tools, BiocGenerics, knitr, xtable
bit64, BiocStyle, knitr, rmarkdown, testthat, microbenchmark,
dplyr, ggplot2
knitr, testthat, BiocStyle, DT, reticulate
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, RUnit,
enviPat
readxl, knitr, rmarkdown, reshape2, pander, testthat
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, qvalue, 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, knitr, multtest, rmarkdown, testthat
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, RUnit, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
e1071, parallel, doParallel
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, readr, rmarkdown
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
Fletcher2013b, 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
knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
RUnit, BiocGenerics, knitr, knitcitations, formatR,
org.Sc.sgd.db, BioNet, DLBCL, msm
BiocStyle, biomaRt, beachmat, cowplot, destiny, knitr,
mvoutlier, rmarkdown, Rtsne, uwot, testthat, magrittr,
pheatmap, Biobase, limma
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot
testthat, knitr, rmarkdown, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
BiocStyle, covr, knitr, Matrix, rmarkdown, scales, scater,
testthat
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase,
BiocGenerics, ggplot2, ggthemes
BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2,
rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork
testthat, BiocStyle, knitr, beachmat, HDF5Array, irlba,
org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, aroma.light
BiocStyle, knitr, rmarkdown, Rsubread, testthat
testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db,
MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, Rsamtools, VariantAnnotation
knitr, BiocStyle, rmarkdown, testthat, BiocManager
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
testthat, BiocStyle, knitr, rmarkdown, covr
BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr,
cowplot, knitr, rmarkdown, testthat
scales, knitr, rmarkdown, testthat, minfi,
SummarizedExperiment, FlowSorted.CordBloodNorway.450k,
FlowSorted.Blood.450k, dplyr, tidyr, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions,
covr
BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
BiocStyle, optparse, testthat, knitr, rmarkdown
org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0),
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle
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, rmarkdown, scRNAseq, magrittr,
Rtsne, Matrix
testthat, Rsubread, BiocStyle, knitr, bladderbatch,
rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable,
spelling, GSEABase, lintr
BiocGenerics, BiocStyle, destiny, gam, knitr, mclust,
RColorBrewer, rmarkdown, testthat, covr
GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2,
Rtsne, Biobase, BiocStyle
BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
parallel, Matrix, RUnit, knitr, MASS, BiocGenerics
testthat, knitr, parallel,
BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations,
ggdendro, fastICA, sva
testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>=
5.0.0)
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress,
pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa,
phenopath, BASiCS, zinbwave, SparseDC, BiocManager, spelling
igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel,
gridExtra, digest, doParallel, bigmemory
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
qgraph, png, grid
RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>=
1.3), roxygen2, doSNOW
testthat, BiocStyle, knitr, rmarkdown,
gWidgets2,gWidgets2RGtk2,RGtk2
RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz
testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat,
roxygen2, covr, knitr, plyranges, ggbio, biovizBase, circlize,
tictoc, GenomeInfoDb, IRanges, S4Vectors, SummarizedExperiment
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat,
DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter,
scater, rnaseqcomp, biomaRt
annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown,
digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit,
testthat
Hmisc, CPE, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN,
BiocStyle
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt,
BiocParallel, BiocManager
jpeg, png, BiocStyle, rmarkdown, devtools, maftools,
parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame,
pathview, clusterProfiler, igraph, supraHex
testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2,
BiocStyle, animation, pander
BiocFileCache, BiocStyle, curatedTCGAData, devtools, dplyr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr,
magrittr, minfi, mirbase.db, org.Hs.eg.db, readr, RTCGAToolbox
(>= 2.7.5), rtracklayer, R.utils, testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene,
knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2,
GSEABase, DESeq2, BiocGenerics, ggrepel, rcompanion,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, data.table, GSEABase, testthat, AnnotationDbi,
AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges,
Gviz, IRanges, Rsamtools, S4Vectors, org.Hs.eg.db,
EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db,
GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR,
ggplot2, png, gwascat
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap,
GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db,
MASS, RColorBrewer, rmarkdown, UpSetR,
knitr, aroma.light, affxparser, RUnit, BiocGenerics
GenomicFeatures, shiny, BiocManager, rmarkdown, testthat
EBImage, knitr, rmarkdown, testthat, tofsimsData,
BiocParallel, RColorBrewer
BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR,
plotrix, breastCancerVDX, EnrichmentBrowser
limma, edgeR, DESeq2, NBPSeq, dplyr, testthat, knitr,
rmarkdown, reshape2, tidyr, readr, org.At.tair.db,
AnnotationDbi
topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle,
xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
Biostrings, ggplot2, ggtree, knitr, phangorn, prettydoc,
testthat, tidyr
ggtree, BiocStyle, knitr, rmarkdown, testthat
RUnit, plyr, knitr, BiocGenerics, rmarkdown
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer,
GenomeGraphs
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer
BiocStyle, knitr, rmarkdown, testthat, ggplot2
BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways
EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT
(>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>=
1.12), rmarkdown, testthat, covr, pander
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db,
DESeq2, edgeR, devtools
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma,
edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix
knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny,
biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb,
ontoProc
BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr,
org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
testthat, knitr, rmarkdown, BiocGenerics, RUnit
spelling, knitr, BiocStyle, TFBSTools, rmarkdown, MotifDb,
testthat, Logolas, BiocParallel, seqLogo, motifStack
BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics,
r2glmm, readr
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 (>=
1.21.3)
SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown
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, rmarkdown, metagenomeSeq, DESeq2, edgeR
knitr, DESeq, rmarkdown, BiocStyle, testthat
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata, ncdf4,
rgl, microbenchmark, testthat, pander, magrittr, MALDIquant,
pheatmap
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, DESeq2, Seurat
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
parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno,
org.Dm.eg.db, caTools, plotly
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