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 (>= 4.0.0), 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
R (>= 3.6.0), SummarizedExperiment, ROCR
methods, grDevices, stats, utils, parallel, edgeR
R (>= 3.6), methods, Biobase, MSnbase (>= 2.9.3)
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, DT
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 (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
GenomicRanges
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 3.6), GenomicRanges, cowplot, breakpointRdata
R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors
R (>= 3.5), methods, BiocGenerics, GenomicRanges (>= 1.33.6),
SummarizedExperiment (>= 1.17.4)
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)
methods, MultiAssayExperiment, R (>= 3.5.0)
R (>= 2.14.0), Biobase, binom, methods, stats
BiocGenerics, BiocParallel, EBImage, graphics, methods,
S4Vectors (>= 0.23.18), stats, ProtGenerics
R (>= 3.6.0), Biobase, IRanges, methods, GenomicRanges
methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix
R (>= 4.0.0), AnVIL, MultiAssayExperiment
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 (>= 3.5.0), 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),DMRcate,
Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest,
DT
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 (>= 3.0.0), 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)
stats, utils, graphics, grDevices, datasets, base, biomaRt,
GenomicRanges, R (>= 3.1.0)
R (>= 3.3), GenomicRanges, ggplot2, chromstaRData
R (>= 3.5.0), methods, S4Vectors (>= 0.18.0),
MultiAssayExperiment (>= 1.6.0), 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 (>= 3.6), 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
SummarizedExperiment, GenomicRanges, IRanges, S4Vectors,
rtracklayer
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 (>= 4.0), EBImage, SingleCellExperiment, methods
R (>= 3.4), SummarizedExperiment, ggplot2
R (>= 4.0.0), foreach, parallel, doParallel, igraph
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, IRanges,
GenomicRanges, SummarizedExperiment, Biostrings, VGAM,
VariantAnnotation (>= 1.13.44),
R (>= 3.4), methods, stats4, matrixStats, BiocGenerics (>=
0.31.5), S4Vectors (>= 0.25.15), IRanges (>= 2.17.3)
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment,
knitr, KernSmooth, matrixcalc
BiocGenerics (>= 0.7.5), Biobase (>= 2.21.7), locfit, lattice
S4Vectors (>= 0.23.18), IRanges, GenomicRanges,
SummarizedExperiment (>= 1.1.6)
R(>= 4.0.0), R.utils, DESeq2, BiocParallel
BiocParallel, Biobase, SummarizedExperiment, IRanges (>=
2.5.17), GenomicRanges (>= 1.23.7), DESeq2 (>= 1.9.11),
AnnotationDbi, RColorBrewer, S4Vectors (>= 0.23.18)
R (>= 3.5), GenomicRanges, SummarizedExperiment
R (>= 3.5), GenomicRanges, InteractionSet,
SummarizedExperiment
R (>= 3.6.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges
R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges, fdrtool
R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10)
R (>= 3.6.0), minfi, SummarizedExperiment
R (>= 4.0.0), methods, stats, utils, graphics, Rcpp
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
R (>= 3.3), methods, Biobase, BiocParallel, bsseq
blockmodeling, gplots, testthat, R (>= 3.0.0)
isa2, Biobase (>= 2.17.8), AnnotationDbi, methods
R (>= 3.1.2), methods, grid, ComplexHeatmap (>= 2.4.2),
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, pipeFrame
R (>= 3.6), SummarizedExperiment, MultiAssayExperiment,
cluster (>= 2.0.7-1), fpc (>= 2.2-3)
R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment
Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 2.19.3),
BiocFileCache (>= 1.5.1)
utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData
(>= 1.17.3)
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 (>= 2.11.0), flowCore, flowViz,flowClust
R (>= 3.2), methods, flowCore, flowViz, flowStats
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 (>= 3.6), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges, biomaRt,
ggplot2
R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods,
BiocGenerics (>= 0.13.8)
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 (>= 4.0.0), stats, methods, graphics, GGally, network, sna,
scales, matrixStats
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
circlize, GenomicRanges, graphics, R (>= 4.0)
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, 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 (>= 3.6), utils, curl, rhdf5, R6, grid
R (>= 3.6), 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 (>= 2.9.0), Biobase, fdrtool, MASS, survival
Biobase, IRanges, GenomicRanges, RColorBrewer,
rtracklayer,graphics,GenomeInfoDb
R (>= 2.10), methods, Biobase, annotate, plotrix
methods, R (>= 3.6.0), Rcpp (>= 0.12.0), SummarizedExperiment,
StanHeaders (> 2.18.1)
R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>=
2.9.1)
R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
R(>= 3.6), 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 (>= 3.6), 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 (>= 0.25.14)
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 (>= 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, Matrix, 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 (>= 3.4.0), EDASeq, DESeq, limma, qvalue
R (>= 4.0.0), DESeq2, limma, locfit, splines
R (>= 3.4), metagenomeSeq (>= 1.17.1), methods, data.table,
Biobase, digest
R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
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 (>=
1.22.0), GenomicRanges, Biobase (>= 2.34.0), org.Hs.eg.db
R (>= 3.5.0), 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 (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 2.14.0), minpack.lm, MASS, parallel, mitoODEdata,
KernSmooth
R (>= 3.5), Rcpp, 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 (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, 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 (>= 2.10), graphics, BiocGenerics, GenomicRanges
R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment,
limma
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(>= 1.51.7), RcppArmadillo, methods, BH
R (>= 2.15.1), Rgraphviz, methods, minet, mclust, reshape2
R (>= 3.6.0), BiocGenerics, ggplot2, tibble (>= 1.3.1)
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
R(>= 3.6.0), igraph, graphics, methods, utils
R (>= 3.4), webshot, shiny, shinyFiles, scatterplot3d
dplyr, optimalFlowData, rlang (>= 0.4.0)
R (>= 2.14.0), methods, BiocGenerics (>= 0.15.10),
AnnotationDbi (>= 1.33.15), GenomicFeatures (>= 1.39.4)
R (>= 2.9.0), methods, S4Vectors, IRanges, ShortRead (>=
1.23.15), Biobase, vegan
R (>= 3.6), 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
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, Hmisc
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), 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 (>= 3.2.0), 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 (>= 4.0), parallel, GenomicRanges, 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 (>= 3.5.0), methods, GenomicRanges, Rsamtools, baySeq
R (>= 3.2), Biobase, rcellminerData (>= 2.0.0)
R (>= 2.14.1), methods, graph, GOstats, ggplot2
R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2,
ComplexHeatmap
R (>= 3.5.0), BiocGenerics, 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 (>= 2.7.0), RmiR.Hs.miRNA, RSVGTipsDevice
R (>= 3.6), IRanges (>= 2.21.6), S4Vectors (>= 0.25.14),
GenomicRanges, Modstrings
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
boot, SummarizedExperiment, fission, knitr, 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 (>= 1.37.2)
R (>= 3.4.0), biclust, SummarizedExperiment
R (>= 3.3.0), methods, utils, stats, stats4, BiocGenerics (>=
0.31.1)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 3.4), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 3.5), SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4),
tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN,
PMA
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 3.6), SummarizedExperiment, dynamicTreeCut,
SingleCellExperiment
SingleCellExperiment (>= 1.7.4), Seurat, ggplot2 (>= 3.2.1),
shiny
R (>= 2.10), GO.db, RpsiXML, annotate, apComplex
R (>= 3.4), methods, SummarizedExperiment
R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19
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)
R (>= 4.0), 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 (>= 3.6), Seurat, SingleCellExperiment,
SummarizedExperiment, dplyr
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
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 (>= 4.0), ggplot2, ggridges, SummarizedExperiment,
BiocGenerics
R (>= 3.6.0),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 (>= 3.4), Biobase, BiocParallel, cluster, matrixStats,
stats, graphics, utils
GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R
(>= 3.6.0)
R (>= 3.6), 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
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 (>= 3.6), RefFreeEWAS, EpiDISH, limma, nnls
R (>= 3.3.0), methods, utils, ProtGenerics
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R (>= 3.5.0), 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(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18)
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 (>= 3.6.0), ggplot2, limma, foreach, scales, Biobase,
methods
R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb
(>= 1.15.2), GenomicRanges (>= 1.37.4), SummarizedExperiment
(>= 1.9.9), Rsamtools (>= 1.99.0)
R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>=
1.13.0), GenomicRanges, GDSArray (>= 1.3.0), DelayedDataFrame
(>= 1.0.0)
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
R (>= 2.5.0), digest, tools, utils, codetools
R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 3.6.0), 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, grDevices, graphics, methods, stats, splines, utils
bit, ffbase, DNAcopy, tilingArray, waveslim, cluster, aCGH,
snapCGH
methods, graphics, stats, utils, calibrate, origami (>=
1.0.0), SummarizedExperiment, S4Vectors, tmle
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, Glimma
affxparser (>= 1.16.0), affy, graphics, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi,
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, rlang
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
assertthat, BiocParallel, ChIPseeker, corrplot, data.table,
dplyr, GenomicRanges, GGally, genefilter, gghalves, ggplot2,
ggseqlogo, Gviz, magrittr, org.Hs.eg.db, plyr, reshape2,
rtracklayer, stats, stringr, tibble, tidyr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, utils
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, knitr, ggplot2,
gridExtra, utils
methods, log4r, tools, rjson, Biobase, graph
ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils,
plyr, DESeq2
methods, utils, grDevices, graphics, stats, foreach,
doParallel, BiocGenerics (>= 0.31.6), 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 (>=
0.23.19), XML, forcats, scales, lattice, glmnet, tsne, DMwR,
plotROC, DT, reactable, utils, limma, methods, stats, tibble,
biomformat, umap, Matrix
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, BiocVersion,
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 (>=
0.23.10), stats, utils
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
stats, utils, methods, futile.logger, jsonlite, httr, curl,
rapiclient (>= 0.1.3), tibble, BiocManager
GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq,
ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2,
methods, rtracklayer, ensembldb, VariantAnnotation, dplyr,
tidyr, repmis
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.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, mvtnorm,
PepsNMR, plyr, quadprog, ropls, stats, SummarizedExperiment,
utils, Matrix, zoo
BiocParallel, GenomicAlignments, GenomicFeatures,
GenomicRanges, IRanges, IVAS, Rsamtools, biomaRt, limma,
S4Vectors, stats, DRaWR, GenomeInfoDb, Gviz, Matrix, dplyr,
fgsea, reshape2, igraph, graphics, e1071, methods, rtracklayer,
scales, grid, ggplot2, mGSZ, utils
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
BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table,
ggplot2, grDevices, graphics, grid, motifStack, rappdirs,
stats, testit, utils
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, BiocGenerics,
S4Vectors, utils
RColorBrewer, mzR, assertthat, scales, entropy, cluster,
grDevices, graphics, stats, 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, R.utils, 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, ggExtra, ggplot2,
graphics, grDevices, KernSmooth, MASS, methods, Rcpp (>=
0.11.3), S4Vectors, scran, stats, stats4, SummarizedExperiment,
viridis, utils, Matrix, matrixStats, assertthat, reshape2,
hexbin
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
DelayedArray, DelayedMatrixStats, scater, BiocParallel
utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva,
corpcor, moments, matrixStats, ggvis, heatmaply, reshape2,
limma, grDevices, graphics, stats, methods, Matrix
Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix,
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,
outliers, abind, stats, graphics, utils, methods
GenomicFeatures, rhdf5, tximport, Biostrings, rtracklayer,
biomaRt, jsonlite, methods, grDevices, graphics, stats, utils
data.table, curl, RCurl, digest, methods, stats, utils, dplyr,
RSQLite, graph, Biobase
stats, utils, GEOquery, graphics, BiocGenerics
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(>= 1.0.5), visNetwork,
htmlwidgets, plyr, tibble, DT (>= 0.12), dplyr (>= 0.8.5)
biocViews (>= 1.33.7), BiocManager, stringdist, graph, httr,
tools, optparse, codetools, methods, utils, knitr
httr, whisker, readr, dplyr, utils, methods
methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, curl,
httr
methods, utils, graphics, stats, parallel
Rgraphviz, geneplotter, graph, BiocGenerics, methods
Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix
ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr,
rjson, dplyr, magrittr, grid, DT, GenomicRanges, IRanges,
ggplot2, SummarizedExperiment, DBI, GenomicFeatures,
curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz
stats, utils, futile.logger, parallel, snow
BiocFileCache, BiocManager, biocViews, tibble, methods, rlang,
tidyselect, stringr, rvest, rex, dplyr, xml2, rappdirs, readr,
httr, htmltools, DT, tools, utils, igraph, tidyr, jsonlite, gh,
RBGL, graph, magrittr
methods, tibble, utils, rlang, plyr, rtracklayer,
AnnotationDbi, KEGGREST
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, irlba, rsvd, Rcpp
bookdown, knitr (>= 1.30), 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, git2r, httr, knitr, rmarkdown,
rstudioapi, stringr, tools, utils, usethis
utils, XML, AnnotationDbi, progress, stringr, httr, openssl,
BiocFileCache, rappdirs, xml2
stats, utils, grDevices, lattice, BiocParallel, glmnet, rms,
nsprcomp, ranger, e1071, variancePartition, ggplot2, pROC,
vioplot, CMplot
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
methods, utils, grDevices, graphics, stats, crayon
BiocGenerics, Biobase, methods, grid, graphics, NMF
igraph, cluster, psych, stringr, GenomicRanges, Hmisc, MASS
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, future, doFuture, drtmle (>= 1.0.4), S4Vectors,
BiocGenerics, BiocParallel, SummarizedExperiment, limma
grDevices, stats, scales, Hmisc, RColorBrewer, dichromat,
BiocGenerics, S4Vectors (>= 0.23.19), 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
readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools,
data.table, Biobase, GenomicRanges, BiocGenerics,
VariantAnnotation, DelayedMatrixStats, SummarizedExperiment,
GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats,
rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools,
BiocParallel
methods, BiocGenerics, Biobase, S4Vectors, IRanges,
GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer,
parallel, betareg, lokern, Formula, globaltest
grid, stats, grDevices, utils, circlize, viridis,
RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla
beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8),
BiocGenerics, grDevices, stats, graphics
Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, 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
Biostrings (>= 2.52.0), BSgenome.Hsapiens.UCSC.hg19 (>=
1.4.0), bumphunter (>= 1.26.0), cowplot (>= 1.0.0), derfinder
(>= 1.18.1), derfinderPlot (>= 1.18.1), GenomicRanges (>=
1.36.0), ggplot2 (>= 3.1.1), RColorBrewer (>= 1.1), utils,
grDevices, GenomicState (>= 0.99.7)
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
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, curl, xml2, grDevices, rlang,
BiocFileCache, rappdirs
GenomicRanges, parallel, IRanges, stats, Rsamtools,
GenomicAlignments, DESeq2, SummarizedExperiment, utils, methods
methods, utils, stats, matrixStats, BiocGenerics, S4Vectors,
IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings,
Rsamtools, rtracklayer
IRanges (>= 2.22.2), GenomeInfoDb, scales, stats, graphics,
Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>=
0.25.14), 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 (>= 0.31.6), 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
AnnotationDbi, AnnotationFilter, biomaRt, BiocGenerics,
Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb,
GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr,
Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr,
tibble, tidyr, utils, zeallot
affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase
beanplot, BiocGenerics, BiocParallel, BSgenome, data.table,
DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments,
GenomicRanges (>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges
(>= 2.18.0), KernSmooth, memoise, 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, irlba, lattice, Matrix, matter, magrittr,
mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite
doParallel, readr, viper, AnnotationDbi, Category, ggplot2,
UniProt.ws, lpSolve, igraph
BiocGenerics (>= 0.31.6), coda, EBarrays, gaga, gtools,
GenomeInfoDb, GenomicFeatures, limma, mgcv, Rsamtools,
rtracklayer, S4Vectors (>= 0.9.25), sqldf, survival, VGAM
circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel,
ggridges, graphics, grDevices, grid, gridExtra, magrittr,
Matrix, matrixStats, methods, nnls, purrr, RColorBrewer,
reshape2, Rtsne, SummarizedExperiment, S4Vectors, scales,
scater, stats
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
BiocFileCache (>= 1.5.3), digest, dplyr, GenomeInfoDb,
GenomicRanges, httr, IRanges, methods, readr, RaggedExperiment,
RTCGAToolbox (>= 2.15.8), S4Vectors, SummarizedExperiment,
stats, tibble, tidyr, TCGAutils, utils
stats, S4Vectors, utils, methods, Matrix,
SummarizedExperiment, SingleCellExperiment, Rtsne, graphics,
grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack
(>= 0.7)
MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang,
BiocGenerics, S4Vectors, readr, tibble, DelayedArray
plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
grDevices, graphics, matrixStats, doParallel, digest,
gridExtra, methods, reshape2, MAST, S4Vectors, data.table,
Rcpp, RcppEigen, uwot, enrichR, stringi, SummarizedExperiment,
MCMCprecision, ggrepel, Rtsne, withr, dendextend, ggdendro,
pROC, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
DelayedArray, Seurat, stringr, Matrix
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, tidyselect, 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, methods, BiocParallel,
BiocGenerics
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, 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, fastcluster
furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr,
future, stats
circlize, ComplexHeatmap, clusterProfiler, DESeq2,
GenomicTools, GenomicTools.fileHandler, ggnetwork, GGally,
ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix,
network, Rcpp, RCy3, S4Vectors, stats, SummarizedExperiment,
utils, WebGestaltR
Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
Biobase, CGHbase, CGHcall, methods, stats, utils
prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
limma,RPMM, DNAcopy, preprocessCore,impute, marray, wateRmelon,
plyr,goseq,missMethyl,kpmt,ggplot2,
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
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 (>= 1.7.1), 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, magick
AnnotationDbi, BiocGenerics, chipenrich.data, GenomeInfoDb,
GenomicRanges, grDevices, grid, IRanges, lattice, latticeExtra,
MASS, 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 (>= 0.23.10), 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, grid, matrixStats,
AnnotationDbi, limma, multtest, RBGL, graph, BiocManager,
stats, regioneR, DBI, ensembldb, Biobase, seqinr, idr,
GenomicAlignments, DelayedArray, SummarizedExperiment,
rtracklayer, Rsamtools, VennDiagram
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,
GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots,
graphics, grDevices, gtools, methods, plotrix, dplyr, parallel,
magrittr, RColorBrewer, rtracklayer, S4Vectors, stats,
TxDb.Hsapiens.UCSC.hg19.knownGene, 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
Biobase (>= 2.17.8), graphics, grDevices, methods, stats,
IRanges, rtracklayer, GenomicRanges
methods, utils, grDevices, graphics, stats, foreach,
doParallel, BiocGenerics (>= 0.31.6), 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
dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2,
edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2,
ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb,
universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
Biostrings, BSgenome,
SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>=
1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid,
dbscan, SNFtool, propr, uwot, Rtsne, S4Vectors (>= 0.24.0),
igraph, scales, scran (>= 1.14.6), graphics, methods, stats,
utils, reshape2, ggridges, randomForest, pheatmap, ggraph,
grDevices, rhdf5, rlang
BSgenome, GenomicRanges, seqinr, e1071, GenomeInfoDb, IRanges,
utils, BSgenome.Drerio.UCSC.danRer7
methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor, RBGL
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, qlcMatrix,
matrixStats, methods
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, downloader, DOSE (>= 3.13.1), dplyr, enrichplot
(>= 1.7.1), GO.db, GOSemSim, magrittr, methods, plyr, qvalue,
rlang, rvcheck, stats, tidyr, utils
methods, pracma, princurve (>= 2.0.5), scatterplot3d,
RColorBrewer, grDevices, graphics, utils, stats
cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, readr, rlang,
scales, stringr, tibble, tidyr, stats, methods,
SingleCellExperiment, SummarizedExperiment, matrixStats,
S4Vectors
methods, rhdf5, data.table, prada, SummarizedExperiment,
matrixStats
DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb,
S4Vectors, exomeCopy
IRanges, GenomicRanges, SummarizedExperiment, pracma,
regioneR, assertthat, karyoploteR, CopyNumberPlots, graphics,
utils, VariantAnnotation, Rsamtools, GenomeInfoDb, Biostrings,
methods
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, 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, simpleCache, fitdistrplus
affy, siggenes, GEOquery, vsn, igraph, acde, Biobase, limma,
graphics, stats, utils, STRINGdb, SummarizedExperiment, minet,
rmarkdown
BiocParallel, cluster, 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, stringr, tibble, tidyr, dplyr, devtools
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.4.2), 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
ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix, BB,
reshape2, alabama, cobs, Biobase, vegan, grDevices, graphics,
methods, SummarizedExperiment
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, methods
GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods
data.table, grDevices, clue, cluster, gplots, BiocGenerics (>=
0.31.6), S4Vectors, IRanges, GenomicRanges, 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, rhdf5, 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
Biobase, S4Vectors, SummarizedExperiment, piano, BiocParallel,
methods, stats, utils, graphics, grDevices, lsa
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, methods
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, utils,
lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats,
VGAM, parallel, graphics, limma, beanplot
data.table, methods, MergeMaid, ConsensusClusterPlus, limma,
cluster, dplyr, Biobase, grDevices, stats, graphics, utils
Rcpp, BiocGenerics, Rsamtools, edgeR, limma, GenomicFeatures,
AnnotationDbi, methods, S4Vectors, IRanges, GenomeInfoDb,
stats, BiocParallel, utils
GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2,
grDevices, stats, utils
Biobase, BiocGenerics, graphics, grDevices, ggplot2, igraph,
Matrix, methods, Matrix, utils, sincell, TSCAN, HSMMSingleCell
biomaRt, cowplot, data.table, dplyr, fgsea, ggplot2, ggrepel,
graphics, httr, limma, methods, pbapply, R.utils, readxl,
reshape2, rhdf5, scales, stats, tools, utils
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
viridis, methods, shiny, graphics, stats, grDevices, utils,
BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment,
flowCore, Biobase, Rcpp, BiocNeighbors
doParallel, dplyr, glmnet, rpart, rpart.plot, stats,
flowCore,grDevices, graphics, utils
flowCore, ggplot2, ggridges, RColorBrewer, reshape2, stats,
grDevices, Rdpack, methods, grid, FlowSOM
S4Vectors, RColorBrewer, viridis, utils, SummarizedExperiment,
tools, graphics, raster, grDevices, stats
cytolib(>= 2.0.3), flowCore (>= 1.99.10), flowWorkspace (>=
3.99.15), openCyto (>= 1.99.2), XML, data.table, jsonlite,
RBGL, Rgraphviz, Biobase, methods, graph, graphics, utils,
base64enc, plyr, dplyr, grDevices, methods, ggcyto (>= 1.11.4),
yaml, lattice, stats, corpcor, RUnit, tibble, RcppParallel,
xml2
pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils,
biomaRt, grid, motifStack, grImport2, methods
stats, GenomeInfoDb, GenomicRanges, IRanges, S4Vectors, readr,
SummarizedExperiment, GenomicAlignments, stringr, plyr,
VariantAnnotation, parallel, ggplot2, Rsamtools, BiocGenerics,
methods, limma, bumphunter, Biostrings, reshape2, cowplot,
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,
plyr
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 (>= 0.7.0), DAPARdata (>= 1.16.0),
siggenes, graph, lme4, readxl, clusterProfiler, dplyr,
tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra,
visNetwork
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
CompQuadForm, ggplot2, KernSmooth, matrixStats, methods,
parallel, pbapply, stats, statmod
shiny, jsonlite, shinyjs, shinydashboard, shinyBS, gplots, DT,
ggplot2, RColorBrewer, annotate, AnnotationDbi, DESeq2, DOSE,
igraph, grDevices, graphics, stats, utils, GenomicRanges,
IRanges, S4Vectors, SummarizedExperiment, stringi, reshape2,
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), GenomicRanges, stats,
GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr,
utils, graphics, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
SummarizedExperiment, ggseqlogo, gridExtra, data.table,
GenomeInfoDb
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
graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL,
Rgraphviz, rrcov, NCIgraph
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 (>= 0.56.0), Matrix, S4Vectors (>=
0.17.5), IRanges, HDF5Array (>= 1.16.1), BiocParallel
IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2
matrixStats, stats, truncdist, base64enc, ggplot2
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 (>=
0.23.19), stats, utils
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3),
GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>=
1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28),
limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>=
0.9.38), scales, utils
BiocParallel, BiocGenerics, ChIPpeakAnno, data.table,
DelayedArray, GenomeInfoDb, GenomicAlignments, glue, IRanges,
plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>= 0.23.19),
SummarizedExperiment, tools, utils
genefilter, geneplotter, methods, MASS, RColorBrewer
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,
methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0)
methods, graphics, grDevices, utils, stats, Matrix, Rcpp (>=
0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba, pcaMethods,
Biobase, BiocGenerics, SummarizedExperiment,
SingleCellExperiment, ggplot2, ggplot.multistats, tidyr,
tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW,
smoother, scales, scatterplot3d
graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq,
DESeq, stats, grDevices, graphics, pheatmap, utils, ggplot2,
Matrix, jsonlite, tools, DESeq2, methods
BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb,
GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats,
utils
BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
zoo (>= 1.8-3), dplyr, tidyr, rlang, mzR (>= 2.18), signal,
ggplot2, scales, gridExtra, RSQLite, DBI, Rcpp
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, zip, reshape2
Rcpp, stats, SummarizedExperiment, SingleCellExperiment,
methods, Matrix, foreach, parallel, doParallel, doRNG, ggplot2,
limma, scater
methods, colorspace (>= 1.4), gridExtra, cowplot, reshape2,
pheatmap, grDevices, ggrepel, ggridges, stats, utils,
SummarizedExperiment, SingleCellExperiment, edgeR, S4Vectors
utils, stats, speedglm, MASS, data.table, splines, arm,
rtracklayer, benchmarkme, tibble, matrixStats, fastDummies,
graphics
utils, stats, grDevices, rtracklayer, multcomp, calibrate,
graphics
parallel, Rcpp, RcppRoll, betareg, grDevices, graphics,
methods, stats, utils
ExperimentHub, bsseq, GenomeInfoDb, limma, edgeR, DSS,
missMethyl, GenomicRanges, 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, methods
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, SummarizedExperiment, utils
methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy,
limma, stringr, ggplot2, graphics, grDevices, calibrate,
corrgram, gridExtra, DT, shiny, shinydashboard, readxl,
prodlim, matrixStats
AnnotationDbi, BiocParallel, DO.db, fgsea, ggplot2, GOSemSim
(>= 2.0.0), methods, qvalue, reshape2, stats, utils
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
MASS, IRanges, BSgenome, grDevices, parallel
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
utils, graphics, stats, splines, DelayedArray
BiocParallel, SummarizedExperiment, mclust, utils, ggplot2,
dplyr, tidyr, RColorBrewer, magrittr, gganimate, purrr
Biobase (>= 2.44.0), BiocFileCache (>= 1.7.10), BiocGenerics
(>= 0.30.0), BiocParallel (>= 1.18.1), biomaRt (>= 2.40.5),
Biostrings (>= 2.52.0), DESeq (>= 1.36.0), edgeR (>= 3.26.8),
GenomeInfoDb (>= 1.20.0), genomeIntervals (>= 1.40.0),
GenomicAlignments (>= 1.20.1), GenomicRanges (>= 1.36.1),
SummarizedExperiment (>= 1.14.1), graphics, IRanges (>=
2.18.3), LSD (>= 4.0), locfit, methods, parallel, rappdirs (>=
0.3.1), Rsamtools (>= 2.0.3), S4Vectors (>= 0.22.1), ShortRead
(>= 1.42.0), 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
methods, graphics, stats, utils, 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,
methods
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)
graphics, stats, GenomicRanges, GenomicFeatures, S4Vectors,
IRanges, AnnotationDbi, limma, edgeR, methods,
SummarizedExperiment, BiocGenerics, rtracklayer, utils
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, reshape2, ggpubr, rtracklayer,
DelayedArray
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
methods, tools, jsonlite, RCurl, tidyr, data.table, dplyr,
stringr, stringi, utils, AnnotationHub, GenomicRanges,
rtracklayer, S4Vectors, GenomeInfoDb, ENCODExplorerData
foreach, doParallel, parallel, stats, survivalROC, glmnet,
survivalsvm, ggplot2, minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19, survival, utils
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
AnnotationDbi, BiocFileCache, BiocManager, ComplexHeatmap,
GSEABase, GO.db, KEGGREST, KEGGgraph, Rgraphviz, S4Vectors,
SPIA, biocGraph, edgeR, geneplotter, graphite, hwriter, limma,
methods, pathview, rappdirs, safe, topGO
AnnotationDbi, cowplot, DOSE (>= 3.13.1), europepmc, ggplot2,
ggplotify, ggraph, ggridges, GOSemSim, graphics, grDevices,
grid, gridExtra, igraph, methods, plyr, purrr, RColorBrewer,
reshape2, stats, utils, scatterpie
BSgenome, rtracklayer, motifmatchr, TFBSTools, R.utils,
methods, JASPAR2018, GenomeInfoDb, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, utils, parallel, stats, ggpubr,
heatmap3, ggplot2, clusterProfiler, rmarkdown, grDevices,
magrittr
methods, RSQLite (>= 1.1), DBI, Biobase, GenomeInfoDb,
AnnotationDbi (>= 1.31.19), rtracklayer, S4Vectors (>=
0.23.10), 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,
locfdr
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
data.table, doParallel, EntropyExplorer, graphics, stats,
grDevices, pheatmap, utils, qvalue, WGCNA, ReactomePA
BoolNet, e1071, gtools, stats, igraph, utils, lattice,
latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph,
mnem
methods, utils, httr, xml2, curl, GenomicFeatures,
GenomicRanges, GenomeInfoDb, BiocGenerics, BiocFileCache,
S4Vectors, IRanges, RSQLite, DBI, Biostrings, tRNAdbImport
epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4),
GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb
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 (>= 0.23.18), BiocGenerics,
GenomicRanges, SummarizedExperiment, ggplot2, GenomeInfoDb,
Biobase, shiny, BiocParallel, IRanges, AnnotationDbi
Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer,
ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph,
rJava, magrittr, digest, BSgenome, AnnotationDbi,
GenomicFeatures, R.utils, GenomeInfoDb, BiocGenerics,
S4Vectors, IRanges, rmarkdown, tools, VennDiagram, grid,
JASPAR2018, TFBSTools, grDevices, graphics, stats, utils,
parallel, corrplot, BiocManager, motifmatchr
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2,
ggdendro, plotrix, stats, matrixStats, 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
shiny, shinydashboard, DT, cowplot, utils, dplyr, magrittr,
tidyr, ggplot2, stats, methods, rintrojs, scales, tibble, MASS,
limma, S4Vectors
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,
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
FCBF, parallel, progress, dplyr, ggplot2, ggrepel, igraph,
grid, intergraph, stringr, clusterProfiler, data.table,
grDevices, methods, network, scales, sna, utils, stats,
SingleCellExperiment, pathwayPCA
stats, plyr, VariantAnnotation, SummarizedExperiment,
rtracklayer, GenomicRanges, methods, IRanges
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, methods, stats, utils, graphics, grDevices
Rcpp, 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, Rcpp,
Matrix
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
gplots, graphics, MASS, methods, SparseM, stats, utils
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), grDevices, graphics,
methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>=
1.9.15)
flowCore, graphics, flowViz (>= 1.46.1), car, sp, rgeos,
gplots, RFOC, flowWorkspace (>= 3.33.1), 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
stats, utils, flowCore, ConsensusClusterPlus, BiocGenerics,
tsne, CytoML, flowWorkspace, XML, RColorBrewer
FlowSOM, Rtsne, ggplot2, destiny, gmodels, flowUtils, Biobase,
Matrix, flowCore, sva, matrixStats, methods, mclust, prettydoc,
RANN(>= 2.5), Rcpp (>= 0.12.0), BiocNeighbors, cluster,
pheatmap, scatterpie, umap, scatterplot3d, limma, stringr,
grDevices, grid, stats
BiocGenerics, MASS, flowCore (>= 1.99.6), flowWorkspace,
ncdfFlow(>= 2.19.5), flowViz, fda (>= 2.2.6), Biobase, methods,
grDevices, graphics, stats, cluster, utils, KernSmooth,
lattice, ks, RColorBrewer, rrcov
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, cytolib (>= 1.99.26), lattice,
latticeExtra, XML, ggplot2, graph, graphics, grDevices,
methods, stats, stats4, utils, RBGL, tools, Rgraphviz,
data.table, dplyr, Rcpp, stringr, scales, matrixStats,
RcppParallel, RProtoBufLib, digest, flowCore(>= 1.99.20),
ncdfFlow(>= 2.25.4)
RUnit, methods, ChemmineR, BiocGenerics, parallel
Biobase, Biostrings, GenomicRanges, SummarizedExperiment,
Rsamtools, ggbio, reshape2, rtracklayer, fda,
GenomicAlignments, gtools, Matrix, methods
AnnotationDbi, BBmisc, Biobase, BiocGenerics, biomaRt,
BSgenome, cowplot, DelayedArray (>= 0.5.11),
DelayedMatrixStats, extraDistr, GenomeInfoDb,
GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges,
grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods,
pcaMethods, pheatmap, plotly, PRROC, RColorBrewer, rhdf5,
Rsubread, R.utils, S4Vectors, stats, tibble, tools, utils, VGAM
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,
SummarizedExperiment
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
Rcpp (>= 1.0.2), httr, googleAuthR, googleCloudStorageR,
methods, jsonlite, utils
BiocManager, Biobase, utils, methods, RSQLite, devtools, dplR,
stringr, graphics, stats, affxparser, data.table
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
dplyr, grDevices, ggplot2, magrittr, mixtools, scales,
pbmcapply, parallel, stats, 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
utils, methods, stats, Biobase, BiocGenerics
BiocGenerics (>= 0.31.2), 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,
data.table
AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils
S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser,
RColorBrewer, Biostrings
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
AnnotationDbi, bs4Dash, ComplexHeatmap, dendextend, DESeq2,
dplyr, DT, dynamicTreeCut, ggforce, ggplot2, ggrepel, GO.db,
graphics, grDevices, grid, igraph, matrixStats, methods,
plotly, RColorBrewer, rintrojs, rlang, rmarkdown, S4Vectors,
scales, shiny, shinycssloaders, shinyWidgets, stats,
SummarizedExperiment, tidyr, tools, utils, viridis, visNetwork
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
grDevices, stats, utils, plyr, gridExtra, sjstats, parallel,
ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack
stats, utils, XML, Biobase, IRanges (>= 2.3.23), Biostrings,
GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
S4Vectors (>= 0.23.18), 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),
gridExtra (>= 2.0.0), gtable, gtools, IRanges (>= 2.7.5), plyr
(>= 1.8.3), reshape2, Rsamtools, scales, viridis, data.table,
BSgenome, 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, hexbin, 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, aplot (>= 0.0.4), dplyr, ggplot2 (>= 3.0.0), grid,
magrittr, methods, purrr, rlang, rvcheck, tidyr, tidytree (>=
0.2.6), treeio (>= 1.8.0), 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
Rcpp, pracma, DelayedMatrixStats, DelayedArray, HDF5Array,
SummarizedExperiment, methods, stats, 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
AnnotationDbi, ape, bnlearn, Category, DT, doParallel,
foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db,
org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics,
reshape2, stats, utils
grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics,
Biostrings, GenomeInfoDb, methods, GenomicAlignments,
GenomicFeatures, IRanges, rtracklayer, pracma, colorspace,
S4Vectors
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, grDevices, utils,
stats, GenomeInfoDb
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
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
SummarizedExperiment, nloptr, fGarch, methods, BiocParallel,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel,
edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics,
KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods,
rappdirs, S4Vectors, stats, utils
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, stats, utils, graphics, BiocGenerics, S4Vectors,
Biobase, SummarizedExperiment, GSEABase, parallel,
BiocParallel, shiny, shinythemes, fastmatch
circlize (>= 0.3.3), GetoptLong, grDevices, utils
BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno,
data.table, matrixStats, BSgenome, parallel, IRanges (>=
2.5.5), S4Vectors (>= 0.9.6), GenomicAlignments (>= 1.7.3),
GenomeInfoDb, Rsamtools, hash, limma,dplyr
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), ensembldb
(>= 2.11.3), 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), graphics, grDevices, stats, utils
methods, BiocGenerics, S4Vectors (>= 0.9.25), IRanges,
GenomeInfoDb, GenomicRanges (>= 1.29.6), GenomicFeatures,
Biostrings, Rsamtools, rtracklayer, AnnotationDbi, utils,
ggplot2
graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth, dplyr
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
Rcpp (>= 0.11.2), graphics, stats, methods
BiocFileCache, S4Vectors, curl, googleAuthR, httr, jsonlite,
methods, plyr, readr, rlang, stringr, tibble, tidygraph, tidyr,
utils
S4Vectors, vctrs, curl, httr, jsonlite, methods, plyr, rlang,
tibble, tidygraph, utils
utils, stats, tools, Matrix, BiocGenerics (>= 0.31.5),
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, tibble, jsonlite, BiocParallel,
R.utils, readr, methods
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq,
KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
methods, utils, HilbertVis, png, grDevices, circlize (>=
0.3.3), IRanges, GenomicRanges, polylabelr
R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges,
S4Vectors, XVector, Biostrings, GenomicFeatures,
BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices,
stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp
coin, stats, limma, grDevices, utils, graphics,
preprocessCore, servr, DelayedArray, matrixStats, methods,
S4Vectors
ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap,
dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment,
ggrepel
sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl,
methods
Biostrings, graphics, grDevices, rtracklayer, RColorBrewer,
Matrix, parallel, GenomeInfoDb
graphics, grDevices, stats, utils, BiocGenerics
dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils,
gridExtra
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
BiocGenerics (>= 0.2.0), S4Vectors (>= 0.9.25), IRanges (>=
1.21.39), GenomicRanges (>= 1.23.21), Rsamtools (>= 1.8.5),
Biostrings (>= 2.24.1), chipseq (>= 1.6.1), hwriter (>= 1.3.0),
Cairo (>= 1.5.5), GenomicFeatures (>= 1.9.31), BiocParallel,
parallel, tools, rtracklayer (>= 1.17.19), GenomicAlignments,
VariantTools (>= 1.7.7), GenomeInfoDb, SummarizedExperiment,
methods
edgeR (>= 3.9.14), DESeq2 (>= 1.10.1), DESeq (>= 1.22.1),
BiocParallel (>= 1.4.3), Biobase, utils, stats, grDevices,
graphics, methods
shiny, ssrch, S4Vectors, SummarizedExperiment, utils
ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr,
scales, rlang, httr, openxlsx, reactable, msigdbr, kableExtra,
rmarkdown, igraph, visNetwork
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), heatmaply, plotly, 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
dplyr (>= 0.7.6), futile.logger (>= 1.4.3), GenomeInfoDb (>=
1.14.0), GenomicRanges (>= 1.30), ggplot2 (>= 3.1.1),
grDevices, idr (>= 1.2), IRanges (>= 2.18.0), magrittr (>=
1.5), methods, reticulate (>= 1.13), scales (>= 1.0.0), stats,
stringr (>= 1.3.1), utils
methods, BiocGenerics, httpuv, utils, MotifDb, seqLogo,
rtracklayer, VariantAnnotation, RColorBrewer
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 (>= 2.3.1),
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, digest, 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, KernSmooth, gdata, GenomicFeatures,
GenomicRanges, IRanges, BiocGenerics, GenomicAlignments,
Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer,
SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny
methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.25.14),
IRanges, GenomeInfoDb
interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer,
ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi
seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), 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, graphics, grDevices,
viridisLite, shinyWidgets, ComplexHeatmap, circlize
methods, S4Vectors, shiny, SummarizedExperiment,
SingleCellExperiment, ggplot2, DT, stats
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, VariantAnnotation
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
stringr, kernlab, ggplot2 (>= 3.3.0), rlist, rmarkdown,
reshape2, gplots, caret, XML, class, praznik, R.utils, e1071,
randomForest, httr, jsonlite, sva (>= 3.30.1), edgeR (>=
3.24.3), limma (>= 3.38.3), Biobase, multtest, pathview (>=
1.22.3), grDevices, graphics, stats, utils, Hmisc (>= 4.4.0),
gridExtra
graphics, grDevices, igraph, parallel, RColorBrewer, Rfast,
stats, SummarizedExperiment, utils
Biobase, graphics, grDevices, methods, stats, tools, utils
Matrix, snpStats, VariantAnnotation, GenomeInfoDb, httr,
BiocGenerics, ensembldb, EnsDb.Hsapiens.v75, Rsamtools,
GenomicFiles (>= 1.13.6), BiocGenerics (>= 0.25.1)
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
scales, cluster, graphics, ggpubr, gridExtra, vegan, rio,
MultiAssayExperiment, emmeans, reshape2, data.table
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, data.table, 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
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
reshape2, utils, stats, methods
DelayedArray, GenomicRanges, HDF5Array, Matrix, stats,
stringr, 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
data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
Biostrings, phangorn, stringdist, UpSetR
ggplot2, Matrix, doSNOW, cluster, parallel, foreach,
doParallel, matrixcalc, Rtsne, 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
robustbase, biglm, pcaPP, edgeR, metagenomeSeq, lpsymphony,
pscl, pbapply, car, dplyr, vegan, chemometrics, ggplot2,
pheatmap, cplm, logging, data.table, lmerTest, hash, optparse,
MASS, MuMIn, grDevices, stats, utils
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
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, RColorBrewer, methods, grDevices, survival
clusterProfiler, DOSE, enrichplot, gridExtra, biomaRt, sva,
ggsci, ggplot2, ggrepel, ggpubr, data.table, pheatmap, png,
grDevices, grid, stats, utils, dendextend, scales, Biobase,
msigdbr, KEGGgraph, KEGGREST, graph, graphics, pathview, XML
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, SummarizedExperiment(>= 1.5.3), progress
methods, TFBSTools, IRanges, XVector, Biostrings
BiocGenerics, ProtGenerics, digest, irlba, utils
methods, DelayedArray, Rcpp, SingleCellExperiment,
SummarizedExperiment, ClusterR, benchmarkme, Matrix,
BiocParallel
Biobase, graphics, methods, utils, grDevices
stats, graphics, utils, limma (>= 3.30.13),
SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0),
BiocFileCache, rappdirs, rpx, xml2, RCurl, ggplot2, PairedData
BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db,
org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA
biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2,
graphics, grDevices, Gviz, IRanges, limma, methods, parallel,
S4Vectors, stats, SummarizedExperiment, utils
AnnotationDbi, DBI, GO.db, KEGG.db, cluster, Matrix
GenomicAlignments, GenomicRanges, IRanges, Biostrings,
DNAcopy, Rsamtools, parallel, stringr
GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges,
S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute,
Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA,
graphics, stats, utils, matrixStats
impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0),
grDevices, graphics, stats, utils, stringr, tibble, RPMM (>=
1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon
GenomicRanges, Biostrings, graphics, gtools, IRanges, methods,
stats, utils, edgeR, DNAcopy, biomaRt, rtracklayer,
preprocessCore
data.table, parallel, ROCR, matrixcalc, mclust, 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, reshape2
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench
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
ABSSeq, baySeq, Biobase, BiocParallel, biomaRt, Biostrings,
corrplot, DESeq, DSS, DT, EDASeq, edgeR, GenomeInfoDb,
GenomicAlignments, GenomicFeatures, GenomicRanges, gplots,
graphics, grDevices, heatmaply, htmltools, httr, IRanges,
jsonlite, log4r, NOISeq, magrittr, methods, NBPSeq, pander,
parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite,
rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment,
survcomp, utils, VennDiagram, vsn, zoo
epivizr, epivizrData, epivizrServer, epivizrStandalone, vegan,
GenomeInfoDb, phyloseq, httr
methods, data.table, dplyr, tidyr, plotly, ggplot2, cowplot,
parallel, metafor, metap, rlang, topconfects, grDevices,
graphics, stats, htmlwidgets
methods, utils, stats, S4Vectors, bsseq, DSS, methylKit,
DNAcopy, GenomicRanges, IRanges, GenomeInfoDb, BiocParallel
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
DelayedArray, HDF5Array, BSgenome, rjson, DelayedMatrixStats,
parallel, methods, ggplot2, matrixStats, graphics, stats, utils
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
Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr,
minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter,
genefilter, methods, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler,
missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db,
AnnotationDbi, shiny,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.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
bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges,
GenomeInfoDb, GenomicRanges, methods, parallel, stats,
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 (>= 1.4.0.1), 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, tibble, tidyr, utils,
vegan
graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply,
stats, phyloseq, metagenomeSeq, Biobase
ape, plyr, tidyr, ggplot2, phyloseq, magrittr, dplyr,
Biostrings, ggrepel, vegan, rentrez, reshape, zoo, ggtree,
tidytree, gtools, MASS, methods, randomForest, rlang, tibble,
grDevices, stats, utils, coin, ggsignif, scales, Rmisc,
DECIPHER, biomformat, yaml, phangorn, patchwork
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, dplyr, tidyr, rlang
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 (>= 0.23.18),
IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16),
SummarizedExperiment (>= 1.15.4), 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, iBBiG, fabia, BicARE, isa2, s4vd, BiBitR, rqubic,
Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero,
ppclust, miRspongeR, Rcpp, utils, SummarizedExperiment,
GSEABase, org.Hs.eg.db, MatrixCorrelation, energy
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
AnnotationDbi, BiasedUrn, Biobase, BiocGenerics,
GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, IRanges, limma,
methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors,
statmod, stringr, SummarizedExperiment
stats, grDevices, graphics, utils, MASS, plyr, reshape2,
parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2,
gplots, beeswarm, echarts4r
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, utils
gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats
methods, DESeq2, edgeR, limma, Biobase, SummarizedExperiment,
plyr, foreach, utils, sSeq, xtable
ensemblVEP (>= 1.20.0), gmapR, Rsamtools, VariantAnnotation,
BiocParallel, Biobase, BiocGenerics, dplyr, GenomeInfoDb,
GenomicRanges, IRanges, S4Vectors, tidyr, VariantTools,
magrittr, methods, grDevices, graphics, stats, utils, stringr,
data.table
GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr,
cowplot, utils, stats, grDevices
cluster, graph, Rgraphviz, flexclust, lattice, naturalsort,
snowfall, stats4, tsne, methods, graphics, stats, utils,
Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices,
e1071
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges,
XVector, stringi, stringr, crayon, grDevices
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
circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics,
grid, grDevices, magrittr, methods, MKmisc,
MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr,
reshape2, rlang, stats, stringr, tibble, tidyr, 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
HiddenMarkov, zoo, methods, matrixStats, dplyr, stringi,
lazyeval, rlang, stats, utils, purrr, scales, stringr, tibble,
tidyr, ggplot2, Biobase, IRanges, 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, ggplot2
methods, stats, grid, S4Vectors, IRanges (>= 1.13.5),
Biostrings, 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
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,
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid
ggplot2, BiocParallel, caret, gridExtra, reshape2, stats,
utils, grDevices, graphics, MSstats
limma, lme4, lmerTest, dplyr, tidyr, statmod, methods,
reshape2, data.table, matrixStats, stats, utils, ggplot2,
grDevices, graphics, MSstats
graphics, grDevices, stats, methods, fields
methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors
(>= 0.23.19), 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
BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr,
edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest,
lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors,
scales, scater, sctransform, stats, SingleCellExperiment,
SummarizedExperiment, variancePartition, viridis
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 (>= 1.17.3),
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
graph, KEGGgraph, methods, RBGL, RCy3, R.methodsS3
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
RColorBrewer, DT, stats, clusterProfiler, data.table, gplots,
jsonlite, plyr
glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust,
parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
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
(>= 1.15.13)
Biostrings, checkmate, dplyr (>= 0.8.0), DT, FactoMineR,
forcats, ggdendro, grDevices, grid, 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)
KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,
S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl,
dbplyr,utils,ggplot2,igraph,stats,reshape2,readr,
GO.db,zlibbioc,
biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi
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)
dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr,
stats, methods
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, grDevices
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), foreach, BiocManager, utils, S4Vectors (>= 0.9.25),
RSQLite, DBI, ff
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
utils, ape, Biostrings, GenomicRanges, IRanges, methods,
topGO, jsonlite
compositions, DT, grDevices, knitr, jsonlite, 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, Rtsne,
dendextend, clusteval, ggplot2, ggfortify
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
Rtsne, plotly, gplots, grDevices, graphics, stats, utils,
methods, flowCore
Biobase, S4Vectors, methods, AnnotationDbi, stats, utils,
shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT
methods,Biobase,BiocGenerics,gtools,flowCore(>=
1.99.17),flowViz,ncdfFlow(>= 2.11.34),flowWorkspace(>=
3.99.1),flowStats(>= 3.99.1),flowClust(>=
3.11.4),MASS,clue,plyr,RBGL,graph,data.table,ks,RColorBrewer,lattice,rrcov,R.utils
MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist,
summarytools, graphics, stats, utils
fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt,
Biobase, RcppParallel, Rcpp
limma, stats, reshape, ggplot2, grDevices, RColorBrewer,
pheatmap, knitr, methods, devtools
transport, parallel, Rfast, robustbase, dbscan, randomForest,
foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse
RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges,
GenomicFeatures, AnnotationDbi, methods, tools, utils,
BiocFileCache, DBI, dbplyr, tibble
Biobase, BiocManager, GenomicRanges (>= 1.31.13), graph,
IRanges, RBGL, DBI, S4Vectors (>= 0.9.25), stats
BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics,
GenomicRanges, ggplot2, grDevices, heatmaply, pheatmap,
graphics, IRanges, matrixStats, plotly, plyr, pcaMethods,
PRROC, RColorBrewer, Rcpp, reshape2, S4Vectors, scales,
splines, stats, utils
stats, utils, methods, BiocParallel, SummarizedExperiment,
limma, fdrtool, Rcpp
e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR,
sva
Biostrings, GenomicRanges, kmer, ape, methods, IRanges,
S4Vectors
limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db,
hgu133a.db, KEGGREST, 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, GenomicRanges,
S4Vectors
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,
org.Hs.eg.db, 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
DESeq2, SummarizedExperiment, GenomicRanges, IRanges,
S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly,
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
methods, stats, utils, Matrix, DelayedMatrixStats,
DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng
AnnotationDbi, Biobase, Category, GO.db, graph, graphics,
GSEABase, KEGG.db, methods, ScISI, stats, stats4
ROTS, limma, affy, genefilter, preprocessCore,
aroma.affymetrix, aroma.core
assertthat, circular, conicfit, doParallel, foreach, genlasso
(>= 1.4), graphics, methods, parallel, scater,
SingleCellExperiment, SummarizedExperiment, stats, utils
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, dplyr,
processx, readr, seqinr
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, pheatmap, scales, ccaPP, grid,
grDevices, AnnotationDbi, DESeq2
Biobase, S4Vectors, SummarizedExperiment, BiocParallel,
ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods,
downloader, stats, utils, graphics, grDevices, reshape2,
testthat, jsonlite
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, phateR, reticulate
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
survival, limma, gplots, Category, AnnotationDbi, hopach,
biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
hgu133a.db, ellipse
SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf,
knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4,
graphics, grDevices, utils, stats
ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table,
DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply,
RColorBrewer, shiny, shinyBS, shinyjs, OmaDB, plyr, xml2, zoo
Matrix, ggbio, GenomicRanges, GenomeInfoDb, supraHex, scales,
grDevices, ggrepel, ROCR, randomForest, glmnet, Gviz, lattice,
caret, plot3D, stats, methods, MASS, IRanges, BiocGenerics,
dplyr, tidyr, ggnetwork, osfr, RCircos, purrr, readr, tibble
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods
utils, stats, graphics, grDevices, methods, IRanges,
GenomicRanges, Rsamtools, GenomicAlignments
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), dplyr, gdata
methods, PICS, graphics, grDevices, stats, Gviz, fda,
BSgenome, stats4, BiocGenerics, IRanges, GenomicRanges,
S4Vectors
BSgenome, digest, visNetwork, magrittr, methods, Biostrings,
GenomeInfoDb, parallel, stats, utils
Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2,
Biobase
utils, Biobase (>= 2.5.5), MASS, methods
BiocGenerics, CGHbase, graphics, grDevices, ic.infer, marray,
methods, quadprog, Rcsdp, stats, stats4, utils
methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>=
1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb,
Rsamtools, S4Vectors (>= 0.23.10), utils
stats, impute, pcaMethods, missForest, ggplot2, methods,
SummarizedExperiment, S4Vectors, matrixStats, grDevices,
reshape2, 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, reshape2, rlang,
scales, stats, sva, tidyr, tibble, tools, utils, viridis,
wesanderson, WGCNA
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, utils, methods, BiocGenerics, SummarizedExperiment,
S4Vectors, extraDistr
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
Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra
methods, cluster, stats, limma, CoGAPS, NMF, ROCR, ggalluvial,
RColorBrewer, dplyr, reshape2, viridis, scales, ggplot2
stats4, 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 (>= 1.19.16), DAPARdata (>= 1.16.0), rhandsontable,
data.table, shinyjs, DT, shiny, shinyBS, shinyAce, highcharter,
htmlwidgets, webshot, R.utils, shinythemes, XML,later,
rclipboard, shinycssloaders, future, promises, colourpicker,
BiocManager, shinyjqui,shinyTree, shinyWidgets, sass, tibble
mzR (>= 2.3.2), MSnbase, Biostrings, GenomeInfoDb, utils,
Biobase, BiocManager, RCurl
gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, cluster,
colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR,
fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices,
highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma,
pairsD3, plyr, Rcpp (>= 0.12.14), recount, Rfast, 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
ggplot2, igraph, ggrepel,rentrez, progress, graphics, dplyr,
utils, methods, intergraph, network, sna
robustbase, methods, R.utils, taRifx, S4Vectors,
SummarizedExperiment, ggplot2, ggridges, stats, utils, UpSetR,
cowplot, grid, MuMIn
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
doParallel, abind, truncnorm, CpGassoc, shiny, ggplot2,
parallel, shinyWidgets, BiocManager, doSNOW, limma, genefilter,
stats, grDevices, methods, utils, graphics, pwrEWAS.data
magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table,
reshape2, grDevices, graphics, stats, utils, Rcpp, rlang,
RSeqAn
Biobase, methods, knitr, tools, Nozzle.R1, xtable, pander,
S4Vectors
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, KernSmooth, MASS
SummarizedExperiment, utils, sva, stats, methods, graphics
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
methods, grDevices, graphics, utils, BiocGenerics, S4Vectors,
IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools,
GenomicFeatures, ShortRead, 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
methods, graphics, utils, stats, Rdpack (>= 0.7)
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 (>=
0.23.19), IRanges, GenomeInfoDb, GenomicAlignments
GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer,
GenomicFeatures, rmarkdown (>= 0.9.5), genomation (>= 1.5.5),
knitr (>= 1.12.3), BiocGenerics, S4Vectors, plotrix, pbapply,
RSQLite, proxy, pheatmap, ggplot2, cowplot, ggseqlogo, utils,
ranger, gprofiler2
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
jsonlite, httr, progress, ggplot2, methods, gplots,
RColorBrewer
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2, ggraph,
reactome.db, igraph, graphite
dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment
phyloseq, KernSmooth, reshape2, ggplot2, stats, methods, MASS,
graphics, grDevices
BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb,
GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer
(>= 1.35.3), S4Vectors, stats, utils
BiocGenerics, biomaRt, circlize, graphics, grDevices, methods,
rtracklayer, S4Vectors, stats, utils
AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils
memoise, GenomicRanges, IRanges, BSgenome, Biostrings,
rtracklayer, parallel, graphics, stats, utils, methods,
GenomeInfoDb, S4Vectors, tools
BiocStyle (>= 2.5.19), derfinder (>= 1.2.5), DEFormats,
DESeq2, GenomeInfoDb, GenomicRanges, knitcitations (>= 1.0.1),
knitr (>= 1.6), knitrBootstrap (>= 0.9.0), methods, RefManageR,
rmarkdown (>= 0.9.5), S4Vectors, SummarizedExperiment, utils
glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats,
pbapply, utils, methods
AnnotationDbi, AnnotationHub, Biostrings, DBI, GenomicRanges,
Gviz, IRanges, RCy3, RSQLite, S4Vectors, methods, stats, utils,
BiocFileCache
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, 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
httr, stringi, rsvg, magick, data.table, Biostrings, utils
Biostrings, GenomicRanges, 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
dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors,
tidyr, tools, yaml
Rsamtools, IRanges, baySeq, GenomeInfoDb, seqLogo
AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq,
GenomicAlignments, GenomicFeatures, GenomeInfoDb, IRanges,
methods, motifStack, rtracklayer, Rsamtools, RUVSeq, Rsubread,
S4Vectors, XVector, ggplot2, ggfittext, scales, ggrepel, utils,
cluster, stats, graphics, grid
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, gsubfn, hash, png, sqldf, igraph, BgeeDB,
knitr, RITANdata
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb,
S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods,
grDevices
Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges,
SummarizedExperiment, devtools, TBX20BamSubset,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2,
BiocStyle
ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats,
SummarizedExperiment, methods
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr,
scales
RColorBrewer, ICS, ICSNP, cellHTS2, geneplotter, gplots, grid,
hwriter, lattice, latticeExtra, limma, methods, splots (>=
1.13.12)
geneplotter, limma, biomaRt, car, splots, methods
methods, stats, grDevices, matrixStats, BiocGenerics,
Biostrings (>= 2.55.7), BiocParallel, GenomicFeatures,
GenomicAlignments, GenomeInfoDb, rtracklayer, Rsamtools,
BSgenome, RColorBrewer, colorRamps, ggplot2, Gviz (>= 1.31.0),
reshape2, graphics, ROCR
methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz
methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges,
stats, ranger
methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz
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
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
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)
graphics, grDevices, methods, MultiDataSet, stats
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
GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel,
treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), zlibbioc, bitops,
BiocParallel, stats
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, httr, limma, methods, RaggedExperiment, RCircos,
RCurl, RJSONIO, S4Vectors (>= 0.23.10), stats, stringr,
SummarizedExperiment, survival, TCGAutils, XML
RedeR, minet, viper, mixtools, snow, stats, limma, data.table,
IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr,
pheatmap, grDevices, graphics, utils
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,
graphics
GENLIB, gRain, snpStats, kinship2, methods, stats, utils
httr, utils, XML, rjson, data.table, tidyr
methods, stats, utils, RcppParallel, SPAtest (>= 3.0.0)
rJava, Biostrings, IRanges, utils, stats, cluster, binom
methods, reshape2, scales, gridExtra, XML
Rdpack, grDevices, methods, stats, utils, xml2, rsvg, igraph,
rmarkdown, knitr, SummarizedExperiment, AnnotationDbi
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
BiocGenerics, SummarizedExperiment, Matrix, ggbeeswarm, rlang,
grid, DelayedArray, DelayedMatrixStats, methods, S4Vectors,
stats, utils, viridis, Rcpp, BiocNeighbors, BiocSingular,
BiocParallel
SingleCellExperiment, SummarizedExperiment, Seurat, MASS,
zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods,
Matrix
S4Vectors, limma, ggraph, igraph, methods, cluster,
minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix,
ggplot2, hopach, diptest, mgcv, stats, graphics, statmod
igraph, Matrix, matrixStats, BiocParallel, BiocNeighbors,
BiocSingular, SummarizedExperiment, SingleCellExperiment,
scran, scater, data.table, dplyr, ggplot2, randomForest,
graphics, methods, stats, DelayedArray
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, dplyr, pROC
SingleCellExperiment, SummarizedExperiment, methods, stats,
bit, dplyr, hash, reshape2, Rcpp(>= 0.12.12)
glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1),
fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel,
grDevices, graphics, stats, utils, DESeq, locfit
hexbin, stats, methods, cluster, dplyr, entropy, ggforce,
scales, grid, concaveman
S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix,
SummarizedExperiment, IRanges, methods, stats, BiocParallel,
reshape, ggplot2, igraph, grDevices, ggforce, graphics
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, BiocSingular, cluster, DelayedArray,
DelayedMatrixStats, distr, dplyr, igraph, M3Drop (>= 1.9.4),
parallel, pdist, proxy, Rcpp (>= 0.12.18), RcppEigen (>=
0.3.3.4.0), ruv, S4Vectors (>= 0.23.19), SingleCellExperiment
(>= 1.7.3), 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)
SingleCellExperiment, SummarizedExperiment, stats, methods,
graphics, grDevices, parallel, quantreg, cluster, moments,
data.table, BiocParallel, S4Vectors, ggplot2, forcats,
BiocGenerics
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
stats, grDevices, graphics, utils, DescTools, RColorBrewer,
gplots, foreach, parallel, doParallel, DNAcopy, BSgenome,
Biostrings, BiocGenerics, S4Vectors
Biostrings, methods, snpStats, VariantAnnotation,
GenomicRanges, BiocParallel, graphics, SummarizedExperiment
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
cluster, kernlab, origami
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, hash, dplyr, GenomicRanges,
magrittr, glue (>= 1.3.0), rlang, scater (>= 1.11.0)
SummarizedExperiment, S4Vectors, IRanges, BiocGenerics,
BiocParallel, Rcpp, stats, methods, utils, Matrix, scater,
edgeR, limma, 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,
Rsubread
glmpca (>= 0.2.0), Matrix, 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,
schex, ggplot2
GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly,
tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr,
S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor,
methods, scales, msigdbr, schex, tibble, ggplot2, igraph
BiocParallel, Rtsne, grDevices, graphics, stats
Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils,
abind
nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
methods, parallel, IRanges, GenomicRanges, GenomeInfoDb,
Biostrings, S4Vectors
dplyr (>= 0.5.0), GenomeInfoDb (>= 1.13.4), ggplot2 (>=
2.2.1), grid (>= 3.5.0), IRanges (>= 2.8.2), methods,
rtracklayer, rlang, scales (>= 0.4.1), S4Vectors (>= 0.12.2),
stats, SummarizedExperiment (>= 1.4.0), tidyr (>= 0.6.1), utils
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, grDevices, utils, illuminaio, MASS,
GenomicRanges, IRanges, grid, preprocessCore, stats, S4Vectors,
randomForest, wheatmap, ggplot2, parallel, matrixStats,
DNAcopy, HDF5Array, SummarizedExperiment
S4Vectors, SummarizedExperiment, data.table, pheatmap,
seriation, ComplexHeatmap, circlize, methods, BiocParallel,
randomcoloR, edgeR, openxlsx
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, data.table
AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>=
2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>=
1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19),
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)
AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array,
magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue,
stats, utils, reshape2, visNetwork, BiocParallel, fastmatch,
Matrix, clusterProfiler, readr, DOSE, rhdf5, GSEABase,
DelayedArray
BiocGenerics, Biostrings, class, graphics, grDevices,
GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats,
utils, PMCMR
graph, igraph, RBGL, graphics, utils, stats, methods
quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0),
VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb,
GenomicRanges, rtracklayer, SummarizedExperiment, graphics,
stats, utils
mzR, ggplot2, grid, reshape2, grDevices, stats, utils
dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges,
Rsamtools, parallel, graphics, stats, utils, methods
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 (>= 0.23.19), methods, BiocGenerics, utils, stats
BiocManager, circlize, limma, igraph, gplots, grDevices,
edgeR, SIMLR, data.table, pheatmap, stats, Rtsne, graphics,
stringr, foreach, multtest, scran, utils,
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, shinyBS, sva,
reshape2, AnnotationDbi, shinyalert, circlize, enrichR, celda,
shinycssloaders, shinythemes, umap
methods, Matrix, S4Vectors, BiocGenerics, DelayedArray,
DelayedMatrixStats, BiocNeighbors, BiocParallel, BiocSingular,
stats, utils, Rcpp, ExperimentHub
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, 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, graphics, grDevices, igraph, matrixStats, methods,
SingleCellExperiment, SummarizedExperiment
SummarizedExperiment, curl, dplyr, foreach, httr, stats,
utils, methods, readr, rhdf5, jsonlite, tidyr
magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0)
scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2,
reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph,
Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics,
stats, utils
aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma,
methods, stats, tilingArray, utils
R6, httr, rlang, purrr, jsonlite, assertthat, data.table,
Matrix, magrittr, methods, stringr, stats, IRanges,
GenomicRanges, SummarizedExperiment
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
methods, ggplot2, scater (>= 1.13.27), shiny, jpeg, magrittr,
utils, S4Vectors
stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack
Rcpp, Matrix, MatrixGenerics, matrixStats, methods
methods, glmnet, huge, stats, graphics, utils
BiocGenerics (>= 0.31.6), 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
ggplot2, class, concaveman, grid, BiocParallel, spatstat,
lmerTest, BiocGenerics, S4Vectors, lme4, methods, mgcv,
pheatmap, purrr, rlang, grDevices, IRanges, stats
httr, igraph, utils, stats, miRNAtap, miRNAtap.db,
AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots,
grDevices, lattice, latticeExtra, visNetwork, TCGAbiolinks,
gdata, MAGeCKFlute,networkD3
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
akima, BiocGenerics, BiocParallel, checkmate (>= 2.0.0),
edgeR, fitdistrplus, ggplot2, locfit, matrixStats, methods,
scales, scater (>= 1.15.16), stats, SummarizedExperiment,
utils, crayon, S4Vectors
methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>=
0.17.5), BiocParallel, IRanges (>= 2.21.2), 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,
DBI, lazyeval, methods, tools, stats, BiocGenerics, RSQLite,
tibble
graphics, grDevices, methods, RColorBrewer, stats, utils
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils, graphics
Rcpp (>= 0.12.8), methods, devtools, S4Vectors, GenomeInfoDb,
rtracklayer, SummarizedExperiment, IRanges, GenomicRanges,
DESeq2, Rsamtools, GenomicFeatures, GenomicAlignments,
grDevices, Gviz, BiocParallel, BiocManager, BiocStyle
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, ontologyIndex, datasets, graphics, stats, utils,
knitr, SummarizedExperiment, S4Vectors
methods, BiocGenerics, XVector, stringr, stringi, crayon,
grDevices
ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats
assertthat, Biostrings, stringr, dplyr, methods, rlang
Rtsne, scatterplot3d, caret, e1071, ggplot2, gridExtra,
networkD3, ggrepel, graphics, stats, org.Hs.eg.db,
AnnotationDbi
data.table, dplyr, tidyr, ggplot2, magrittr, qvalue (>= 1.99),
digest, Biobase
utils, stats, tools, Matrix, BiocGenerics (>= 0.15.3),
S4Vectors (>= 0.25.14), IRanges (>= 2.21.6), GenomeInfoDb (>=
1.13.1)
ape, MASS, grDevices, graphics, stats, utils, methods
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma, edgeR
methods, stats, SummarizedExperiment, edgeR, ggplot2, limma,
lmtest, parallel, pls
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)
methods, Biostrings, S4Vectors, IRanges, utils, stats
doBy, dplyr, grid, magrittr, RColorBrewer, RankProd, reshape2
seqinr, methods, Biostrings, stringr, BiocGenerics
GenomicRanges, GenomicFeatures (>= 1.31.3),
SummarizedExperiment, VariantAnnotation (>= 1.25.11), rjson,
ggplot2, grid, limma, edgeR, DESeq2, GOstats, GO.db, annotate,
pheatmap, batchtools, yaml, stringr, assertthat, magrittr, DOT,
rsvg
methods, GenomicAlignments, GenomicRanges, IRanges,
BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome,
GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel
BiocGenerics, GenomicRanges, IRanges, matrixStats, methods,
stats, graphics, shiny
graphics, grDevices, methods, stats, utils, stringr,
assertthat
grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics,
reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot,
graphics, GenomicAlignments, Hmisc
ASSIGN (>= 1.23.1), GSVA, SummarizedExperiment, S4Vectors,
methods, BiocParallel, ComplexHeatmap, RColorBrewer, ggplot2,
reshape2, circlize, glmnet, ROCit, bioDist, readr, boot,
DESeq2, caret, ggfortify, e1071, DT, edgeR, singscore, gdata,
shiny
downloader (>= 0.4), grDevices, dplyr, graphics, tibble,
GenomicRanges, XML (>= 3.98.0), data.table, jsonlite (>=
1.0.0), plyr, knitr, methods, biomaRt, ggplot2, stringr (>=
1.0.0), IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors,
R.utils, SummarizedExperiment (>= 1.4.0), readr, tools, tidyr,
purrr, xml2, httr (>= 1.2.1)
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, stringr, methods,
stats, gplots
GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices,
dplyr, stats, utils, R.utils, methods, org.Hs.eg.db
GenomicRanges, S4Vectors, grDevices, graphics, stats, utils,
IRanges, methods
methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase
tibble, readr, dplyr, magrittr, tidyr, rlang, purrr,
preprocessCore, stats, parallel, utils, lifecycle
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
dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr,
ggrepel, propr, lmtest
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, splines,
stats, stringr, tibble, utils, VennDiagram, VGAM
ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl,
parallel, MASS, BiocParallel, limma
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
mgcv, edgeR, SingleCellExperiment, SummarizedExperiment,
slingshot, magrittr, RColorBrewer, BiocParallel, Biobase,
pbapply, ggplot2, princurve, methods, S4Vectors, tibble, dplyr,
monocle, igraph, clusterExperiment
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), grDevices, 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 (>= 0.2.6), utils
methods, BiocGenerics, utils, ape, rlang, dplyr,
SummarizedExperiment
RSQLite, RMySQL, lassopv, randomForest, vbsr, xgboost,
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 (>= 1.6.1)
stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector,
Biostrings, Modstrings, ggplot2, scales
Biostrings, BiocGenerics, stringr, xml2, S4Vectors, methods,
httr, IRanges, utils
methods, stringr, BiocGenerics, Biostrings, Structstrings,
S4Vectors, IRanges, XVector, GenomeInfoDb, rtracklayer,
BSgenome, Rsamtools
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
gridExtra, methods, dtw, class, kmlShape, graphics, cluster,
RColorBrewer, grDevices, knitr, rmarkdown, prettydoc, grid,
ggplot2, latex2exp, stats, SummarizedExperiment, GenomicRanges,
IRanges, S4Vectors
AnnotationHub, BiocGenerics, BiocParallel, dplyr,
GenomicAlignments, GenomeInfoDb, GenomicRanges, gtools,
IRanges, methods, readxl, Rsamtools (>= 1.14.3), rtracklayer,
S4Vectors, SummarizedExperiment, tools, utils
AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel,
Biostrings, ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges,
GGally, ggplot2, Gviz, limma, IRanges (>= 2.21.6), reshape2,
Rsamtools, S4Vectors (>= 0.25.14), SummarizedExperiment,
VariantAnnotation (>= 1.19.9)
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges,
GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb,
BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb,
rappdirs, utils, methods, Matrix
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, moments,
Organism.dplyr, S4Vectors, shiny, shinydashboard, shinyFiles,
shinyjs, Sushi, yaml
stringr, R.utils, WriteXLS, stats, doParallel, foreach,
GenomicRanges, IRanges, VariantAnnotation
methods, stats, utils, MASS, ggplot2, ape, ggtree, ggseqlogo,
yaml, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics,
processx, S4Vectors, rlang
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
Biobase, S4Vectors (>= 0.23.18), 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)
tools, utils, stats, methods, gdsfmt, SNPRelate, SeqArray,
SeqVarTools, DelayedArray, Biostrings, IRanges
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
IRanges, GenomicRanges, S4Vectors, Sushi, parallel,
matrixStats, GenomicAlignments, GenomeInfoDb, Rsamtools,
cluster, stats, graphics, methods
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
data.table, AnnotationDbi, AnnotationForge, biomaRt,
dendextend, DiagrammeR, DT, dynamicTreeCut, GOSemSim, ggplot2,
GO.db, grDevices, heatmaply, htmlwidgets, igraph, methods,
plotly, topGO, RColorBrewer, R.utils, scales, stats, UpSetR,
utils, webshot
wordcloud, csaw, gplots, stats, utils, caTools, graphics,
DESeq, Biobase
Rcpp (>= 1.0.1), arm (>= 1.10-1), BiocFileCache, BiocParallel,
SingleCellExperiment, parallel, methods, stats
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
multtest, qvalue, stats, utils, BiocManager
methods, utils, stats, assertthat, S4Vectors, DelayedArray,
DelayedMatrixStats, BiocParallel, BiocGenerics, limma, dplyr,
purrr, ggplot2, scales, reshape2, RhpcBLASctl
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
stats, utils, data.table, IRanges, VariantAnnotation,
seqminer, ggplot2, biomaRt, readxl, S4Vectors
mzR (>= 2.19.5), BiocGenerics, ProtGenerics (>= 1.17.2),
lattice, RColorBrewer, plyr, RANN, MassSpecWavelet (>= 1.5.2),
S4Vectors, robustbase, IRanges, SummarizedExperiment
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, doParallel, PMCMR, ggbeeswarm,
ComplexHeatmap, KEGGREST, grDevices, Biostrings,
BSgenome.Hsapiens.UCSC.hg19, magrittr, pracma, dplyr, utils
biomaRt, downloader, edgeR, gplots, graphics, limma,
matrixStats, preprocessCore, readr, RColorBrewer, stats,
quantro
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
Rcpp, BH(>= 1.72.0-2), RProtoBufLib(>= 1.99.8),Rhdf5lib,
RcppArmadillo, RcppParallel(>= 4.4.2-1)
Rcpp, BH(>= 1.62.0-1), RProtoBufLib, cytolib ( >=
2.0.3),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1),
flowWorkspace
Rcpp, RcppArmadillo, BH(>= 1.65.0.1), cytolib(>= 1.7.2),
RProtoBufLib
Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>=
2.0.1),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1)
Rcpp, RcppArmadillo, beachmat (>= 2.0.0)
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings
Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats
Matrix, testthat, rmarkdown, knitr, BiocStyle, SuperLearner,
earth, gam, nnls, airway
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
knitr, rmarkdown, ComplexHeatmap, circlize, testthat
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
knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi,
TBX20BamSubset, Rsamtools, testthat
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, doSNOW, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh,
devtools, Rtsne, tsne, testthat, zoo
testthat (>= 2.1.0), covr, devtools, knitr, rmarkdown, mtbls2
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
BiocStyle, knitr, rmarkdown, testthat, magick
knitr, rmarkdown, BiocStyle, testthat, callr
knitr, rmarkdown, BiocStyle, testthat, BiocFileCache
testthat, BiocStyle, knitr, beachmat, scran, scRNAseq
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, 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
knitr, testthat, rmarkdown, AnnotationHub, httr
BiocGenerics, RUnit, 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
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0)
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, GenomicRanges, DelayedArray,
Biostrings, Rsamtools, AnnotationDbi, oligoClasses, oligo,
affyPLM, flowClust, affy, DESeq2, MSnbase, annotate, RUnit
testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy,
RcppHNSW
knitr, dbplyr, 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,
visNetwork, clipr, blastula, kableExtra
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
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, org.Hs.eg.db, ineq, covr
BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db,
knitr, omicade4, 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
knitr, markdown, base, rmarkdown, ggplot2
testthat, knitr, rmarkdown, BiocStyle, arm, earth, xgboost,
SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1)
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer,
EnsDb.Hsapiens.v75, RUnit
DSS, covr, knitr, rlang, scmeth, pkgdown, roxygen2, testthat,
QDNAseq.hg19, QDNAseq.mm10
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl
xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db,
lumi, knitr
BiocStyle, knitcitations, knitr, rmarkdown, sessioninfo,
testthat (>= 2.1.0), covr
BiocStyle, knitr, rmarkdown, testthat, apeglm, remotes,
ggplot2, reshape2, Biostrings
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,
BSgenome.Hsapiens.NCBI.GRCh38,
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, testthat, BiocStyle, TENxBUSData,
TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38,
EnsDb.Hsapiens.v86
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,
gplots
BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto,
rmarkdown, testthat
EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6),
hgu95av2.db, KEGG.db, karyoploteR, 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, biomaRt, covr,
BiocManager, BiocStyle, M3DExampleData, TENxPBMCData
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, 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
airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
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,
BSgenome.Hsapiens.UCSC.hg38, 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 (>= 3.15.4), ggimage, ggplotify, ggupset,
ReactomePA, org.Hs.eg.db, knitr, rmarkdown, testthat, tibble
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
testthat, knitr, roxygen2, rmarkdown, citr, devtools,
gridExtra, ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BiocManager,
knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle
limma, genefilter, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0),
gridExtra (>= 2.0.0), 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, knitr, org.Hs.eg.db, prettydoc, ReactomePA,
testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel,
BiocStyle
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
AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked,
BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment,
TCGAutils, curatedTCGAData, ensembldb, grid, 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, ReactomePA, DOSE, AnnotationDbi, gplots,
hu6800.db
flowWorkspace (>= 3.33.1), 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), rmarkdown
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, gridtext
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, minfiData, RCurl
BiocStyle, knitr, panelcn.mops,
BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat
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
rmarkdown, testthat, knitr, shiny, shinydashboard,
shinyWidgets, shinycssloaders, DT, ggthemes, ggplot2, pheatmap,
RColorBrewer, tibble, ggalluvial
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, biomaRt, irlba, knitr, destiny, VGAM
testthat, knitr, covr, rmarkdown, spelling
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle,
flowStats
testthat, flowWorkspaceData , knitr, parallel
XML, BiocStyle, knitr, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
BSgenome.Hsapiens.UCSC.hg19
EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust,
minqa, SummarizedExperiment, Biobase, knitr, rmarkdown,
BiocStyle, edgeR
mgcv, testthat, BiocStyle, knitr, rmarkdown
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr,
RColorBrewer, matrixStats
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL,
rrcov, Rgraphviz, NCIgraph
BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown,
statmod, testthat
BiocParallel, 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), 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,
covr
sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6),
BiocStyle (>= 2.5.19), rmarkdown (>= 0.3.3), testthat, covr
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, RefManageR,
rmarkdown (>= 0.3.3), testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene, covr
BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq,
RUVSeq, RColorBrewer, statmod
testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer,
apeglm, ashr, tximport, tximeta, tximportData, readr, pbapply,
airway, pasilla (>= 0.2.10)
nbconvertR (>= 1.3.2), igraph, testthat, FNN, tidyr
knitr, rmarkdown, testthat, BiocStyle, IHW
GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22),
parathyroidSE, BiocStyle, knitr, rmarkdown, testthat
knitr, lattice, latticeExtra, rmarkdown, BiocStyle, testthat
(>= 2.1.0)
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
plotly, testthat, Seurat (>= 2.2), DESeq2, knitr, BiocStyle,
scRNAseq
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, testthat
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, knitr, readxl, edgeR, limma, EDASeq, statmod
BiocStyle (>= 2.12.0), BSgenome (>= 1.52.0),
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
jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi,
SummarizedExperiment, org.Hs.eg.db
igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust,
MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db,
org.Hs.eg.db
knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie,
Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb
DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer,
hgu133plus2cdf, hgu133plus2probe
BiocStyle, knitr, testthat, data.table, DT,
GenomicInteractions, webshot, R.utils, covr, sesameData
RUnit,BiocGenerics,knitr, curl, httr, shiny, shinythemes, DT
RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway,
gridExtra, magrittr
SummarizedExperiment, testthat, Biobase, survminer,
affycoretools, knitr, plotROC, prognosticROC
testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer
ALL, BiocStyle, ReportingTools, airway, hgu95av2.db, knitr
clusterProfiler, dplyr, ggupset, knitr, org.Hs.eg.db,
prettydoc, tibble, tidyr
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
BiocStyle, knitr, rmarkdown, testthat, httptest,
AnnotationHub, ggplot2, EpiTxDb.Hs.hg38,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3,
TxDb.Hsapiens.UCSC.hg38.knownGene
testthat, roxygen2, knitr, Biobase, SummarizedExperiment,
antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle,
minfi
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, 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
testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle
caret, mlbench, SingleCellExperiment, knitr, rmarkdown,
testthat, BiocManager
testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData,
scater, gridExtra, scran, Seurat, knitr
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
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, 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 (>= 3.43.4), testthat,
flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto,
gridExtra
testthat, knitr, rmarkdown, BiocStyle, flowVS, DepecheR
BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat,
BiocStyle
knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments,
stats
testthat, flowWorkspaceData (>= 2.23.2), knitr, ggcyto,
parallel, CytoML, openCyto
BiocStyle, knitr, rmarkdown, testthat, covr,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
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, 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, 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, Matrix, RUnit, knitr, crayon, 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, BiocStyle, magick
RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown,
Fletcher2013b, geneplast.data.string.v91, ggplot2, ggpubr, plyr
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db
CompQuadForm, poibin, SPAtest, survey, testthat, BiocStyle,
knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, BiocStyle, htmltools, clusterProfiler, macrophage,
org.Hs.eg.db, magrittr, testthat (>= 2.1.0)
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, GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.NCBI.GRCh38, 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, snpStats,
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,
shiny, shinythemes, shinyjs, shinycustomloader, data.table, DT
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,
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, stats, testthat, tibble
roxygen2, knitr, rmarkdown, testthat, BiocStyle
BiocStyle, IRanges, GenomicRanges, SummarizedExperiment,
DESeq2, limma, testthat, knitr, rmarkdown, pryr
testthat (>= 2.1.0), zoo, DESeq2, edgeR, beachmat, MASS,
statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData
testthat, knitr, rmarkdown, survival, survcomp, pROC,
VennDiagram, BiocStyle, curatedTCGAData, TCGAutils
GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz
vsn, golubEsets, KEGGREST, 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
testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle,
BiocManager
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
RUnit, limma, RColorBrewer, genefilter, edgeR, 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, rmarkdown,
testthat
DO.db, DT, knitr, RBGL, RUnit, snpStats, Gviz,
VariantAnnotation, AnnotationHub, gQTLstats, graph, ggbio,
DelayedArray, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
BiocStyle
ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
VariantAnnotation, parallel
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
BiocParallel, GenomicRanges, SummarizedExperiment (>=
1.15.1), h5vcData, ExperimentHub, TENxBrainData,
GenomicFeatures, BiocStyle
parallel, knitr, gdsfmt, SNPRelate, SeqArray, ggplot2,
reshape2
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong
org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat
knitr, BiocStyle, beeswarm, tximportData, DT, tximport,
dplyr, magrittr, BiocFileCache, testthat
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
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, gridExtra, ggrepel
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, RColorBrewer, viridis, htmltools
scRNAseq, scater, scran, airway, edgeR, AnnotationDbi,
org.Hs.eg.db, GO.db, knitr, rmarkdown, BiocStyle, htmltools,
Rtsne, uwot, testthat (>= 2.1.0)
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,
BSgenome.Hsapiens.UCSC.hg19.masked,
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
MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments,
testthat
knitr, rmarkdown, igraph, reshape2, limma,
knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr,
spelling, testthat
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, NMF, mclust,
berryFunctions
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, readr, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, AnnotationHub
knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(>
6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF,
TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer,
BiocStyle, scater, DelayedArray, Matrix, HDF5Array, zinbwave,
dplyr
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
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
BiocStyle, rmarkdown, brgedata
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0)
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, IHW
BiocGenerics, GenomicRanges, rtracklayer, Rsamtools,
survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager,
BSgenome, RSQLite
BiocGenerics, BiocManager, BSgenome, knitr, RMySQL, RUnit
knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
testthat, gss, curatedMetagenomicData
BiocStyle, knitr, rmarkdown, RUnit, methylInheritance
knitr, rmarkdown, DSS, bsseq, plotly,
BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38,
MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings,
RColorBrewer, GenomicRanges, GenomeInfoDb, IRanges, testthat
(>= 2.1.0)
BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC,
RUnit
knitr, testthat (>= 2.1.0), BiocGenerics, BiocStyle, tidyr,
ggplot2
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit,
methInheritSim
testthat (>= 2.1.0), knitr, rmarkdown, genomation,
BiocManager
BiocStyle, doParallel, testthat, knitr, rmarkdown
BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0),
covr
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
DT, prettydoc, treeio, tidyverse, testthat, knitr, nlme
BiocStyle, breastCancerMAINZ, breastCancerNKI,
breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP,
breastCancerVDX, knitr, 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, future, future.apply
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, 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
BiocStyle, edgeR, knitr, minfiData, rmarkdown,
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, klaR,
testthat
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
testthat, mockery, roxygen2, knitr, rmarkdown, BiocStyle,
MMAPPR2data
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
testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan,
phyloseq, curatedMetagenomicData, genefilter
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM
BiocStyle, knitr, rmarkdown, testthat, viper
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, seqLogo, BiocStyle, knitr, rmarkdown
RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr,
httr, htmltools
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, preprocessCore
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, RPostgres, RMySQL
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)
BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr,
phylogram, RColorBrewer, reshape2, rmarkdown, testthat, UpSetR
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
paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown,
testthat, cgdsr
curatedTCGAData, TCGAutils, rmarkdown, testthat, knitr
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, uwot
knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics
(>= 0.8.0)
knitr,
TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Drerio.UCSC.danRer10.refGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,TxDb.Dmelanogaster.UCSC.dm6.ensGene,
testthat,TxDb.Celegans.UCSC.ce11.refGene,rmarkdown,
TxDb.Rnorvegicus.UCSC.rn6.refGene,TxDb.Hsapiens.UCSC.hg19.knownGene,
org.Mm.eg.db,
org.Rn.eg.db,org.Hs.eg.db,org.Dr.eg.db,BiocGenerics,
org.Sc.sgd.db, org.Ce.eg.db,org.Dm.eg.db, methods,
knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
BiocStyle, testthat (>= 1.0), knitr, rmarkdown
testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2,
BiocStyle
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, ACME, 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, 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
tidyr, dnet, gprofiler2, BiocStyle, testthat, knitr,
rmarkdown, ggplot2, ggraph
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,
SingleCellExperiment, SingleR
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
biomartr, knitr, rmarkdown, testthat, dendextend, biocViews,
BiocCheck, BiocStyle
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, foreach,
doSNOW, parallel, org.Hs.eg.db, clusterProfiler
testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat, scran, BiocGenerics, knitr, Biobase, GEOquery,
biomaRt, ggplotify, beachmat
testthat, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle
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, ggforce, fgsea, RColorBrewer, ggpubr,
rtracklayer
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 (>= 2.1.0),
HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19,
pasillaBamSubset, covr, ggplot2
testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra,
magick
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, ggpubr, gtable, gridExtra,
roxygen2, testthat (>= 2.1.0), spelling
testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr,
tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown
BiocStyle, testthat, knitr, rmarkdown, png, Rsamtools,
ggplot2
airway, biomaRt, BiocFileCache, broom, Seurat,
SingleCellExperiment, DESeq2, knitr, readr, readxl, pheatmap,
tibble, testthat (>= 2.1.0)
BiocStyle, gridExtra, grid, testthat, devtools, knitr,
rmarkdown, ComplexHeatmap
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2,
synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3),
dplyr, akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>=
0.13), nipals, reshape
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
FCBF, plotly, SummarizedExperiment, SingleCellExperiment,
knitr, rmarkdown, testthat (>= 2.1.0), BiocManager, biomaRt
testthat (>= 2.1.0), knitr, rmarkdown, gridExtra
pumadata, affydata, snow, limma, ROCR,annotate
BiocParallel, BiocStyle, PSCBS,
TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr,
optparse, org.Hs.eg.db, rmarkdown, 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
knitr, BiocParallel, lme4, rmarkdown, BiocStyle, testthat (>=
2.1.0), limma, sva
h5vcData, testthat, knitr, optparse,
BSgenome.Hsapiens.UCSC.hg19
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL,
igraph
limma, biomaRt, RUnit, BiocGenerics, BiocStyle
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW,
parallel
Biobase, BiocStyle, BiocParallel, doParallel, DT, tibble,
foreach, igraph, knitr,
RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat,
visNetwork, arrow
testthat, knitr, rmarkdown, BiocStyle, dplyr
RUnit, BiocStyle, RefNet, knitr, rmarkdown
testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase,
devtools
BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc,
testthat
knitr, rmarkdown, testthat (>= 2.1.0), here
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), covr, pheatmap
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 (>= 1.35.2),
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
R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics
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
RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10,
edgeR, limma, testthat
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
readxl, knitr, rmarkdown, reshape2, pander, testthat
BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
Biostrings, RNAmodR.Data
BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data,
RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer,
keras
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
RNAmodR.Data
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,
MethylSeekR
GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat,
lubridate, DT, rmarkdown,
BiocGenerics, BiocStyle, knitr, multtest, omicade4,
rmarkdown, testthat
knitr, rmarkdown, testthat, RUnit, BiocGenerics
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
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0),
shinydashboard, DT, plotly, heatmaply, magrittr, utils,
clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db,
org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db,
org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db,
org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pf.plasmo.db,
org.Pt.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db,
org.Xl.eg.db
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
Biostrings, methods, knitr, rmarkdown, BiocStyle
devtools, testthat, pander, Biobase, GenomicRanges, IRanges,
S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations,
RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation,
RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr
BiocStyle, Homo.sapiens, knitr, readr, 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
parallel, crayon, RUnit, knitr, BiocGenerics, SNPRelate
BiocStyle, BiocFileCache, biomaRt, beachmat, cowplot,
destiny, knitr, scRNAseq, robustbase, rmarkdown, Rtsne, uwot,
NMF, testthat, pheatmap, Biobase, limma, DropletUtils
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot
testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown,
RColorBrewer, ReactomePA, clusterProfiler, cowplot,
org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne,
BiocParallel, e1071, WGCNA, devtools, DOSE
ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr,
TENxPBMCData, scater, shinydashboard, iSEE, igraph, scran
knitr, rmarkdown, scater, scattermore, scales, matrixStats,
deldir
BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales,
scater, testthat, badger
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,
doParallel, BatchJobs
knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0)
testthat (>= 2.1.0), covr, knitr, rmarkdown, BiocStyle,
Matrix, ggplot2, ggpubr, splatter, SingleCellExperiment,
microbenchmark
testthat, BiocStyle, knitr, beachmat, HDF5Array, scRNAseq,
dynamicTreeCut, DESeq2, monocle, Biobase, pheatmap
BiocGenerics, knitr, testthat, covr, rmarkdown, ggplot2,
DuoClustering2018
testthat, LRBase.Hsa.eg.db, MeSH.Hsa.eg.db, LRBase.Mmu.eg.db,
MeSH.Mmu.eg.db, LRBaseDbi, Seurat, Homo.sapiens
knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
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,
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
testthat, parallel, knitr, rmarkdown, BiocStyle
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
knitr, testthat, rmarkdown, BiocStyle, org.Hs.eg.db
IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr,
rmarkdown
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, Rtsne,
Matrix
testthat, Rsubread, BiocStyle, knitr, lintr, bladderbatch,
rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable,
spelling, GSEABase
testthat, knitr, rmarkdown, BiocStyle, beachmat,
SingleCellExperiment, scater, scRNAseq, scran, ggplot2,
pheatmap, grDevices, gridExtra, viridis, AnnotationHub,
AnnotationDbi
BiocGenerics, BiocStyle, clusterExperiment, destiny, gam,
knitr, mclust, mgcv, RColorBrewer, rgl, rmarkdown, testthat,
covr
GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2,
Rtsne, Biobase, BiocStyle
BiocManager, bit64, covr, knitcitations, knitr (>= 1.6),
JunctionSeq, devtools, BiocStyle (>= 2.5.19), rmarkdown (>=
0.9.5), testthat (>= 2.1.0)
BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
parallel, Matrix, RUnit, knitr, MASS, BiocGenerics
testthat, knitr, parallel,
BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations,
ggdendro, fastICA, sva
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
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, covr
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress,
pscl, testthat, rmarkdown, scDD, scran, mfa, phenopath, BASiCS
(>= 1.7.10), zinbwave, SparseDC, BiocManager, spelling, igraph,
DropletUtils, BiocSingular
igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel,
gridExtra, digest, doParallel, bigmemory
BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3),
RUnit
RMySQL, bigrquery, testthat, knitr, rmarkdown, DelayedArray
knitr, BiocStyle, rmarkdown, tinytest, doFuture
BiocStyle, knitr, rmarkdown, genefilter, edgeR, DESeq
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, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx,
ggplot2, magick
testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
agricolae, BiocFileCache, BiocStyle, car, covr, cowplot,
e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls,
pmp, reshape2, ropls, rmarkdown, Rtsne, testthat
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
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN,
BiocStyle
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
BiocGenerics, ape, RUnit, BiocStyle, knitr, rmarkdown,
biomaRt, BiocParallel, BiocManager, systemPipeRdata,
GenomicAlignments
testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer
testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS,
covr
testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle
jpeg, png, BiocStyle, rmarkdown, devtools, maftools,
parmigene, c3net, minet, dnet, Biobase, affy, testthat, sesame,
pathview, clusterProfiler, ComplexHeatmap, circlize,
ConsensusClusterPlus, igraph, TCGAbiolinksGUI.data, supraHex,
limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra,
survival, doParallel, parallel, ggrepel (>= 0.6.3), scales,
grid
testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2,
BiocStyle, animation, pander
BiocFileCache, BiocStyle, curatedTCGAData, ComplexHeatmap,
devtools, dplyr, IlluminaHumanMethylation450kanno.ilmn12.hg19,
impute, knitr, magrittr, mirbase.db, org.Hs.eg.db,
RColorBrewer, readr, RTCGAToolbox (>= 2.17.4), rtracklayer,
R.utils, testthat, TxDb.Hsapiens.UCSC.hg18.knownGene,
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, 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, MotifDb,
motifStack, RColorBrewer
testthat, AnnotationDbi, BiocManager, Rsubread, e1071, edgeR,
limma, org.Hs.eg.db, sva, GGally, knitr, qpdf, covr, Seurat,
KernSmooth, Rtsne, EGSEA, SummarizedExperiment, S4Vectors,
ggplot2, widyr, clusterProfiler, msigdbr
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse,
igraph, gplots
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
BiocStyle, knitr, rmarkdown, csSAM, gplots, matrixStats,
Matrix
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, httr,
htmltools
knitr, rmarkdown, cowplot, tidyr, testthat, covr
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
RColorBrewer, geneplast
Biostrings, ggplot2, ggtree, igraph, knitr, phangorn,
prettydoc, testthat, tidyr, vroom, xml2
ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
RUnit, plyr, knitr, BiocGenerics, rmarkdown,
BSgenome.Scerevisiae.UCSC.sacCer3
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer
BiocStyle, knitr, rmarkdown, testthat, ggplot2,
BSgenome.Scerevisiae.UCSC.sacCer3
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, limma, devtools
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma,
edgeR, csaw, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats,
Matrix, fishpond
knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, shiny,
biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb,
ontoProc, rjson, graph, TFutils (>= 1.5.4)
BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr,
org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
testthat, knitr, rmarkdown, BiocGenerics, RUnit
spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr
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
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager
affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat
knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown,
scater
knitr, rmarkdown, tidyverse, airway, edgeR, topconfects,
EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi, testthat (>=
2.1.0)
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 (>=
0.25.1), ncdf4, rgl, microbenchmark, testthat, pander,
magrittr, multtest, MALDIquant, pheatmap
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
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
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