a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
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, limma,
AnnotationDbi
R (>= 4.0.0), methods, Biobase, MSnbase (>= 2.14.2)
R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R(>= 4.0.0), SummarizedExperiment(>= 1.1.6), S4Vectors(>=
0.22.1), IRanges
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 (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4),
methods, minfi (>= 1.21.0), Biobase, methylumi
R (>= 4.0.0), 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
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, metafor, methods
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
GenomicRanges
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 4.0), biomaRt, SummarizedExperiment
R (>= 3.5), GenomicRanges, cowplot, breakpointRdata
R (>= 4.0), rtracklayer, GenomeInfoDb, S4Vectors
R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5),
SummarizedExperiment (>= 1.19.5)
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 (>= 0.27.3), 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, RPMM
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 (>= 3.5.0), BiocGenerics (>= 0.1.0), methods, stats
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>=
1.15.4), 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 (>= 3.5.0), 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, Matrix, BiocGenerics (>= 0.31.5),
MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2), 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
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 (>= 4.0), GenomicRanges, SummarizedExperiment
R (>= 3.5), GenomicRanges, InteractionSet,
SummarizedExperiment
R (>= 4.0.0), 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 (>= 2.5.1),
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 (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14),
flexmix (>= 2.3.15)
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 (>= 4.0.0), SummarizedExperiment, SingleCellExperiment
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 (>= 2.8.0), Biobase, coda, EBarrays, mgcv
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),
MatrixGenerics, GenomicRanges (>= 1.31.16),
SummarizedExperiment, BiocParallel (>= 1.1.0), Rsamtools (>=
1.17.29), rtracklayer (>= 1.25.3)
R (>= 4.0.0), 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 (>= 3.1), 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 (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.36.0),
S4Vectors (>= 0.27.12)
R (>= 3.5), DiscriMiner, SummarizedExperiment
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (> 3.0.0),GenomicFeatures, ggplot2, Biobase
R (>= 3.4), regioneR, GenomicRanges, methods
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 2.13.2), methods, graphics, fdrtool
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 (>= 3.5.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
R (>= 4.0), methods, CAMERA, xcms (>= 1.35)
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 (>= 2.10), 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 (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
AnnotationDbi, affy, plotrix, gplots, gmodels, gdata, gtools
R (>= 3.5.0), methods, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings
R (>= 3.4.0), methods, BiocGenerics, SummarizedExperiment,
limma
R (>= 4.0.0), 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 (>= 4.0), SummarizedExperiment, SharedObject(>= 1.3.15)
R (>= 4.0.0), BiocGenerics, ggplot2, tibble (>= 1.3.1)
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
R(>= 4.0), igraph, graphics, methods, utils, jsonlite
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 (>= 4.0.0), SummarizedExperiment, S4Vectors
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 3.0.0), methods, Biobase, BiocGenerics,
R (>= 3.4), cn.mops, methods, utils, stats, graphics
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.3.0), methods, ggplot2, gridExtra
R (>= 2.10), Category, ScISI (>= 1.3.0), SLGI, ppiStats,
ppiData, annotate (>= 1.17.4)
R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome,
BiocParallel
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 (>= 2.14.0), 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 (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1)
R (>= 3.5.0), methods, grid, BiocGenerics, Biostrings
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 (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet,
SummarizedExperiment
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 (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9),
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
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 (>= 3.3), methods, GenomicRanges (>= 1.37.2)
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.36.0)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 3.6.0), stringr, ape, Biostrings, DECIPHER, parallel,
reshape2, phangorn, sangerseqR, gridExtra, shiny,
shinydashboard, shinyjs, data.table, plotly, DT, zeallot,
excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx,
tools, rmarkdown, kableExtra, seqinr, BiocStyle, logger
R (>= 3.4), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
parallel, preprocessCore, splines, splines2, xgboost,
SCATEData, Rtsne, mclust
R (>= 4.0), S4Vectors, SingleCellExperiment,
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
dplyr, ggalluvial, ggplot2, reshape2, R (>= 4.0)
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)
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 (>= 4.0), 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 (>= 4.0.0), methods, SingleCellExperiment
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics (>=
1.17.4)
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, MatrixGenerics (>= 1.1.3), GenomicRanges
(>= 1.41.5), Biobase
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, 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, BiocParallel, scales, Biobase,
methods
R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3),
MatrixGenerics, GenomeInfoDb (>= 1.15.2), GenomicRanges (>=
1.41.5), SummarizedExperiment (>= 1.19.5), 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 (>= 3.5.0), 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 (>= 4.0), GenomicRanges, IRanges, ggplot2
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 (>= 3.5.0), methods, Biobase, BiocParallel (>= 1.8.0),
MSnbase (>= 2.15.3)
R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 3.6.0), GenomicRanges, ggplot2, grid
R (>= 3.4), methods, SummarizedExperiment,
SingleCellExperiment
methods, graphics, grid, Biobase, annaffy, mpm, genefilter,
limma, multtest, glmnet, gplots
methods, Biobase, ROCR, pamr, glmnet, varSelRF, utils,
graphics, stats
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
ArgumentCheck, BiocParallel, data.table, DrImpute, kernlab,
MASS, Matrix, methods, rsvd, S4Vectors, SAVER,
SingleCellExperiment, stats, SummarizedExperiment, utils
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
stats, methods, S4Vectors, SummarizedExperiment,
SingleCellExperiment, Matrix, tibble, rlang
BiocParallel, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, multtest
rmarkdown (>= 2.5), tools, methods, ggplot2, GGally, dplyr,
rjson, shiny, shinydashboard, DT, stats, utils, tximport (>=
1.17.4), 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
ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils,
plyr, DESeq2
stats, MASS, nloptr, Rdpack, phyloseq, microbiome
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), httr
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, 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, tidyselect, rlang, BiocManager
methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr,
dplyr, lubridate, plotly, ggplot2
AnVIL, httr, rmarkdown, whisker, tools, utils, stats,
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
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, glmnet, 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, Rsamtools, BiocStyle,
igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid,
graphics
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, testthat, utils, lifecycle
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
BiocGenerics, BiocParallel, data.table, dplyr, GenomeInfoDb,
GenomicAlignments, GenomicFeatures, GenomicRanges, stats,
glmnet, Rsamtools, methods, Rcpp
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, MASS, methods, Rcpp (>= 0.11.3),
S4Vectors, scran, stats, stats4, SummarizedExperiment, viridis,
utils, Matrix, matrixStats, assertthat, reshape2, BiocParallel,
hexbin
utils, methods, parallel, reticulate, filelock, basilisk.utils
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
DelayedArray, DelayedMatrixStats, BiocParallel, scuttle,
ResidualMatrix
utils, rmarkdown, knitr, pander, gplots, MCMCpack, shiny, sva,
corpcor, moments, matrixStats, ggvis, heatmaply, reshape2,
limma, grDevices, graphics, stats, methods, Matrix
Rcpp (>= 1.0.4.6), stats, purrr, scater, scran,
SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix,
assertthat, mclust, RCurl, DirichletReg, xgboost, utils,
ggplot2, scales, BiocFileCache
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
methods, DelayedArray (>= 0.15.14), BiocGenerics, Matrix
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,
rslurm
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, memoise
methods, stats, utils, dplyr, RSQLite, DBI, rappdirs, curl,
httr
methods, utils, graphics, stats, parallel
Rgraphviz, geneplotter, graph, BiocGenerics, methods
BiocGenerics, GenomicRanges, RCurl, S4Vectors, methods, tools
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, S4Vectors, BiocIO,
AnnotationDbi, KEGGREST, ontologyIndex, tidyr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, irlba, rsvd, Rcpp, beachmat
bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1)
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,
precrec, nsprcomp, ranger, e1071, ggplot2, vioplot, CMplot,
imager, topGO, xlsx
igraph (>= 1.0.1), AnnotationDbi, Biobase
BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr,
utils, stats, RColorBrewer, Hmisc, psych, knitr, rmarkdown,
markdown
methods, utils, grDevices, graphics, stats, crayon
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
stats, methods, utils, Matrix, Rcpp, igraph, S4Vectors,
BiocParallel, BiocNeighbors
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)
data.table, lsa, methods, S4Vectors, utils, BiocFileCache
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 (>= 0.29.3), GenomeInfoDb, GenomicRanges,
Biostrings, Rsamtools, rtracklayer
IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, graphics,
Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors (>=
0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats (>= 1.5.2),
permute, limma, DelayedArray (>= 0.15.16), Rcpp, BiocParallel,
BSgenome, Biostrings, utils, HDF5Array (>= 1.15.19), 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 (>= 0.27.5), som, stringdist, stringi,
SummarizedExperiment, utils, vegan, VGAM
methods, xcms, RBGL, graph, graphics, grDevices, stats, utils,
Hmisc, igraph
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 (>= 2.19.7), S4Vectors, SummarizedExperiment,
stats, tibble, tidyr, TCGAutils (>= 1.9.4), 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, 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, ComplexHeatmap, multipanelfigure, circlize
dplyr, tibble, stringr, Biostrings, Rcpp, reshape2, methods,
rlang (>= 0.3), purrr, Matrix, S4Vectors, BiocGenerics, tidyr,
forcats, progress, stats, utils
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, 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
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
AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>=
2.47.6), DBI, dplyr, ensembldb, GenomeInfoDb,
GenomicAlignments, GenomicFeatures, RBGL, Rsamtools,
SummarizedExperiment, VennDiagram, biomaRt, ggplot2, grDevices,
graph, graphics, grid, KEGGREST, matrixStats, multtest,
regioneR, rtracklayer, stats, utils
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
shiny, colourpicker, shinyjs, rtracklayer, shinyFiles,
shinyhelper, shinycssloaders, Matrix, plotly, shinydashboard,
colorRamps, kableExtra, viridis, batchelor, BiocParallel,
parallel, Rsamtools, ggplot2, qualV, stringdist, fs, DT, scran,
scater, ConsensusClusterPlus, Rtsne, dplyr, tidyr,
GenomicRanges, IRanges, irlba, rlist, umap, tibble, methods,
jsonlite, edgeR, stats, graphics, grDevices, utils, S4Vectors,
SingleCellExperiment, SummarizedExperiment, msigdbr
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, rJava
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, gwascat, BSgenome,
SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>=
1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid,
dbscan, 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, mbkmeans
AnnotationDbi, downloader, DOSE (>= 3.13.1), dplyr, enrichplot
(>= 1.9.3), 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, proxy, httr
methods, rhdf5, data.table, flowCore, 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
BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq,
IRanges, Rsamtools, exomeCopy, foreach, ggplot2, plyr,
GenomeInfoDb, gplots, reshape2, stringr, testthat, graphics,
methods, shiny, shinyFiles, shinyjs, grid, openxlsx
BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges,
S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR,
gdsfmt, grDevices, lattice, limma, methods, plyr, qqman,
rappdirs, reshape2, stats, utils
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 (>=
2.5.4), 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, foreach,
coda
tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16),
gplots, gtools, gdata, caTools, grid, KernSmooth, MASS,
ggplot2, stringr, modeest, edgeR, limma, vioplot, methods,
utils, stats, grDevices, graphics
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, Cairo,
digest, S4Vectors (>= 0.26.1), IRanges, matrixStats
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,
BiocGenerics, methods, stats, utils, graphics, grDevices, lsa,
data.table, crayon
ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix,
methods, MultiAssayExperiment, pals, SingleCellExperiment,
SummarizedExperiment, transport
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 (>= 2.5), 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,reticulate,rhdf5
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
Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma,
GenomicFeatures, AnnotationDbi, methods, S4Vectors, IRanges,
GenomeInfoDb, stats, BiocParallel, utils
GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2,
grDevices, stats, utils
Biobase, BiocGenerics, graphics, grDevices, igraph, methods,
utils, sincell, TSCAN, destiny, HSMMSingleCell
biomaRt, binr, cowplot, data.table, dplyr, DT, fgsea, ggplot2,
ggrepel, graphics, highcharter, httr, limma, methods, pbapply,
R.utils, readxl, reshape2, rhdf5, scales, shiny, stats, tools,
utils
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats,
rappdirs, BiocFileCache
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, ggplot2, ggbeeswarm,
svgPanZoom, svglite, shiny, shinydashboard, matrixStats
cytolib(>= 2.1.18), flowCore (>= 1.99.10), flowWorkspace (>=
4.1.8), 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
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
pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils,
biomaRt, motifStack
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
Biobase, MSnbase, tibble, 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), forcats, methods, highcharter, DAPARdata (>=
1.18.0), siggenes, graph, lme4, readxl, clusterProfiler, dplyr,
tidyr,AnnotationDbi, tidyverse, vsn, FactoMineR, factoextra,
multcomp, purrr, visNetwork, foreach, parallel, doParallel,
igraph, dendextend, Mfuzz, apcluster, diptest, cluster
basilisk, BiocFileCache, BiocParallel, data.table, dplyr,
GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges,
magrittr, megadepth, methods, plyranges, readr, reticulate,
S4Vectors, stringr, SummarizedExperiment, tidyr
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
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
methods, rJava, BiocParallel, stats, Biobase,
SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR,
pcaPP, apcluster, graphics
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, apeglm, ashr
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
Rcpp (>= 1.0.2),GenomicFeatures, parallel, foreach, S4Vectors,
doParallel, Rsamtools (>= 1.31.2), GenomicAlignments,
heatmaply, data.table, stats, ggplot2, GenomicRanges, IRanges,
plyr, plotly, utils,viridis
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), sparseMatrixStats, Matrix,
S4Vectors (>= 0.17.5), IRanges, HDF5Array (>= 1.17.2),
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
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,
methods, stats4, locfit, geneplotter, ggplot2, Rcpp (>= 0.11.0)
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, gplots, grDevices, limma,
GenomicAlignments, locfit, stats, utils, IRanges, lattice,
systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel,
parallel, S4Vectors, Rsamtools (>= 2.0), DESeq2, methods,
graphics, ggrepel, apeglm, ashr, GreyListChIP
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, checkmate, 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
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors,
SummarizedExperiment, BiocParallel, DelayedArray, HDF5Array,
rhdf5, edgeR, R.utils, dqrng, beachmat, scuttle
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),
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, MASS, RCurl, 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,
rms, survivalsvm, ggplot2, minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19, survival, utils
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db,
KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR,
graphite, hwriter, limma, methods, pathview, safe
cowplot, DOSE, ggplot2, ggraph, graphics, grid, igraph,
methods, plyr, purrr, RColorBrewer, reshape2, stats, utils,
scatterpie, shadowtext, GOSemSim, magrittr
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, Matrix
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
grDevices, dplyr, ggplot2, GSEABase, GSVA,
SingleCellExperiment, limma, ggridges, msigdbr, stats,
BiocParallel, Matrix
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2,
ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class,
prabclus, mclust, kableExtra
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 (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr,
magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales,
tibble, MASS, limma, S4Vectors, shinyjs
methods, isa2, eisa, GO.db, KEGG.db, AnnotationDbi
methods, graphics, grDevices, stats, utils
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
KEGGREST, MPINet, dplyr, gprofiler2, rWikiPathways,
reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny,
shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler,
org.Hs.eg.db
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
foreach, doParallel, GenomicRanges, IRanges, Rsamtools,
parallel, S4Vectors
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), S4Vectors
flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics,
stats,methods
flowCore, graphics, flowViz (>= 1.46.1), car, sp, rgeos,
gplots, RFOC, flowWorkspace (>= 3.33.1), methods, stats,
grDevices
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
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
utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang
flowCore, methods, flowViz, stats, flowClust
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 (>= 2.1.20), lattice,
latticeExtra, XML, ggplot2, graph, graphics, grDevices,
methods, stats, stats4, utils, RBGL, tools, Rgraphviz,
data.table, dplyr, Rcpp, scales, matrixStats, RcppParallel,
RProtoBufLib, digest, aws.s3, aws.signature, flowCore(>=
2.1.1), 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, generics, GenomeInfoDb,
GenomicAlignments, GenomicFeatures, GenomicRanges, IRanges,
grDevices, ggplot2, ggrepel, HDF5Array, matrixStats, methods,
OUTRIDER, 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
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, 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
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, Rsamtools, igraph, kernlab, FactoMineR,
IRanges, GenomicRanges, data.table,grDevices, graphics,stats,
utils, methods, GGtools
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, foreach, graphics, grDevices, igraph, Matrix,
methods, reshape2, stats, utils
AnnotationDbi, bs4Dash, colorspace, ComplexHeatmap,
dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, 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, lsr, parallel,
ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack
stats, utils, XML, Biobase, BiocManager, BiocFileCache,
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 (>= 0.27.3), 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 (>= 2.45.8), 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 (>= 0.35.3),
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, scales
ggplot2, utils, rlang, ggnewscale, stats
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
htmlwidgets, edgeR, DESeq2, limma, SummarizedExperiment,
stats, jsonlite, methods, S4Vectors
Rcpp, DelayedMatrixStats, matrixStats, DelayedArray,
HDF5Array, SummarizedExperiment, methods, stats, utils, splines
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,
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 (>= 1.67.1), 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,
S4Vectors, stats, utils
dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud,
stringr, gridExtra, rlang, grDevices, graphics, stats, methods
cluster, doParallel, foreach, matchingR, nsga2R, survival,
proxy, stats, methods,
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, stats, utils, graphics, BiocGenerics, S4Vectors,
IRanges, Biobase, SummarizedExperiment, GSEABase, parallel,
BiocParallel
circlize (>= 0.4.8), GetoptLong, grDevices, utils
BiocParallel, Biostrings, CRISPRseek, ChIPpeakAnno,
data.table, matrixStats, BSgenome, parallel, IRanges (>=
2.5.5), S4Vectors (>= 0.9.6), GenomicAlignments (>= 1.7.3),
GenomeInfoDb, Rsamtools, hash, limma,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
S4Vectors (>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges
(>= 1.29.6), GenomicFeatures, readr, Biostrings, AnnotationDbi,
BiocFileCache, snpStats, VariantAnnotation
graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth, data.table
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, googleAuthR, httr, methods, readr, rlang, utils
BiocFileCache, HCAMatrixBrowser, S4Vectors, LoomExperiment,
vctrs, curl, httr, jsonlite, methods, plyr, readr, rlang,
tibble, tidygraph, utils, xml2
BiocFileCache, digest, dplyr, httr, jsonlite, Matrix, methods,
progress, rlang, SingleCellExperiment, stats, 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
utils, stats, scales, stringr, tibble, shiny, data.table
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices,
graphics, methods
shiny, ssrch, S4Vectors, SummarizedExperiment, utils
Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr,
scales, rlang, httr, openxlsx, htmltools, reshape2, reactable,
msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny
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
Matrix, parallel, foreach, aricode, LiblineaR, SparseM,
ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster,
parallelDist, cluster, dendextend, DescTools, plyr, scales,
pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment,
SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils
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
methods, stats, graphics, grid, lattice, grDevices
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
stats, grDevices, utils, graphics, pbapply, matlab, png,
raster, grid, uwot, gtools, Biobase, generics, parallel,
methods, xgboost
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 (>= 0.27.12),
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
utils, reactable, htmltools, dplyr, readr, tidyr, purrr,
rlang, forcats, tibble, BiocParallel, stringr, fs, zip,
lubridate, lifecycle, ggplot2, ggrepel, stats, upsetjs, psych,
grDevices, data.table, readxl, tools
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2,
ggrepel, colourpicker, igraph, vipor, mgcv, graphics,
grDevices, viridisLite, shinyWidgets, ComplexHeatmap, circlize,
grid
methods, S4Vectors, shiny, SummarizedExperiment,
SingleCellExperiment, ggplot2, DT, stats, colourpicker
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), tximeta (>=
1.7.12), edgeR, futile.logger, stringr, dplyr, magrittr, readr,
tibble, XVector, BiocGenerics, RCurl
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
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 (>= 0.27.3), 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, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab,
rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML,
praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3),
limma (>= 3.38.3), 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,
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
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, imputeLCMD,
magrittr
Biobase, graphics, grDevices, methods, stats
pheatmap, wordcloud, RColorBrewer, data.table, methods,
grDevices, stats, graphics, GenomicRanges, BiocParallel,
S4Vectors
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
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,
pbapply, car, dplyr, vegan, chemometrics, ggplot2, pheatmap,
logging, data.table, lmerTest, hash, optparse, MuMIn,
grDevices, stats, utils, glmmTMB, MASS, cplm, pscl
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
Biobase, clusterProfiler (>= 3.16.1), enrichplot, gridExtra,
ggplot2, ggrepel, grDevices, grid, reshape2, stats, utils
Biobase, affy, methods, stats, utils, zlibbioc
multtest, clusterSim, apcluster, limma, e1071, AnnotationDbi,
methods, parmigene,igraph,reactome.db
Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr,
magrittr, rlang, S4Vectors
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, S4Vectors, SingleCellExperiment,
SummarizedExperiment, bluster, 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
xfun, utils, fs, GenomicRanges, readr, cmdfun
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, enrichplot, GOSemSim, 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
methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape
(>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges,
circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3),
ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors
methods, mgcv, caret, S4Vectors, stats, utils, rlang,
graphics, matrixStats
data.table, httr, jsonlite, methods, MultiAssayExperiment,
struct, SummarizedExperiment, utils
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, purrr, data.table, methods, dplyr,
magrittr, reshape2
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench
Matrix, tools, robustbase, BiocGenerics, graphics, stats,
utils
grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4),
Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2),
gplots (>= 3.0.1), RColorBrewer (>= 1.1.2),
SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph,
dplyr, tidyr, tibble, ggplot2
edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots,
corrplot, vsn, brew, rjson, log4r
ABSSeq, baySeq, Biobase, BiocGenerics, BiocParallel, biomaRt,
Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter,
GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, gplots, graphics, grDevices, harmonicmeanp,
heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r,
magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel,
qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer,
S4Vectors, stats, stringr, SummarizedExperiment, survcomp,
utils, VennDiagram, vsn, yaml, 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
dplyr, plyr, GenomicRanges, SummarizedExperiment,
DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors,
sesameData, stringr, readr, methods, stats, Matrix, MASS,
rlang, pscl, IRanges, sfsmisc, progress
rtracklayer, DelayedArray, HDF5Array, BSgenome,
DelayedMatrixStats, parallel, methods, ggplot2, matrixStats,
graphics, stats, utils, GenomicRanges, IRanges
grDevices, stats, utils, lumi, methylumi, Gviz, genoset,
SummarizedExperiment, IRanges, GenomicRanges,
VariantAnnotation, rtracklayer,
bigmemoryExtras,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
shinyjs, shinydashboard, shinycssloaders, shinyWidgets,
rmarkdown (>= 1.9.0), DESeq2, RColorBrewer, dplyr, tidyr,
rlang, knitr, readr, DT (>= 0.12.0), biomformat, tools,
stringr, vegan, matrixStats, heatmaply, car, broom, limma,
reshape2, tibble, forcats, lubridate, methods, plotly (>=
4.9.1)
ape, plyr, tidyr, ggplot2, phyloseq, magrittr, dplyr,
Biostrings, ggrepel, vegan, reshape, zoo, ggtree, tidytree,
gtools, MASS, methods, rlang, tibble, grDevices, stats, utils,
coin, ggsignif, Rmisc, patchwork, ggstar
AnnotationDbi, Biobase, BiocParallel, compiler, data.table,
edgeR, futile.logger, ggdendro, ggplot2, GO.db, GOstats, graph,
graphics, grDevices, grid, GSEABase, ismev, jsonlite, limma,
matrixStats, org.Hs.eg.db, RBGL, reshape2, Rgraphviz, 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 (>= 0.15.16), HDF5Array, BiocParallel
methods, BiocGenerics, MatrixGenerics, 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
AnnotationDbi, BiasedUrn, Biobase, BiocGenerics,
GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICmanifest, 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, ggrepel, BiocParallel, 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
rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods,
GGally, RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array,
grDevices, stats, magrittr, forcats, utils, corrplot,
DelayedArray, Rtsne, uwot, basilisk
stats, utils, RCy3, stringr, graphics, grDevices, RUnit,
BiocParallel, igraph
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
ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets,
stats, stats4, utils, XML
httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales,
gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb,
methods, biomaRt, stats, IRanges
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
softImpute, methods, stats, graphics, pdist, reticulate,
scran, data.table, FNN, matrixStats, rdetools, limma, mvtnorm
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, BiocStyle, msmsTests,
ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang,
stringr, tibble, AnnotationHub, AnnotationDbi, xtable
SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), VIM,
crmn, preprocessCore, sva, dplyr (>= 0.7), tidyr, tibble (>=
1.2), magrittr, rlang, stats, stringr, methods, ddpcr
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,
data.table, log4r, methods, checkmate, utils
broom, dplyr, rlang, stats, tibble, tidyr, tidyselect,
Biostrings
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
dplyr, gridExtra, stringr, reshape2, stats, utils, ggplot2,
grDevices, graphics, MSstatsTMT, Rcpp
graphics, grDevices, stats, methods, fields
methods, GenomicRanges (>= 1.25.93), BiocGenerics, S4Vectors
(>= 0.23.19), IRanges, Biobase, stats, tidyr, utils
Matrix, ggplot2, MultiAssayExperiment, ropls, graphics,
methods
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
assertive, BiocGenerics, Biostrings, BSgenome, CRISPRseek,
data.table, GenomeInfoDb, GenomicFeatures, GenomicRanges,
ggplot2, grid, karyoploteR, magrittr, methods, parallel,
plyranges, Rbowtie, reticulate, rtracklayer, stats, stringi,
tidyr, tidyselect, utils
BiocGenerics, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, methods, utils, ggplot2, ggrepel, qqman,
limma
magrittr, graphite, AnnotationDbi, dplyr, fgsea, metap,
rappdirs, rlang, methods
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
SummarizedExperiment, VariantAnnotation, cowplot, Biostrings,
base, methods, magrittr, tibble, tidyr, gtools, gridExtra,
maftools, MCMCprecision, data.table, dplyr, rlang, BSgenome,
GenomeInfoDb, GenomicFeatures, GenomicRanges, IRanges,
S4Vectors, uwot, ggplot2, stringr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Mmusculus.UCSC.mm10, deconstructSigs, decompTumor2Sig,
topicmodels, ggrepel, withr, plotly, utils
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
S4Vectors, SummarizedExperiment, bsseq, forcats, assertthat,
AnnotationDbi, Rcpp, dplyr, data.table, e1071, fs,
GenomicRanges, ggthemes, glue, patchwork, purrr, readr, rlang,
RSQLite, Rsamtools, scales, stats, stringr, tibble, tidyr,
utils, zlibbioc
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
DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods,
stats,
edgeR, stats, MASS, car, mppa, BiocParallel, ggplot2, reshape2
httr, xml2, utils, methods, grDevices, ggplot2, IRanges,
GenomicRanges, S4Vectors
R.utils, matrixStats, plyranges, transport, Rsamtools,
S4Vectors, grDevices, graphics, rtracklayer, dplyr,
GenomeInfoDb, methods, GenomicRanges, utils, stats, magrittr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots,
BiocGenerics, rlang
Seurat, SingleCellExperiment, SummarizedExperiment,
SeuratObject, ks, Matrix, stats, methods
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)
methods, SingleCellExperiment, parallel, irlba, Matrix,
DelayedArray, BiocSingular, stats
Biostrings, checkmate, dplyr (>= 1.0.0), DT, FactoMineR,
forcats, ggdendro, grDevices, grid, lifecycle, lubridate,
methods, pander, parallel, plotly, readr, reshape2, rmarkdown,
Rsamtools, scales, ShortRead, stats, stringr, tidyr, tidyselect
(>= 0.2.3), utils, viridisLite, 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
dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr,
tidyselect, grid, stats, stringr
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,
BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr,
magrittr, DT, igraph
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
S4Vectors (>= 0.21.3), GenomeInfoDb (>= 1.15.5),
GenomicFeatures (>= 1.31.10), AnnotationDbi (>= 1.45.0),
rtracklayer (>= 1.43.0), Rcpp (>= 1.0.0), data.table (>=
1.11.8), Biostrings (>= 2.51.1), biomartr, BiocGenerics (>=
0.29.1), BiocParallel (>= 1.19.0), BSgenome, DESeq2 (>=
1.24.0), ggplot2 (>= 2.2.1), gridExtra (>= 2.3), cowplot (>=
1.0.0), GGally (>= 1.4.0), methods (>= 3.6.0), R.utils, RCurl,
Rsamtools (>= 1.35.0), utils, stats, SummarizedExperiment (>=
1.14.0), fst (>= 0.9.2), xml2 (>= 1.2.0), tools
RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges,
GenomicFeatures, AnnotationDbi, rlang, 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
FactoMineR, MultiAssayExperiment, methods, graphics, stats,
utils
limma, AnnotationDbi, GSA, foreach, doRNG, hgu133plus2.db,
hgu133a.db, KEGGREST, nlme
GenomicRanges, igraph, motifmatchr, stats, utils, grDevices,
graphics
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
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
lattice, grDevices, cowplot, methods, reshape2, stats, Matrix,
DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel,
Rcpp, dqrng
AnnotationDbi, Biobase, Category, GO.db, graph, graphics,
GSEABase, KEGG.db, methods, ScISI, stats, stats4
circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2,
grDevices, grid, gridExtra, methods, plyr, stats, utils
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
S4Vectors, rtracklayer, stats, GenomeInfoDb, magrittr, zoo,
ggplot2, methods, parallel, cowplot
dplyr, ggplot2, tidyr, assertthat, lme4, splines, igraph,
foreach, parallel, doParallel, diffusr, lazyeval, tibble, grid,
utils, graphics, scales, magrittr, formula.tools, rlang
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, curl
Biobase, S4Vectors, SummarizedExperiment, BiocParallel,
ggplot2, magicaxis, RColorBrewer, parallel, caTools, methods,
downloader, stats, utils, graphics, grDevices, reshape2,
jsonlite, data.table
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
plyr, stats, graphics, matrixStats, methods
ruv, e1071, calibrate, dendextend, limma, pcaMethods, stats,
RColorBrewer, circlize, dplyr, igraph, pheatmap,
preprocessCore, tidyr, rlang, graphics, grDevices, utils
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
BiocParallel, S4Vectors, ComplexHeatmap, SingleCellExperiment,
SummarizedExperiment, Seurat, matrixStats, Matrix, cluster,
aricode, methods, utils, dplyr, grid, scales, scran,
viridisLite, clue, randomcoloR, ggplot2, cowplot,
intrinsicDimension, scater, knitr, reshape2, stats, Rtsne,
uwot, circlize, RColorBrewer
BSgenome, digest, visNetwork, magrittr, methods, Biostrings,
GenomeInfoDb, parallel, stats, utils
Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2,
Biobase
utils, Biobase (>= 2.5.5), MASS, methods
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
Biobase, broom, caret, clisymbols, ComplexHeatmap, crayon,
dplyr, e1071, ggcorrplot, ggplot2, ggraph, ggrepel, glasso (>=
1.11), glmnet, impute, knitr, limma, magrittr, mixOmics,
MSnbase (>= 2.12), patchwork, plotly, qpdf, randomForest,
RankProd (>= 3.14), reshape2, rmarkdown, tibble, tidyr, vegan
stats, CompQuadForm, Matrix, survival, Biobase, GSEABase
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, truncdist, vegan, VGAM
Biobase, Category, graph, graphics, grDevices, lattice,
methods, RColorBrewer, stats
Rcpp (>= 0.12.3), GenomicRanges, IRanges, S4Vectors, methods
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
S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics,
e1071, PRROC, pROC, caret, DMwR, utils, cluster, dbscan,
doSNOW, foreach, pbapply, stats, parallel
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
dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments,
GenomeInfoDb, IRanges, S4Vectors, methods, rlang,
SummarizedExperiment, AnnotationDbi, DESeq2, data.table,
tibble, Gviz, BiocParallel
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, ggplot2, EnrichedHeatmap, ComplexHeatmap, grid,
circlize, BiocParallel, rtracklayer, GenomeInfoDb, grDevices,
rlang, Cairo, tiff
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, shinydashboardPlus, colourpicker, shinyhelper,
shinyWidgets, shinyjs, colorspace, shinydashboard, stats,
grDevices, grid, BiocGenerics
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.22.8), DAPARdata (>= 1.20.0), 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, 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, stats, utils, S4Vectors, IRanges,
SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.19.3),
AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.1.2),
methods, parallel, Matrix (>= 1.0), grid, annotate, graph (>=
1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi,
IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm,
qtl, Rgraphviz
assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0),
ggdendro, ggplot2, graphics, grDevices, IRanges, limma,
magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang,
scales, stats, stringr, tibble, tidyr, tidyselect, utils
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, 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)
SummarizedExperiment, S4Vectors, Biobase, parallel,
BiocParallel, RColorBrewer, caTools, magicaxis, methods,
reshape2, scales, grDevices, graphics, stats, utils,
assertthat, matrixStats, downloader
BiocGenerics, GenomeInfoDb, IRanges, Matrix, MatrixGenerics,
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, 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
utils, methods, knitr, callr, rmarkdown, CodeDepends,
BiocStyle
dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment
phyloseq, KernSmooth, reshape2, ggplot2, stats, methods,
graphics, grDevices, matrixStats
BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb,
GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer
(>= 1.35.3), S4Vectors, stats, utils
BiocFileCache, methods, rtracklayer, S4Vectors, utils, RCurl,
data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools
minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl,
R.utils, BiocFileCache
BiocGenerics, biomaRt, circlize, GenomeInfoDb,
GenomicFeatures, graphics, grDevices, httr, methods, parallel,
RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr,
utils
AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils
randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA,
ggplot2 (>= 2.2.0), methods, reshape2, magrittr
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, 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,
rvest, xml2, IRanges, S4Vectors
Biostrings, GenomicRanges, methods, graphics, seqLogo
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
GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb,
bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot
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 (>= 2.57.2), 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
biomaRt,edgeR,heatmap3,matlab,KEGGREST,methods,grDevices,
graphics, stats, utils,Rcpp (>= 0.11.2)
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
BiocFileCache, rappdirs, xml2, RCurl, utils
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 (>= 1.9.4), 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
Biobase, methods, ggplot2, pROC, fdrtool, splines, utils,
tibble
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, RCurl
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, httr,
KEGGREST, bookdown
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
stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics,
S4Vectors, SummarizedExperiment, DelayedArray,
DelayedMatrixStats, BiocNeighbors, BiocSingular, BiocParallel,
scuttle, rlang, ggbeeswarm, viridis
SingleCellExperiment, SummarizedExperiment, Seurat, MASS,
zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods,
Matrix
SingleCellExperiment, SummarizedExperiment, Matrix, methods,
utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel,
iterators, foreach, Seurat
S4Vectors, limma, ggraph, igraph, methods, cluster,
minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix,
ggplot2, hopach, diptest, mgcv, stats, graphics, statmod
ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales,
RColorBrewer, corrplot, stats, grDevices, graphics, utils,
MASS, matrixStats, methods
igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors,
BiocSingular, S4Vectors, SummarizedExperiment,
SingleCellExperiment, scran, scater, scuttle, bluster, methods,
DelayedArray, xgboost, stats, utils
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
matrixStats, keras, tensorflow, BiocParallel, igraph, Matrix,
cluster, clusterCrit, psych, glmnet, RhpcBLASctl, stats, utils,
methods, survival
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, igraph, M3Drop (>= 1.9.4), parallel,
pdist, proxy, 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
methods, stats, utils, SingleCellExperiment,
SummarizedExperiment, MultiAssayExperiment, S4Vectors, dplyr,
magrittr, rlang
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
cluster, kernlab, origami, RSpectra, coop, Matrix, DelayedArray
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, BiocGenerics, BiocParallel,
Rcpp, stats, methods, utils, Matrix, scuttle, edgeR, limma,
BiocNeighbors, igraph, statmod, DelayedArray,
DelayedMatrixStats, BiocSingular, bluster, dqrng, beachmat
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)
Biostrings, RColorBrewer, colorRamps, ggdendro, ggfittext,
stringr, vegan, powerTCR, SummarizedExperiment,
SingleCellExperiment, Seurat
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
DelayedArray, glmpca (>= 0.2.0), HDF5Array, Matrix,
SingleCellExperiment, SummarizedExperiment, BiocSingular
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
methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors,
BiocParallel, GenomicRanges, SummarizedExperiment,
DelayedArray, DelayedMatrixStats, beachmat
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,
pbapply, pbmcapply, 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, BiocGenerics,
gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW,
logistf, Matrix, data.table,
BiocParallel, grDevices, utils, stringr, tibble, illuminaio,
MASS, GenomicRanges, IRanges, grid, preprocessCore, S4Vectors,
randomForest, wheatmap, ggplot2, parallel, matrixStats,
DNAcopy, stats, 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
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,
reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5,
GSEABase, DelayedArray
BiocGenerics, Biostrings, class, graphics, grDevices,
GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats,
utils, PMCMR
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
GOSemSim, ComplexHeatmap (>= 2.5.4), circlize, GetoptLong,
digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods,
clue, grDevices, graphics, stats, utils, proxyC, Matrix,
cluster (>= 1.14.2)
graphics, stats, gbm, Hmisc, GenomicRanges, methods
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
methods, utils, stats, S4Vectors, BiocGenerics
BiocManager, circlize, limma, igraph, gplots, grDevices,
edgeR, SIMLR, data.table, pheatmap, stats, Rtsne, graphics,
stringr, foreach, multtest, scran, utils,
ape, batchelor, BiocGenerics, BiocParallel, colourpicker,
colorspace, cowplot, cluster, ComplexHeatmap, data.table,
DelayedMatrixStats, DESeq2, dplyr, DT, ExperimentHub, fields,
ggplot2, ggplotify, ggrepel, ggtree, gridExtra, GSVA (>=
1.26.0), GSVAdata, igraph, KernSmooth, limma, MAST, Matrix,
matrixStats, methods, msigdbr, multtest, plotly, RColorBrewer,
ROCR, Rtsne, S4Vectors, scater, scMerge (>= 1.2.0), scran,
Seurat (>= 3.1.3), shiny, shinyFiles, shinyWidgets, shinyjs,
shinyBS, shinyjqui, sva, reshape2, AnnotationDbi, shinyalert,
circlize, enrichR, celda, shinycssloaders, shinythemes, uwot,
DropletUtils, scds (>= 1.2.0), reticulate (>= 1.14), tools,
withr, GSEABase, R.utils, zinbwave, scRNAseq (>= 2.0.2),
TENxPBMCData, yaml, rmarkdown, magrittr, kableExtra,
scDblFinder
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocNeighbors, BiocParallel, BiocSingular, stats, utils, Rcpp,
beachmat
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree,
graphics, grDevices, gridExtra, methods, parallel, seqinr,
stats, tidytree, utils
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
methods, glmnet, huge, stats, graphics, utils
nnlasso, nnls, parallel, data.table, Biostrings,
GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2,
gridExtra, reshape2
logNormReg, grDevices, stats, utils, graphics,
av, DESeq2, edgeR, WGCNA, flashClust, htmlwidgets, genefilter,
ggplot2, ggdendro, grImport, grid, gridExtra, gplots, igraph,
rsvg, shiny, dynamicTreeCut, grDevices, graphics, ggplotify,
plotly, rols, stats, SummarizedExperiment, shinydashboard,
utils, visNetwork, methods, xml2, yaml
methods, IRanges, MsCoreUtils (>= 1.1.5), graphics, grDevices,
stats, tools, utils, fs
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges
ggplot2, concaveman, BiocParallel, spatstat.core,
spatstat.geom, lmerTest, BiocGenerics, S4Vectors, lme4,
methods, mgcv, pheatmap, rlang, grDevices, IRanges, stats,
data.table, dplyr, tidyr
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
BiocGenerics, BiocParallel, checkmate (>= 2.0.0), edgeR,
fitdistrplus, ggplot2, locfit, matrixStats, methods, scales,
scater (>= 1.15.16), stats, SummarizedExperiment, utils,
crayon, S4Vectors, grDevices
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,
stats, methods, SingleCellExperiment, fitdistrplus, graphics,
edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
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, utils
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 (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>=
1.13.1), DelayedArray (>= 0.15.10)
ape, MASS, grDevices, graphics, stats, readr, tibble, tidyr,
dplyr, stringr, purrr, magrittr, igraph, methods
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma, edgeR
data.table, reshape2, ggplot2, stats, grDevices, graphics,
utils, biomaRt, methods
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, limma, edgeR, DESeq2, GOstats, GO.db, annotate,
pheatmap, batchtools, yaml, stringr, assertthat, magrittr, DOT,
rsvg, IRanges
DT, assertthat, bsplus, crayon, dplyr, ggplot2, glue,
magrittr, methods, plotly, rlang, rstudioapi, shinyAce,
shinyFiles, shinyWidgets, shinydashboard, shinydashboardPlus
(>= 2.0.0), shinyjqui, shinyjs, shinytoastr, stringr, stats,
styler, tibble, utils, vroom (>= 1.3.1), yaml
dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2,
tidyr, ggpubr, RColorBrewer, reshape2, cowplot
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, 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, biomaRt, dplyr, graphics,
tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite
(>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0),
IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils,
SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data, 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,
rjson, BiocFileCache, DT, httr, readxl
tibble, readr, dplyr, magrittr, tidyr, stringr, rlang, purrr,
preprocessCore, stats, parallel, utils, lifecycle, scales,
SummarizedExperiment, methods
dplyr, tibble, tidyr, ggplot2, plotly, magrittr, rlang, purrr,
lifecycle, methods, utils, S4Vectors, tidyselect, ellipsis,
pillar, stringr, cli, fansi
tibble (>= 3.0.4), dplyr, magrittr, tidyr, ggplot2, rlang,
purrr, lifecycle, methods, plotly, utils, S4Vectors,
tidyselect, ellipsis, pillar, stringr, cli, fansi
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
biomaRt, clusterProfiler, dplyr (>= 0.8.4), FreqProf, gtools
(>= 3.8.1), gplots, ggdendro, gghighlight, ggplot2, graphics,
grDevices, igraph (>= 1.2.4.2), RCy3, readxl, reshape2,
rWikiPathways, scales, stats, tidyr (>= 1.0.2), stringr (>=
1.4.0)
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, alsace, signal, KernSmooth, graphics,
grDevices, stats
methods, stats, grDevices, reshape2, Rtsne, umap,
RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
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)
SummarizedExperiment, S4Vectors, Biobase, BiocParallel,
ggplot2, tibble, dplyr, caTools, downloader, magrittr, methods,
reshape2, tidyr, data.table, assertthat, scales, graphics,
grDevices, parallel, stats, utils, limma
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, monocle, igraph,
S4Vectors, tibble, Matrix, viridis, matrixStats
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 (>= 1.0.4.8), 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 (>= 0.3.0), 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, methods, stats, Matrix, SummarizedExperiment,
SingleCellExperiment, DelayedArray, S4Vectors
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
magick, cowplot, scales, GenomicRanges, ShortRead, zoo,
ggplot2, reshape2, regioneR, IRanges, S4Vectors, magrittr,
dplyr, BSgenome, Biostrings, DESeq2, R.utils, Rsamtools,
stringr, Rbowtie2, methods, GenomeInfoDb, GenomicAlignments,
RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate,
TxDb.Hsapiens.UCSC.hg19.knownGene, rlang, GenomicFeatures,
BiocFileCache, rappdirs, fda
markdown, shiny, shinyjs, shinyBS,
shinyWidgets,shinycssloaders, DT, Gviz, Homo.sapiens, openxlsx,
condformat, stringr, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, BiocFileCache,rappdirs,
TxDb.Hsapiens.UCSC.hg19.knownGene, rlist, utils,
EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi,
BSgenome.Hsapiens.UCSC.hg19, processx, Rsamtools, GenomicRanges
stringr, R.utils, WriteXLS, stats, doParallel, foreach,
GenomicRanges, IRanges, VariantAnnotation
methods, stats, utils, MASS, ggplot2, ggseqlogo, yaml,
IRanges, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics,
S4Vectors, rlang, grid
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
MatrixGenerics, 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,
foreach, doParallel, colorRamps, gplots, progress, reshape2,
lme4 (>= 1.1-10), grDevices, graphics, utils, stats
utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.27.12), IRanges
(>= 2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.57.2),
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
methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors,
DelayedArray, basilisk, zellkonverter, scuttle,
SingleCellExperiment, BiocParallel, BiocSingular
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, fgsea, GOSemSim,
ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph,
methods, plotly, processx, topGO, RColorBrewer, R.utils,
scales, stats, UpSetR, utils
cowplot, magrittr, GenomeInfoDb, GenomicAlignments,
RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2,
methods, graphics, stats
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
multtest, qvalue, stats, utils, BiocManager
methods, utils, stats, grDevices, assertthat, S4Vectors,
DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics,
limma, topconfects, dplyr, purrr, ggplot2, rlang, scales,
reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl
dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer,
cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb
utils, methods, cli, Biobase, SummarizedExperiment, config,
golem, shiny, DT, ggplot2, dplyr, rlang, stringr,
shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer,
logging
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,
MsCoreUtils
BiocGenerics, genefilter, graphics, grDevices, gtools,
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, tools, zlibbioc, BiocGenerics, S4Vectors,
IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
limSolve, 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
Matrix, basilisk, reticulate, SingleCellExperiment (>=
1.11.6), SummarizedExperiment, DelayedArray, methods,
S4Vectors, utils
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 ( >=
1.99.26),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1),
flowWorkspace
Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Rcpp, RcppArmadillo, BH(>= 1.65.0.1), cytolib(>= 1.7.2),
RProtoBufLib
Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>=
2.1.15),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1)
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 1.17.7), S4Vectors, IRanges, XVector, Biostrings
Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Rcpp, Rhtslib (>= 1.13.1), zlibbioc, testthat
S4Vectors, IRanges, XVector, Biostrings, Rhtslib, zlibbioc
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats
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
BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics,
DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext,
RColorBrewer, pheatmap, viridis
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
DT (>= 0.5), testthat (>= 2.0.0), plotly (>= 4.7.1),
ChemoSpec, knitr
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
knitr, microbiome, tidyverse, testthat, DT, magrittr, qwraps2
(>= 0.5.0)
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,
rmarkdown
RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData,
rmarkdown
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, testthat, withr, readr
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
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
AnnotationDbi, Biostrings, BiocFileCache, ggplot2,
ComplexHeatmap, circlize, ggbio, gridExtra, knitr, rmarkdown,
testthat, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3),
DESeq2, NanoporeRNASeq, BSgenome, apeglm, utils, DEXSeq
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, rmarkdown, scran, scater,
bluster, scRNAseq
testthat, knitr, rmarkdown, igraph, spatialLIBD, dplyr,
viridis, patchwork, RColorBrewer, Seurat
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel
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, affy, affyPLM, DESeq2,
flowClust, 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, 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, DiagrammeR,
SummarizedExperiment
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
BiocStyle, covr, devtools, knitr, pkgdown, RefManageR,
rmarkdown, sessioninfo, testthat, utils
annotate, BiocStyle, knitr, rmarkdown, testthat, mockery
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
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis
BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 2.1.0), covr
BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr,
plotly
testthat, BiocStyle, knitr, rmarkdown, devtools
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
testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl,
gplots
BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto,
rmarkdown, testthat, uwot
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
testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle,
ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment,
scater, broom.mixed, cowplot
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, Rtsne
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
scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14),
devtools (>= 2.3.0), BiocStyle, testthat
ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, 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
BSgenome, limma, reactome.db, BiocManager, BiocStyle,
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,
DelayedArray, idr, seqinr, EnsDb.Hsapiens.v75,
EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR,
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, devtools, gridExtra,
ggpubr, VennDiagram, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BiocManager,
knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle,
pkgdown
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, 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), samr, pamr, kohonen,
NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE,
AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree,
dendextend
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2, doMC, progress
BiocStyle, EBSeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0),
genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown, testthat
BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr,
rtracklayer
testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,
fastcluster, dendextend (>= 1.0.1), grImport, grImport2, glue,
GenomicRanges, gridtext, pheatmap (>= 1.0.12), shiny
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
pander, BiocStyle, rmarkdown, knitr, formatR, testthat
ade4, BiocStyle, CellBench, DuoClustering2018, knitr,
testthat
knitr, kableExtra, BiocStyle, Biobase, roxygen2,
RColorBrewer, devtools, xtable
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown,
rtracklayer, sangerseqR, testthat, VariantAnnotation
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
RUnit
knitr, rmarkdown, lydata, org.Hs.eg.db, testthat
org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat,
GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
testthat, knitr, covr, rmarkdown, spelling
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet,
BiocStyle, flowStats
testthat, flowWorkspaceData , knitr, parallel
BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat,
BiocStyle
XML, grImport, grImport2, BiocStyle, knitr, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
BSgenome.Hsapiens.UCSC.hg19
BiocStyle, covr, testthat, GenomicState, ggplot2, ggpubr,
ggrepel, grid, knitcitations, knitr, recount, rmarkdown,
sessioninfo, rtracklayer, tibble
EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust,
minqa, SummarizedExperiment, Biobase, knitr, rmarkdown,
BiocStyle, edgeR
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
testthat, rmarkdown, BiocStyle, knitr, R.rsp
knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr,
RColorBrewer, matrixStats
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown,
statmod, testthat
BiocParallel, HDF5Array (>= 1.17.12), genefilter,
SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr,
BiocStyle, RUnit
testthat, knitr, rmarkdown, SeqArray, GDSArray
testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark,
profmem
knitr, rmarkdown, BiocStyle, ggplot2, Rtsne, uwot, testthat
uwot, testthat, knitr, rmarkdown, BiocStyle
BiocStyle (>= 2.5.19), sessioninfo, derfinderData (>=
0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma,
RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0),
TxDb.Hsapiens.UCSC.hg19.knownGene, covr
sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19),
RefManageR, rmarkdown (>= 0.3.3), testthat, covr
biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData
(>= 0.99.0), sessioninfo, 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), glmGamPoi, BiocManager
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, utils
lattice, parallel, MASS, RColorBrewer, xtable
plotly, testthat, Seurat (>= 2.2), DESeq2, ggplot.multistats,
knitr, rmarkdown, BiocStyle, scRNAseq, ggrastr (>= 0.2.0),
ComplexHeatmap
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, knitr, BiocStyle, rmarkdown, jsonlite,
DropletTestFiles
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, DESeq2
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,
org.Hs.eg.db, gridExtra, magrittr
SummarizedExperiment, testthat, Biobase, survminer,
affycoretools, knitr, plotROC, prognosticROC
testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer
ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools,
airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr,
rmarkdown
clusterProfiler, dplyr, europepmc, ggupset, knitr,
org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi,
ggplotify, ggridges, grDevices, gridExtra, ggnewscale, ggrepel
BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat,
BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>=
1.20.0), magrittr, rmarkdown, 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, ensembldb, 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
Seurat, SeuratObject, knitr, rmarkdown, BiocStyle, testthat,
dittoSeq (>= 1.1.2)
ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
kableExtra
GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown
BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran,
scater, scds, TENxPBMCData
testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, BiocManager
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, tximportData,
SingleCellExperiment
testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown,
openCyto
Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat,
flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto,
gridExtra
testthat, knitr, rmarkdown, BiocStyle, DepecheR
knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats,
flowClust, openCyto, flowStats, ggcyto
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, 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
edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db,
org.Hs.eg.db, RUnit, BiocGenerics
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
testthat, knitr, rmarkdown, BiocStyle, GCSConnection
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, 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, COMPoissonReg, poibin, SPAtest, survey,
testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr,
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.ce11, BSgenome.Dmelanogaster.UCSC.dm3
(>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Celegans.UCSC.ce11.ensGene,
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, stats, testthat, tibble
ggtree, treeio, ggstar, patchwork, knitr, rmarkdown,
prettydoc, markdown
roxygen2, knitr, rmarkdown, testthat, BiocStyle
testthat, knitr, rmarkdown, BiocStyle, IRanges,
GenomicRanges, pryr
testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat,
MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData, scran
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, 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
knitr, rmarkdown, BiocStyle, clusterProfiler, testthat
SummarizedExperiment, knitr, plotly, RANKS, WGCNA, rmarkdown
knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp,
Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP,
iC10TrainingData, pamr, testthat
RUnit, limma, RColorBrewer, genefilter, edgeR, GSVAdata,
shiny, shinythemes, ggplot2, data.table, plotly
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
BiocStyle, knitr, rmarkdown, formatR, rrBLUP, qqman
DO.db, DT, knitr, RBGL, testthat, Gviz, AnnotationHub,
Rsamtools, IRanges, 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
BiocStyle, knitr, rmarkdown, stringr, testthat
BiocStyle, knitr, HCABrowser, LoomExperiment (>= 1.5.3),
readr
BiocParallel, GenomicRanges, SummarizedExperiment (>=
1.15.1), h5vcData, ExperimentHub, TENxBrainData,
GenomicFeatures, BiocStyle
BiocStyle, testthat, knitr, rmarkdown, seqCNA
parallel, knitr, gdsfmt, SNPRelate, ggplot2, reshape2
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong
org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat
EDASeq, testthat, knitr, rmarkdown, BiocStyle
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
knitr, rmarkdown, msa, ape, testthat, seqinr
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
knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071
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, covr, knitr, BiocStyle, knitcitations, sessioninfo,
rmarkdown, roxygen2, vegan, withr
testthat, BiocStyle, knitr, rmarkdown, scRNAseq,
TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer,
viridis, htmltools
scRNAseq, scater, scran, airway, edgeR, AnnotationDbi,
org.Hs.eg.db, GO.db, KEGGREST, knitr, igraph, rmarkdown,
BiocStyle, htmltools, Rtsne, uwot, testthat (>= 2.1.0), covr
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
knitr, rmarkdown, curatedMetagenomicData, BiocStyle,
testthat, pkgdown, covr, withr
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
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
biomaRt, BiocStyle, DOSE, dendextend, graphics, knitr,
msigdbr, pheatmap, png, pathview, scales, sva, testthat,
amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
rgl, som
BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit,
BiocGenerics
knitr, rmarkdown, BiocStyle, testthat, covr
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
sparseMatrixStats, DelayedMatrixStats, SummarizedExperiment,
testthat (>= 2.1.0)
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, knitr, rmarkdown, fgsea, BiocManager
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
BiocStyle, rmarkdown, brgedata
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0)
covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer,
derfinder, GenomeInfoDb, tools, RefManageR, testthat
shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>=
1.4.0), org.Hs.eg.db, clusterProfiler,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
BiocStyle, covr, knitr, rmarkdown, testthat
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
knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2),
UpSetR
BiocGenerics, GenomicRanges, rtracklayer, Rsamtools,
survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager,
BSgenome, RSQLite
BiocManager, BSgenome, knitr, RMySQL, RUnit
knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
testthat, gss, curatedMetagenomicData
BiocGenerics, graphics (>= 3.5), grDevices (>= 3.5), knitr
(>= 1.11), methods (>= 3.5), stats (>= 3.5), testthat (>=
2.2.1)
BiocStyle, knitr, rmarkdown, RUnit, methylInheritance
rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel,
downloader, R.utils, doParallel, reshape2, JASPAR2020,
TFBSTools, motifmatchr, matrixStats, biomaRt, dorothea, viper,
stageR, BiocFileCache, png, htmltools, knitr, jpeg
knitr, rmarkdown, DSS, bsseq, plotly,
BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38,
MafDb.1Kgenomes.phase3.hs37d5, GenomicScores, Biostrings,
RColorBrewer, GenomeInfoDb, 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, rmarkdown, prettydoc, treeio, tidyverse, testthat, knitr,
nlme, phangorn, DECIPHER, randomForest, biomformat, scales,
yaml
BiocStyle, breastCancerMAINZ, breastCancerNKI,
breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP,
breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit
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, DMRcate, ExperimentHub
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
testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan,
phyloseq, curatedMetagenomicData, genefilter
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM
knitr, testthat, Seurat, ggpubr, foreach, psych,
MultiAssayExperiment, SummarizedExperiment,
SingleCellExperiment, ggrastr
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
grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer,
BiocStyle, knitr
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, preprocessCore
RUnit, BiocGenerics, BiocStyle, knitr, testthat (>= 2.1.0)
BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
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, knitr, rmarkdown, testthat (>= 1.0.2)
testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData,
CAMERA, RPostgres, RMySQL
knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle
BiocStyle, knitr, rmarkdown, testthat, MSstats, covr
BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array,
RaggedExperiment, UpSetR, survival, survminer
knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase,
GEOquery
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges, knitr,
magick, rmarkdown, testthat, TxDb.Mmusculus.UCSC.mm10.knownGene
brgedata, minfi, minfiData, knitr, rmarkdown, testthat,
omicade4, iClusterPlus, GEOquery, MultiAssayExperiment,
BiocStyle, RaggedExperiment
org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Ss.eg.db,
org.Bt.eg.db, org.Ce.eg.db, org.Dm.eg.db, org.Dr.eg.db,
org.Gg.eg.db, org.Xl.eg.db, org.Cf.eg.db, metaboliteIDmapping,
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0)
BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2)
BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr,
phylogram, RColorBrewer, reshape2, rmarkdown, testthat, UpSetR
testthat, BiocStyle, knitr, rmarkdown, survival, XVector,
qpdf, covr
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), ccfindR
(>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr,
rmarkdown
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML
RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
testthat, BiocManager
DSS, Mus.musculus, Homo.sapiens, knitr, rmarkdown
roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown
knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics
testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran,
DropletUtils, igraph, BiocFileCache
paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown,
testthat, cgdsr
curatedTCGAData, TCGAutils, rmarkdown, testthat, knitr
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI,
pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp,
BiocStyle, knitr
BiocStyle, Cairo, knitr, testthat, truncnorm
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
knitr, rmarkdown, BiocStyle, magick, testthat
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, celldex
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.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, mirbase.db, 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
testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA,
ggplot2, ggrepel, car, cowplot
bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools,
GenomicFeatures, annotate
BiocStyle, knitr, rmarkdown, testthat, digest
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat, scran, BiocGenerics, knitr, Biobase, GEOquery,
hgu133a.db, ggplotify, beachmat, RMTstat, ggalt
testthat, faahKO, msdata, knitr, rmarkdown, pander, BiocStyle
knitr, markdown, rmarkdown, BiocStyle, PepsNMRData
BSgenome.Scerevisiae.UCSC.sacCer3,
BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6,
BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr,
knitr, rmarkdown, pkgdown
testthat, lintr, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, data.table
pander, rmarkdown, knitr, knitcitations, crayon, testthat,
BiocGenerics
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet,
dplyr
testthat, knitr, GGally, network, reshape2, ClueR, directPA,
ggplot2, ggpubr
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, covr, tidyverse, testthat (>= 2.3.2)
BiocStyle, knitr, rmarkdown, colr, metap, repmis
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
BiocStyle, knitr, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle
quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
testthat, mockery, BSgenome, BiocManager,
BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, DEXSeq, Rtsne,
ggplot2, tidyr, vdiffr
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
airway, biomaRt, BiocFileCache, broom, Seurat,
SingleCellExperiment, DESeq2, BiocStyle, 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, jsonlite, rmarkdown, testthat
MotifDb, BSgenome, 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
SingleCellExperiment, msdata, ggplot2, gplots, dplyr, limma,
magrittr, DT, shiny, shinydashboard, testthat, knitr,
BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats,
imputeLCMD, pcaMethods, impute, norm
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
gridExtra, knitr, qPLEXdata, testthat, UniProt.ws, vdiffr
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
BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Ecoli.NCBI.20080805
knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle,
testthat (>= 2.1.0), limma, sva
h5vcData, testthat, knitr, optparse,
BSgenome.Hsapiens.UCSC.hg19
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, 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
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, knitr (>=
1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4),
rmarkdown (>= 0.9.5), testthat (>= 2.1.0), covr, pheatmap
BiocStyle, covr, knitcitations, knitr, RefManageR, rmarkdown,
testthat, pryr, interactiveDisplayBase, recount
knitr, testthat, ggplot2, gridExtra, rmarkdown, BiocStyle,
GenomicRanges, limma, ExperimentHub, AnnotationHub
grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager,
BSgenome, RMySQL
GEOquery, rmarkdown, knitr, BiocManager, testthat
BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot
(>= 1.3.2), sessioninfo, DT, 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
testthat, BiocStyle, knitr, rmarkdown, BiocSingular
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
BiocStyle,gplots,RMassBankData, xcms (>= 1.37.1), CAMERA,
RUnit, knitr
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, RnBeads.mm9, 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
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
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, markdown, rmarkdown,
BiocGenerics, SNPRelate
BiocStyle, biomaRt, cowplot, destiny, knitr, scRNAseq,
robustbase, rmarkdown, Rtsne, uwot, NMF, testthat, pheatmap,
Biobase
testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle,
rmarkdown
PCAtools, cowplot, BiocGenerics, knitr, kableExtra
BiocStyle, knitr, rmarkdown, testthat, scRNAseq, bluster
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, knitr, BiocStyle, rmarkdown, patchwork, ggplot2,
matrixStats, impute, scater, sva, uwot
DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0),
covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter,
SingleCellExperiment, microbenchmark
testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq,
dynamicTreeCut, DESeq2, monocle, Biobase, pheatmap, scater
knitr, rmarkdown, BiocStyle, scater, circlize, scales
BiocGenerics, covr, DuoClustering2018, ggplot2, knitr,
rmarkdown, TENxPBMCData, testthat
testthat, LRBase.Hsa.eg.db, LRBase.Mmu.eg.db, LRBaseDbi,
Seurat, scTGIF, Homo.sapiens
BiocStyle, knitr, scRNAseq, rmarkdown, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, Rsamtools, VariantAnnotation
knitr, BiocStyle, rmarkdown, testthat, BiocManager
testthat, edgeR, BiocStyle, knitr, rmarkdown
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, dplyr, tidyr, BiocStyle,
IlluminaHumanMethylation450kmanifest, minfi,
FlowSorted.CordBloodNorway.450k, FlowSorted.Blood.450k,
HDF5Array
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
knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan,
igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics,
clusterProfiler, msigdbr, DOSE, DO.db, reactome.db, flexclust,
BiocManager
BiocStyle, knitr, biomaRt, stringr, monocle
testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq,
Rtsne
testthat, Rsubread, BiocStyle, knitr, lintr, bladderbatch,
xtable, spelling, org.Mm.eg.db, stringr
testthat, knitr, rmarkdown, BiocStyle, BiocGenerics,
SingleCellExperiment, scuttle, scater, scran, scRNAseq,
ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex
BiocGenerics, BiocStyle, clusterExperiment, knitr, mclust,
RColorBrewer, rgl, rmarkdown, testthat, uwot, 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)
knitr, rmarkdown, scRNAseq, BiocStyle, scater, scran,
scuttle, ggplot2, testthat
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, BSgenome.Hsapiens.1000genomes.hs37d5,
BiocStyle, testthat, knitr,
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, data.table,
ExpressionAtlas, DT, reshape2, Biobase, GEOquery, shinyWidgets
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2,
BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0),
rmarkdown, vdiffr, magrittr
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat, covr
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
BiocStyle, covr, cowplot, magick, knitr, limSolve, lme4,
progress, pscl, testthat, preprocessCore, rmarkdown, scDD,
scran, mfa, phenopath, BASiCS (>= 1.7.10), zinbwave, SparseDC,
BiocManager, spelling, igraph, scuttle, BiocSingular,
VariantAnnotation, Biostrings, GenomeInfoDb, GenomicRanges,
IRanges
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
knitr, rmarkdown, LSD, testthat, BiocStyle
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
HDF5Array (>= 1.7.5), annotate, AnnotationDbi, hgu95av2.db,
GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, jsonlite,
rhdf5, airway, BiocStyle, knitr, rmarkdown, RUnit, testthat,
digest
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, grid
testthat, BiocStyle, knitr, rmarkdown, systemPipeR,
systemPipeRdata, networkD3, rhandsontable, zip, callr, pushbar,
fs, openssl, readr, R.utils, DOT, shinyTree, DESeq2,
SummarizedExperiment, glmpca, pheatmap, grid, ape, ggtree,
Rtsne, UpSetR, tidyr, esquisse, cicerone
BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr,
pheatmap, rGREAT, SpectralTAD
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, 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, rmarkdown, 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
BiocStyle, testthat, vctrs, AnnotationDbi, BiocManager,
Rsubread, e1071, edgeR, limma, org.Hs.eg.db, org.Mm.eg.db, sva,
GGally, knitr, qpdf, covr, Seurat, KernSmooth, Rtsne,
S4Vectors, ggplot2, widyr, clusterProfiler, msigdbr, DESeq2,
broom, survival, boot, betareg, tidyHeatmap, pasilla, ggrepel,
devtools, functional
BiocStyle, testthat, knitr, markdown, SingleCellSignalR,
SingleR, scater, scran, tidyHeatmap, igraph, GGally, Matrix,
uwot, celldex, dittoSeq
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat
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,
BiocManager, kableExtra, knitr (>= 1.27), org.Hs.eg.db,
org.Mm.eg.db, testthat, rmarkdown
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, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat,
reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr,
rmarkdown, BiocStyle
topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle,
xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools,
PharmacoGx, xtable
biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr,
htmltools
knitr, rmarkdown, testthat, covr, clusterExperiment
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
testthat, roxygen2, knitr, BiocStyle, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
RColorBrewer, geneplast
Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml
ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
RUnit, plyr, knitr, BiocGenerics, rmarkdown,
BSgenome.Scerevisiae.UCSC.sacCer3,
BSgenome.Athaliana.TAIR.TAIR9
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
knitr, testthat, beachmat, scuttle, scran, BiocParallel,
BiocNeighbors, batchelor
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
knitr, rmarkdown, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
tidyr, testthat
BiocStyle, knitr, testthat, rmarkdown, dplyr
testthat, knitr, rmarkdown, BiocGenerics, RUnit
spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr,
ape, ggtree, processx
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
BiocStyle, testthat, knitr, rmarkdown, scran, scater,
scRNAseq, ggplot2, Rtsne
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager
GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
testthat, covr, knitr, rmarkdown, pkgdown
affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat
knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown,
scater
knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR,
EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi,
ComplexHeatmap, patchwork, testthat (>= 2.1.0)
knitr, rmarkdown, biomaRt, GenomicFeatures, testthat,
ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi,
AnnotationFilter
MSnbase, testthat, BiocStyle, knitr, rmarkdown
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
covr, spelling, testthat, knitr, rmarkdown, BiocStyle,
scRNAseq, HDF5Array, rhdf5
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
rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb
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