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, BiocManager, GO.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
R (>= 3.6.0), SummarizedExperiment, ROCR
methods, grDevices, stats, utils, parallel, edgeR, limma,
AnnotationDbi
R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>=
0.22.1), BSgenome, 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 (>= 2.14.0), rsbml, hyperdraw, LIM,stringr
R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4),
methods, minfi (>= 1.21.0), Biobase, methylumi
R (>= 4.0.0), methods, utils, graphics, stats
R (>= 4.0), reticulate, methods, SummarizedExperiment, knitr
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
R (>= 4.0), 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 (>= 4.1.0), 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 (>= 4.1.0)
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 (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment
R (>= 4.0.0), 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
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), BSgenome.Drerio.UCSC.danRer7, methods
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 (>= 4.1), GenomicRanges, jsonlite, GenomicFeatures, entropy
R (>= 3.7.0), grid, utils, biomaRt, Gviz, psych
R (>= 4.1.0), SummarizedExperiment, RaggedExperiment,
BiocSingular, HDF5Array
R (>= 3.5.0), methods, grid, graphics, stats, grDevices
R (>= 2.10), BiocGenerics, IRanges, GenomicRanges,
BiocParallel
R (>= 2.14), igraph, shiny, arules, methods
R (>= 4.1), BiocGenerics, SummarizedExperiment
R (>= 4.0.0), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
R (>= 2.10), GenomicFeatures, GSEABase (>= 1.24.0)
R (>= 2.10.0), mclust, nor1mix, stats, preprocessCore,
splines, quantreg
R (>= 3.3.0), shiny, shinyjs, CRISPRseek
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
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 (>= 2.59.1), 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 (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=
0.37.0), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),
IRanges (>= 2.17.3)
MatrixGenerics (>= 1.5.3), DelayedArray (>= 0.17.6)
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, rmarkdown
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 (>= 4.1.0), SummarizedExperiment, methods, S4Vectors,
BiocParallel, GenomicRanges, IRanges, fdrtool
R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10)
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)
R (>= 3.5.0), parallel, doParallel, foreach,
SummarizedExperiment, stats
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 (>= 4.0.0), 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
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
(>= 1.21.3)
R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment,
SpatialExperiment, TreeSummarizedExperiment
R (>= 4.1.1), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2
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 (>= 4.1), mclust, BiocParallel, SummarizedExperiment
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, KEGGREST, RCurl, annotate, Biobase (>=
1.12.0), methods, XML, RSQLite, MASS, Heatplus, RColorBrewer
R(>= 3.2), QDNAseq, CGHcall, CGHbase, GenomicRanges
R (>= 4.1), survcomp, biomaRt, iC10, AIMS
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 (>= 3.6), Biobase, NanoStringNCTools, S4Vectors
methods, BiocGenerics, ggplot2 (>= 1.0.0)
R (>= 4.0.0), stats, methods, graphics, GGally, network, sna,
scales, matrixStats
R (>= 3.5), Matrix, MASS, locfdr, stats, utils
R (>= 4.1), 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), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5),
MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
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
R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>=
2.9.1)
R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
R (>= 3.1), methods, Biobase, GenomicRanges, 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 (>= 0.39.2),
S4Vectors (>= 0.29.19)
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, BiocIO
R (>= 4.1), ExperimentHub, AnnotationHub
S4Vectors, adabag, GenomicRanges, R (>= 4.1)
R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm
R (>= 2.10), convert, graph, limma, marray, methods
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
SingleCellExperiment (>= 1.2.0), R(>= 3.5)
SummarizedExperiment (>= 1.20.0), plotly (>= 4.9.3), shiny (>=
1.6.0)
R (>= 3.5), BiocParallel, Matrix, methods, stats, biglm
RUnit, BiocGenerics, BiocParallel, GenomicRanges,
SummarizedExperiment
R (>= 3.3.0), stats, gplots, gtools,graphics,base,
utils,grDevices
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 (>= 4.1.0), BiocParallel, fields, markdown
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 (>= 4.1.0), methylclockData, devtools, quadprog
R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods
Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
R (>= 4.0), SummarizedExperiment, SingleCellExperiment,
TreeSummarizedExperiment (>= 1.99.3), MultiAssayExperiment
R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment,
mia (>= 0.99), ggplot2, ggraph (>= 2.0)
R (>= 4.1), MultiAssayExperiment (>= 1.8.3)
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
R (>= 4.0), SummarizedExperiment, topGO, stats
data.table, parallel, utils, stats, R (>= 4.1)
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), BiocStyle, Rgraphviz, rmarkdown, methods,
minet, mclust, reshape2
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
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 (>= 4.1.0), SummarizedExperiment, S4Vectors
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 4.1), KEGGREST, S4Vectors, SummarizedExperiment, igraph,
data.table, methods, stats
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 (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome,
BiocParallel
R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2, Hmisc
R (>= 4.1.0), SummarizedExperiment (>= 1.3.81)
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 (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges
R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph,
graph, graphite
R (>= 4.1), Biobase, SingleCellExperiment, MAST
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, BiocGenerics, Biostrings
reshape, ggplot2, Biostrings, biovizBase, brew, xtable,
testthat
R (>= 3.5), Biostrings, BiocGenerics,methods
R (>= 4.1), parallel, GenomicRanges, Rbowtie
GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11),
Biostrings (>= 2.47.6), Biobase
R (>= 4.1), GenomicRanges, parallel, doParallel, foreach,
doRNG, methods
R (>= 3.2.1), stats, methods, Rmpfr, gmp
R (>= 3.5.0), methods, GenomicRanges, Rsamtools, baySeq
R (>= 3.2), Biobase, rcellminerData (>= 2.0.0)
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)
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 (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments
R (>= 3.0.2), methods, GenomicRanges, abind
methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix,
grid, lattice
R (>= 4.0), S4Vectors (>= 0.27.12), IRanges (>= 2.23.9),
GenomicRanges, Modstrings
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, BiocStyle, methods,
rmarkdown
methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8),
Biostrings (>= 2.47.6), R (>= 3.5.0)
R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
R (>= 3.3), methods, GenomicRanges (>= 1.37.2)
R (>= 3.4.0), biclust, SummarizedExperiment
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.37.0)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 4.0.0), stringr, ape, Biostrings, DECIPHER, parallel,
reshape2, phangorn, sangerseqR, gridExtra, shiny,
shinydashboard, shinyjs, data.table, plotly, DT, zeallot,
excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx,
tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle,
logger
R (>= 3.4), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 3.6), SingleCellExperiment (>= 1.4), Seurat (>= 2.3.4),
tensorflow, purrr, irlba, Rtsne, ggplot2, methods, utils, FNN
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment
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 (>= 3.4), methods, SummarizedExperiment
R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19
R (>= 3.4), ggplot2, methods, SingleCellExperiment
R (>= 4.0), methods, epivizr, SummarizedExperiment
R (>= 3.0.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
GenomicRanges, ShortRead, stats
R (>= 3.1), AnnotationDbi, GO.db, annotate
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 (>= 4.0), SummarizedExperiment, SingleCellExperiment,
DelayedArray, Biobase
R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
R (>= 3.1), GenomicRanges, Rsamtools, data.table, checkmate
R (>= 3.2.0), BiocGenerics, SummarizedExperiment
R (>= 3.1.0), VariantAnnotation, GenomicRanges, NMF
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 4.0.0), S4Vectors, BiocParallel, ProtGenerics (>=
1.25.1)
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 (>= 3.4), Biobase, BiocParallel, cluster, matrixStats,
stats, graphics, utils
GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R
(>= 4.1.0)
R (>= 3.6), tidyr, SummarizedExperiment, S4Vectors,
BiocGenerics, methods, UpSetR, rlang, stringr, utils,
BiocParallel, ggplot2, mclust, dplyr, digest, sessioninfo,
crayon, tibble
R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3),
GenomicRanges (>= 1.41.5), Biobase
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
GenomicRanges, rtracklayer, VariantAnnotation,
StructuralVariantAnnotation, BiocGenerics, R (>= 4.0)
GenomicRanges, rtracklayer, BiocGenerics,
StructuralVariantAnnotation, R (>= 4.0)
Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1),
methods
R (>= 3.5.1), methods, GenomicRanges, Rsamtools (>= 1.9.2),
ggplot2, plyr, openxlsx
R (>= 3.0), methods, 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), EpiDISH, limma, nnls, quadprog
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, Rcpp
R (>= 2.15.0), methods, limma, sigPathway, anota, DESeq2,
edgeR, RankProd, topGO, org.Hs.eg.db, GOSemSim, Heatplus,
gplots, plotrix, Biobase
R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18),
Biostrings
R (>= 3.5), GenomicRanges, Structstrings
R (>= 3.5), GenomicRanges, Modstrings, Structstrings, tRNA
R (>= 2.15.2), methods, BiocGenerics, Biobase
R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
R (>= 4.0.0), ggplot2, limma, BiocParallel
R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0),
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,
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 (>= 4.0), ChIPpeakAnno,TxDb.Hsapiens.UCSC.hg19.knownGene,
zoo, GenomicRanges, S4Vectors, viper, DiffBind, locfit
R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi,
lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
illuminaio
R (>= 3.2), GenomicRanges (>= 1.31.8), Rsamtools
R (>= 2.5.0), digest, tools, utils, codetools
R (>= 1.8.0), Biobase, affy, multtest, annaffy, vsn, gcrma,
qvalue
R (>= 3.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 3.6.0), GenomicRanges, ggplot2, grid
R (>= 3.4), methods, SummarizedExperiment,
SingleCellExperiment
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
checkmate, 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, KEGGREST (>= 1.30.1), 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
stats, methods, S4Vectors, SummarizedExperiment,
SingleCellExperiment, Matrix, tibble, rlang
SingleCellExperiment, SummarizedExperiment, S4Vectors, scater,
stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue,
dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2,
ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid,
grDevices, graphics, utils, pbapply
Rfast, 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
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, plotROC,
DT, utils, limma, methods, stats, tibble, biomformat, umap,
Matrix, GUniFrac
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), httr
DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors,
interactiveDisplayBase, httr, yaml, dplyr
GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics,
jsonlite, BiocManager, biocViews, BiocCheck, graph,
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,
rapiclient (>= 0.1.3), tibble, tidyselect, tidyr, rlang,
BiocManager
methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr,
dplyr, lubridate, plotly, ggplot2
AnVIL, httr, jsonlite, rmarkdown, yaml, readr, whisker, tools,
utils, stats
GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2,
ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2,
methods, rtracklayer, ensembldb, VariantAnnotation, dplyr,
tidyr, repmis, Rsamtools
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
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
AnnotationDbi, bit64, circlize, cluster, corrplot, data.table,
dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics,
grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db,
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, pbmcapply
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
methods, stats, Matrix, BiocGenerics, BiocParallel, S4Vectors,
IRanges, GenomicRanges, GenomicAlignments, Rsamtools,
GenomeInfoDb, SQUAREM, sparseMatrixStats
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
abind, assertive, BiocFileCache, BiocGenerics, colorspace,
data.table, edgeR, ggplot2, ggrepel, graphics, grDevices, grid,
gridExtra, limma, magrittr, matrixStats, methods,
MultiAssayExperiment, parallel, pcaMethods, rappdirs, rlang,
R.utils, readxl, S4Vectors, scales, stats, stringi,
SummarizedExperiment, tidyr, tools, 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, tidyr,
GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost
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
cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges,
graphics, grDevices, magrittr, plyr, proxy, RColorBrewer,
rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors,
tibble, tidyr, vegan, viridis, utils
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, scuttle, stats, stats4, SummarizedExperiment,
viridis, utils, Matrix, matrixStats, assertthat, reshape2,
BiocParallel, hexbin
utils, methods, parallel, reticulate, dir.expiry,
basilisk.utils
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
DelayedArray, DelayedMatrixStats, BiocParallel, scuttle,
ResidualMatrix, ScaledMatrix, beachmat
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, BiocSingular
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, Rcpp
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
stats, stats4, utils, methods, phyloseq, BiocParallel,
zinbwave, edgeR, DESeq2, limma, ALDEx2, corncob,
SummarizedExperiment, MAST, Seurat, metagenomeSeq, MGLM,
ggplot2, RColorBrewer, plyr, ffpe, reshape2, ggdendro,
graphics, cowplot
GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt,
jsonlite, methods, dplyr, data.table, sjmisc, grDevices,
graphics, stats, utils, rslurm, rhdf5
R.utils, data.table, curl, RCurl, digest, methods, stats,
utils, dplyr, RSQLite, graph, Biobase,
stats, utils, GEOquery, graphics, BiocGenerics, illuminaio
tidyr, matrixStats, stats, ggplot2, methods, rtracklayer,
S4Vectors, ggforce
DT (>= 0.3), dplyr (>= 0.7.2), shiny (>= 1.0.5), AlgDesign (>=
1.1.7.3), import (>= 1.1.0), methods, AnnotationDbi,
shinythemes, Biobase, geNetClassifier, org.Hs.eg.db,
org.Bt.eg.db, DOSE, clusterProfiler, reactome.db, ReactomePA,
DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr, tibble,
GO.db
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,
filelock, curl, httr
Rgraphviz, geneplotter, graph, BiocGenerics, methods
Rcpp, S4Vectors, BiocParallel, stats, methods, Matrix
ComplexHeatmap, S4Vectors, bigrquery, shiny, stats, httr,
rjson, dplyr, magrittr, grid, DT, GenomicRanges, IRanges,
ggplot2, SummarizedExperiment, DBI, GenomicFeatures,
curatedTCGAData, scales, ggpubr, plyr, car, graph, Rgraphviz
stats, utils, futile.logger, parallel, snow
BiocFileCache, BiocManager, biocViews, tibble, magrittr,
methods, rlang, tidyselect, stringr, rvest, dplyr, xml2, readr,
httr, htmltools, DT, tools, utils, igraph, tidyr, jsonlite, gh,
RBGL, graph
methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO,
AnnotationDbi, KEGGREST, ontologyIndex, tidyr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, 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
BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, jsonlite,
lgr, lifecycle, methods, openssl, plyr, progress, rappdirs,
stats, stringr, tools, withr, yaml
utils, XML, AnnotationDbi, progress, stringr, httr, digest,
BiocFileCache, rappdirs, xml2
stats, utils, grDevices, lattice, BiocParallel, glmnet, rms,
precrec, nsprcomp, ranger, e1071, ggplot2, vioplot, CMplot,
imager, topGO, xlsx
WGCNA, dynamicTreeCut, matrixStats, DESeq2, sva, RColorBrewer,
ComplexHeatmap, ggplot2, reshape2, igraph, ggnetwork,
intergraph, networkD3, ggnewscale, ggpubr, NetRep, stats,
grDevices, graphics, utils, methods, BiocParallel, minet,
GENIE3, SummarizedExperiment
igraph (>= 1.0.1), AnnotationDbi, Biobase
BiocParallel, RJSONIO, whisker, yaml, pheatmap, ggplot2, plyr,
utils, stats, RColorBrewer, Hmisc, psych, knitr, rmarkdown,
markdown
BiocFileCache, GEOquery, graph, methods, utils
methods, utils, grDevices, graphics, stats, crayon
igraph, cluster, psych, stringr, GenomicRanges, Hmisc, MASS
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, 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
SummarizedExperiment, ExperimentHub, methods, grid, graphics,
stats, grDevices, circlize, testthat, ComplexHeatmap(>=
1.99.8), ggplot2, matrixStats, gtools, reshape2,
preprocessCore, randomcoloR, V8, limma
stats, methods, utils, cluster, Matrix, Rcpp, igraph,
S4Vectors, BiocParallel, BiocNeighbors
Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb,
S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage,
utils
CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
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,
shiny
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 (>= 1.19.11), 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
utils, methods, Matrix, S4Vectors, IRanges
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
SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
grDevices, methods, stats, utils
affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase
ggplot2, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges,
reshape2, methods, BioNERO
BiocGenerics, BiocParallel, BSgenome, data.table,
DelayedArray, DelayedMatrixStats, formula.tools, GenomeInfoDb,
GenomicAlignments, GenomicRanges (>= 1.37.16), ggplot2 (>=
2.2.0), gtools, IRanges (>= 2.18.0), KernSmooth, memoise, plyr,
Rsamtools, reshape2, 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
iCluster, cluster, impute, limma, ConsensusClusterPlus,
grDevices, survival
Biobase, dplyr, irlba, lattice, Matrix, matter, magrittr,
mclust, nlme, parallel, signal, sp, stats4, utils, viridisLite
readr, stringr, lpSolve, igraph, dplyr, rjson, rmarkdown,
methods
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, openxlsx
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
utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite,
rapportools, basilisk, reticulate, shinyBS, shinycssloaders,
rintrojs, markdown
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, S4Vectors, data.table, Rcpp, RcppEigen, uwot,
enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne,
withr, scater (>= 1.14.4), scran, SingleCellExperiment, dbscan,
DelayedArray, 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, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr,
ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings
(>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
BiocGenerics, BiocFileCache, BiocParallel, dplyr, rlang, glue,
memoise, purrr (>= 0.3.0), rappdirs, tidyr, tidyselect,
lubridate
Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater,
stringr, irlba, data.table, glue, pbapply, umap, Rtsne,
reticulate, fastmatch, matrixStats, ggplot2, BiocParallel,
SummarizedExperiment, fgsea
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
tiff, graphics, stats, utils, reshape2, parallel, doParallel,
grDevices, matrixStats, FME, SpatialTools, sp, vioplot,
FactoMineR, Hmisc
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
BiocParallel, broom.mixed, dirmult, dplyr, edgeR,
fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp,
purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment,
survival, tibble, tidyr, utils
DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors,
methods, SingleCellExperiment, SummarizedExperiment, ggplot2,
rlang, grDevices, patchwork, reshape2, BiocParallel, stats
furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr,
future, stats
circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr,
GenomicTools, GenomicTools.fileHandler, GGally, ggnetwork,
ggplot2, ggpubr, ggrepel, graphics, grid, igraph, Matrix,
network, Rcpp, RCy3, stats, SummarizedExperiment, S4Vectors,
utils
Rsamtools, GenomeInfoDb, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
Biobase, CGHbase, CGHcall, methods, stats, utils
BiocGenerics, zlibbioc, Rcpp (>= 0.11.0)
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
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, checkmate, 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, InteractionSet, 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
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
graphics, stats, utils, methods, survival
Biobase (>= 2.17.8), graphics, grDevices, methods, stats,
IRanges, rtracklayer, GenomicRanges
shiny, colourpicker, shinyjs, rtracklayer, shinyFiles,
shinyhelper, shinyWidgets, shinydashboardPlus, shinycssloaders,
Matrix, plotly, shinydashboard, colorRamps, kableExtra,
viridis, batchelor, BiocParallel, parallel, Rsamtools, ggplot2,
qualV, stringdist, fs, qs, DT, scran, scater,
ConsensusClusterPlus, Rtsne, dplyr, tidyr, GenomicRanges,
IRanges, irlba, rlist, umap, tibble, methods, jsonlite, edgeR,
stats, graphics, grDevices, utils, S4Vectors,
SingleCellExperiment, SummarizedExperiment, msigdbr, Sushi,
forcats, Rcpp, coop, matrixTests, DelayedArray
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
dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork,
ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat,
tidygraph, expm, Matrix
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
locfit, grid, utils, plyr, MultiAssayExperiment (>= 1.6.0)
BSgenome, GenomicRanges, seqinr, e1071, Biostrings,
GenomeInfoDb, IRanges, utils, stringr, stats
methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor, RBGL
dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome,
Biostrings, utils
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,
BiocSingular, 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, stats, tidyr, utils, yulab.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, utils
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
dplyr, stats, utils, grDevices, plotly, karyoploteR,
CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics
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
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
BiocManager, rmarkdown, GenomeInfoDb, S4Vectors,
AnnotationDbi, graphics, stats, utils, methods, magrittr,
ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene
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, foreach, doParallel,
irlba
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
GenomicRanges, parallel, grid, ggplot2, reshape2, scales,
DelayedArray, rtracklayer, DelayedMatrixStats, Matrix, RMTstat
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, caTools, grid, KernSmooth, MASS, ggplot2,
stringr, modeest, edgeR, limma, vioplot, methods, utils, stats,
grDevices, graphics
circlize (>= 0.4.5), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,
matrixStats, foreach, doParallel
data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr,
rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio,
scales, shinydashboard, shinyjs, stats, tibble, grid
org.Hs.eg.db, org.Mm.eg.db, dbscan, fpc, factoextra, Biobase,
BiocFileCache, parallel, doParallel, foreach,
SummarizedExperiment, biomaRt, AnnotationDbi, methods, dplyr,
scran, scater, pheatmap, ggplot2, gridExtra,
SingleCellExperiment, stats, utils, scales, grDevices,
graphics, Rtsne, GEOquery, clusterProfiler, stringr, tools,
rlang, DT
slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment,
SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume
(>= 0.9.1), methods, pbapply, matrixStats, BiocParallel,
TrajectoryUtils, igraph
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
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, MultiAssayExperiment, MatrixGenerics,
piano, BiocParallel, BumpyMatrix, checkmate, methods, stats,
utils, graphics, grDevices, lsa, data.table, crayon, glue,
rlang
ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix,
methods, MultiAssayExperiment, pals, SingleCellExperiment,
SummarizedExperiment, transport
edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2,
scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics,
stats, methods, compositions, mvtnorm
AnnotationDbi, biomaRt, CARNIVAL, dorothea, dplyr, ggplot2,
GSEABase, igraph, magrittr, org.Hs.eg.db, plyr, purrr, readr,
rlang, scales, stringr, tibble, utils, visNetwork
rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr,
ggplot2, grDevices, tools, SummarizedExperiment, genefilter,
DT, GenomeInfoDbData, caTools, randtests, stats, utils, methods
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, methods,
S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod,
utils
WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2,
grDevices, stats, utils
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache
Biobase, BiocGenerics, graphics, grDevices, igraph, Matrix,
methods, utils, sincell, TSCAN
AnnotationDbi, AnnotationHub, binr, cowplot, data.table,
dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics,
highcharter, htmltools, httr, limma, methods, parallel,
pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang,
scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble,
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
Biobase, flowCore, flowDensity, flowClust, cytometree,
ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats,
utils
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
CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods,
rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix,
SummarizedExperiment, tibble, tidyr
stats, methods, BiocParallel, RColorBrewer, cowplot,
doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr,
mbest, pheatmap, speedglm, stringr, strucchange, tibble,
ggrepel, MASS, logging, Matrix, tidyr, caret, rlang, grDevices
Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap,
circlize, ashr, data.table, BiocParallel, dplyr, stats,
magrittr, rlang, S4Vectors
S4Vectors, BiocParallel, HDF5Array, DelayedArray,
RColorBrewer, viridis, utils, SummarizedExperiment, tools,
graphics, raster, grDevices, stats, ggplot2, ggbeeswarm,
svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5
cytolib(>= 2.3.10), 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
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 (>= 1.1), forcats, methods, DAPARdata (>=
1.24.0), siggenes, graph, lme4, readxl, highcharter,
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, ggplot2, ggpubr,
ggrepel, grid, IRanges, magrittr, megadepth, methods,
plyranges, readr, reticulate, rtracklayer, S4Vectors, stringr,
SummarizedExperiment, tidyr
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
stats, methods, assertthat, graph, pcalg, purrr, tidyverse,
Matrix, ggraph, tidygraph, ggplot2, rlang, expm, MASS,
CombinePValue, edgeR, epiNEM, igraph, metap, mnem, naturalsort,
ppcor, glm2, graphite, reshape2, dplyr, glue, Rgraphviz,
harmonicmeanp, org.Hs.eg.db, logger
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
ggplot2, KernSmooth, matrixStats, methods, patchwork,
parallel, pbapply, stats, statmod, survey, viridisLite
methods, rJava, BiocParallel, stats, Biobase,
SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2,
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, readxl
broom, dplyr, magrittr, Matrix, purrr, rlang, stats, stringr,
tibble, tidyr, tidyselect, withr
GenomicRanges, data.table, stringr, diffr, dplyr, methods,
rjson, utils, R.utils, foreach, withr, rtracklayer,
GenomeInfoDb, settings, filehash
tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers,
webchem, purrr, ttgsea, PRROC, reticulate, stats
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 (>= 0.60.0), sparseMatrixStats, Matrix,
S4Vectors (>= 0.17.5), IRanges (>= 2.25.10)
methods, utils, DelayedArray, HDF5Array, BiocSingular,
rTensor, DelayedRandomArray, irlba, Matrix, einsum,
IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2,
tictoc
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)
methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp
(>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba,
pcaMethods, Biobase, BiocGenerics, SummarizedExperiment,
SingleCellExperiment, ggplot2, ggplot.multistats, tidyr,
tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW,
smoother, scales, scatterplot3d
graph, igraph, RBGL, circlize, limma, edgeR, EBSeq, NBPSeq,
stats, grDevices, graphics, pheatmap, utils, ggplot2, Matrix,
jsonlite, tools, DESeq2, methods
BiocGenerics, data.table(>= 1.11.8), GenomeInfoDb,
GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats,
utils
Biobase, GEOquery, impute, limma, pheatmap, plyr, scales,
snpStats, sva, swamp, stats, methods, utils, bnstruct
BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
zoo (>= 1.8-3), data.table, magrittr, dplyr, tidyr, rlang, mzR
(>= 2.18), signal, bit64, reticulate, ggplot2, RSQLite, DBI,
ape, phangorn, pracma, RMSNumpress, 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
S4Vectors, SummarizedExperiment, limma, edgeR, DEXSeq,
GenomicRanges, Rsubread, ggplot2, rtracklayer, ComplexHeatmap,
ggrepel, stringi, methods, stats, GenomeInfoDb, dplyr,
matrixStats, IRanges, ensembldb, viridisLite
BiocParallel, BiocSingular, SummarizedExperiment,
SingleCellExperiment, S4Vectors, Matrix, Seurat, matrixStats,
parallel, scran, grDevices, stats, methods
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, 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
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,
IRanges, GenomicRanges, SummarizedExperiment, BiocParallel,
DelayedArray, DelayedMatrixStats, HDF5Array, rhdf5, edgeR,
R.utils, dqrng, beachmat, scuttle
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
utils, graphics, stats, splines, DelayedArray
zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors,
rlang, grDevices, stats, utils
BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr,
tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode
progeny, easierData, dorothea (>= 1.0.0), quantiseqr, ROCR,
grDevices, stats, graphics, ggplot2, grid, DESeq2, utils,
dplyr, matrixStats, rlang, arules, BiocParallel, reshape2,
rstatix, ggrepel, coin
Biobase (>= 2.50.0), BiocFileCache (>= 1.14.0), BiocGenerics
(>= 0.36.0), BiocParallel (>= 1.24.1), biomaRt (>= 2.46.0),
Biostrings (>= 2.58.0), edgeR (>= 3.32.0), GenomeInfoDb (>=
1.26.0), genomeIntervals (>= 1.46.0), GenomicAlignments (>=
1.26.0), GenomicRanges (>= 1.42.0), SummarizedExperiment (>=
1.20.0), graphics, IRanges (>= 2.24.0), LSD (>= 4.1-0), locfit,
methods, parallel, rappdirs (>= 0.3.1), Rsamtools (>= 2.6.0),
S4Vectors (>= 0.28.0), ShortRead (>= 1.48.0), 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
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, 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),
htmlwidgets, plotly, DT
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, RcppAnnoy (>= 0.0.9)
graphics, stats, GenomicRanges, S4Vectors, IRanges, limma,
edgeR, methods, SummarizedExperiment, BiocGenerics, 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
BiocGenerics, Biostrings, BSgenome, BiocParallel,
BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges,
jsonlite, motifmatchr, Matrix, rtracklayer, Rcpp, S4Vectors,
stats, utils
foreach, doParallel, parallel, stats, survivalROC, glmnet,
rms, mboost, survivalsvm, ggplot2,
IlluminaHumanMethylation450kanno.ilmn12.hg19, minfi, boot,
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
aplot, DOSE (>= 3.16.0), ggplot2, ggraph, graphics, grid,
igraph, methods, plyr, purrr, RColorBrewer, reshape2, stats,
utils, scatterpie, shadowtext, GOSemSim, magrittr, ggtree,
yulab.utils (>= 0.0.4)
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
stats, methods, utils, GenomicRanges, BiocGenerics,
GenomeInfoDb, SummarizedExperiment, VariantAnnotation, stringi,
data.table
EnvStats, ggplot2, rtracklayer, GenomicRanges, IRanges,
rstatix, ggpubr, methods, stats, utils, dplyr
MASS, e1071, quadprog, parallel, stats, matrixStats, stringr,
locfdr, Matrix
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
Rcpp, magrittr, data.table, SummarizedExperiment, methods,
GenomeInfoDb, GenomicRanges, rtracklayer, IRanges, Rsamtools,
bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5,
Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap,
grDevices
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, latex2exp
GenomicRanges, BiocGenerics, S4Vectors, IRanges, viridisLite,
graphics, plotrix, grDevices, stats
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, Biostrings,
glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport
AnnotationHub, ewceData, ExperimentHub, ggplot2, grDevices,
grid, reshape2, biomaRt, limma, stringr, cowplot, HGNChelper,
ggdendro, gridExtra, Matrix, methods, parallel, future, scales,
SummarizedExperiment, stats, utils
utils, S4Vectors, BiocManager, curl, rappdirs
methods, ExperimentHub, BiocManager, DBI, httr, curl
shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr,
magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales,
tibble, MASS, limma, S4Vectors, shinyjs
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, Matrix
stats, plyr, VariantAnnotation, SummarizedExperiment,
rtracklayer, GenomicRanges, methods, IRanges, foreach,
doParallel, parallel
tcltk, graphics, grDevices, stats, utils
SingleCellExperiment, methods, stats, utils, irlba, TSCAN,
SC3, matrixStats
openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes,
forcats, RColorBrewer, RCy3, utils, stats
methods, igraph, Matrix, KEGGREST, plyr, stats, graphics,
utils
Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache,
curl
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
withr, BiocGenerics, GenomeInfoDb, rtracklayer, S4Vectors,
GenomicFeatures, dplyr, rlang, patchwork, ggplot2,
BiocParallel, qvalue, stringr, utils, stats, ggrepel, tibble,
tidyr, SummarizedExperiment, MultiAssayExperiment, IRanges,
progress, purrr, glmnet, methods
graphics, stats, utils, methods, abind, gtools, qvalue,
S4Vectors, SummarizedExperiment, matrixStats, svMisc, Rcpp,
Matrix, SingleCellExperiment, jsonlite
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
gplots, graphics, MASS, methods, SparseM, stats, utils
basilisk, reticulate, SingleCellExperiment,
SummarizedExperiment, Rsamtools, utils, zlibbioc, scater,
dplyr, tidyr, magrittr, S4Vectors, scuttle, stats
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 (>=
2.3.4), 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
effsize, furrr, future, purrr, ggiraph, ggrepel, ggplot2,
igraph, Matrix, matrixStats, stats, utils, visNetwork,
htmlwidgets, grDevices, methods, stringr, stringi, Rdpack,
data.table (>= 1.9.5), gridExtra,
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, BiocGenerics, colorRamps, ConsensusClusterPlus,
CytoML, dplyr, flowCore, flowWorkspace, ggforce, ggnewscale,
ggplot2, ggpointdensity, ggpubr, ggrepel, grDevices, magrittr,
methods, pheatmap, RColorBrewer, rlang, Rtsne, tidyr, XML,
scattermore
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 (>= 2.3.9), 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), DelayedArray, S4Vectors
RUnit, methods, ChemmineR, BiocGenerics, parallel
clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr,
ontologyIndex, purrr, RecordLinkage, stringr, textclean,
tictoc, tidygraph, tidyr, vroom
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,
SummarizedExperiment, grid, rmarkdown, grDevices, graphics,
methods, ComplexHeatmap, stats, utils, parallel
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, AnnotationDbi, annotate, Biobase, graphics,
methods, stats, survival, grDevices
amap, impute, mclust, limma, graphics, stats, utils
snpStats, mvtnorm, Rsamtools, igraph, kernlab, FactoMineR,
IRanges, GenomicRanges, data.table,grDevices, graphics,stats,
utils, methods
plyr, graph, htmlwidgets, Rgraphviz, rjson, XML, methods,
grDevices, stats, graphics
igraph, snow, ape, grDevices, graphics, stats, utils,
data.table
AnnotationDbi, graphics, grDevices, grid, RColorBrewer, stats,
utils
S4Vectors (>= 0.9.25), Biobase (>= 2.5.5), affxparser,
RColorBrewer, Biostrings
Biobase, BiocGenerics, BiocParallel, GWASTools, gdsfmt,
GenomicRanges, IRanges, S4Vectors, SeqArray, SeqVarTools,
SNPRelate, data.table, graphics, grDevices, igraph, Matrix,
methods, reshape2, stats, utils
AnnotationDbi, backbone, bs4Dash (>= 2.0.0), circlize,
colorspace, colourpicker, 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, shinyAce, shinycssloaders, shinyWidgets, stats,
SummarizedExperiment, tidyr, tippy, 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), 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
data.table, ggplot2, reshape2, methods, utils, Biostrings,
plyr, dplyr, GenomeInfoDb
methods, utils, stats, tools, DBI, RSQLite (>= 2.0), RCurl,
XVector (>= 0.19.7), Biostrings (>= 2.47.6), BiocIO,
rtracklayer (>= 1.51.5), 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
ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr,
dplyr, plotly, BiocFileCache, grid, flextable
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
ggplot2, rtracklayer, BiocGenerics, GenomicRanges,
GenomeInfoDb, IRanges, methods, BiocParallel, graphics, stats
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
Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods,
graphics, stats, testthat, GeomxTools, NanoStringNCTools
DT, htmltools, factoextra, heatmaply, maptools, pheatmap,
scales, shinyHeatmaply, shinybusy, ggplot2, stringr, umap,
GEOquery, impute, grDevices, stats, graphics, utils
xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
BiocGenerics, rjson, readxl, EnvStats, reshape2, methods,
utils, stats, data.table, outliers, lmerTest, dplyr
httr, readr (>= 1.3.1), xml2, dplyr, data.table, tidyr,
magrittr, R.utils, 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
grDevices, graphics, methods, stats, utils, dbscan,
fastcluster, matrixStats
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
Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot,
RColorBrewer, ggalt, ggforce, dplyr, R4RNA, grDevices,
seqmagick, grid, methods
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
ggside, grid, methods, stats
ape, aplot (>= 0.0.4), dplyr, ggplot2 (>= 3.0.0), grid,
magrittr, methods, purrr, rlang, ggfun, yulab.utils, tidyr,
tidytree (>= 0.2.6), treeio (>= 1.8.0), utils, scales
ggplot2, utils, rlang, ggnewscale, stats, ggtree
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, BiocGenerics, methods, stats,
utils, splines
SummarizedExperiment, biomaRt, futile.logger, sparsebn,
sparsebnUtils, forcats, dplyr, glue, readr, httr, ggplot2,
survminer, reshape2, stringr, parallel, methods, loose.rock (>=
1.0.12)
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
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
cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify,
grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap,
purrr, rlang, stats, tibble, tidyr, utils
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, checkmate, graph (>= 1.67.1), httr, rappdirs,
stats, utils, graphics
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, S4Vectors, IRanges, Biobase,
SummarizedExperiment, GSEABase, Matrix, parallel, BiocParallel,
SingleCellExperiment, sparseMatrixStats, DelayedArray,
DelayedMatrixStats, HDF5Array, BiocSingular
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, AnnotationHub
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
httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache,
tools, utils, digest
utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>=
0.31.5), S4Vectors, IRanges
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, GenomeInfoDb
Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape,
dendextend, ggplot2, mclust, patchwork, dplyr, grDevices,
methods, stats
foreach, iterators, rtracklayer, dplyr, BSgenome, ggplot2,
scales, methods
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, QDNAseq,
KernSmooth, methods, utils, graphics, pheatmap, gtools, 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
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
dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble,
utils, stringr, magrittr, caret, corrplot, ggplot2, pROC,
PRROC, igraph, graphics, stats, purrr, grDevices, protr
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices,
graphics, methods
available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager,
utils
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, rlang, 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, grid, 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
S4Vectors, stats, utils, SummarizedExperiment, methods,
pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind,
BiocParallel, viridis, dplyr, magrittr, DT, igraph,
SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph,
tidygraph, ggplot2, data.table, sf, concaveman
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
stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
xml2, maps, rlang
graphics, grDevices, RColorBrewer, gplots, futile.logger,
stats, utils, methods, ape, phyclust, Matrix, fastcluster,
dplyr, HiddenMarkov, ggplot2, edgeR, coin, caTools, digest,
RANN, leiden, 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, preprocessCore,
IRanges, GenomeInfoDb, depmixS4, limma, BiocParallel,
Biostrings, dplyr, magrittr, plyranges, readr, RSQLite, DBI,
purrr, GenomicFeatures, ggplot2, reshape2
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
ComplexHeatmap (>= 2.7.10), grDevices, stats, shiny, grid,
GetoptLong, S4Vectors (>= 0.26.1), digest, IRanges, kableExtra
(>= 1.3.1), utils, svglite, htmltools, clisymbols, jsonlite,
RColorBrewer, fontawesome
interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer,
ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi
config, golem, shiny, DT, shinydashboard, shinyFiles,
shinycssloaders, data.table, fs, dplyr, tidyr, circlize,
colourpicker, dendextend, factoextra, ggplot2, plotly, plyr,
shinyFeedback, shinyalert, tibble, umap, visNetwork,
wordcloud2, readxl, htmlwidgets, colorspace, signal, scales,
htmltools, ComplexHeatmap, grDevices, stats, tools, utils,
biomaRt, rlang, fmsb, igraph
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
Rcpp (>= 1.0.0), MCL, anocva, Polychrome, RColorBrewer,
colorspace, AnnotationDbi, ggplot2, org.Hs.eg.db, org.Mm.eg.db,
pheatmap, AdaptGauss, DEsingle,DrImpute, Matrix, Seurat,
SingleCellExperiment, clusterProfiler, ggpubr, ggraph, igraph,
mixtools, scater, scran, stats, methods, grDevices, graphics,
utils, knitr
utils, dplyr, readr, tidyr, purrr, rlang, tibble,
BiocParallel, stringr, fs, lubridate, lifecycle, ggplot2,
ggrepel, stats, psych, data.table, readxl, tools, Rcapture,
grDevices, zip
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, IRanges, shiny, SummarizedExperiment,
SingleCellExperiment, ggplot2, DT, stats, colourpicker,
shinyAce
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, Biobase
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, Rgraphviz
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
data.tree, 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
ggplot2, class, concaveman, grid, BiocParallel, spatstat.core,
spatstat.geom, BiocGenerics, S4Vectors, methods, spicyR, purrr,
stats, data.table, dplyr, tidyr
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
BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
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
dplyr, rtracklayer, BSgenome, Biostrings, utils, methods,
IRanges, ExperimentHub
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, grDevices,
stats, utils, glmmTMB, MASS, cplm, pscl, lme4
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, grDevices, methods, RColorBrewer, Rhtslib,
survival
doParallel, igraph, bigstatsr, rjson, plyr, data.table,
UpSetR, reshape2, jsonlite, methods, ff, argparse, impute,
RnBeads.hg19, utils, stats
Biobase, clusterProfiler (>= 3.16.1), enrichplot, gridExtra,
ggplot2, ggrepel, grDevices, grid, reshape2, stats, utils
caret, parallel, doParallel, foreach, e1071, future.apply,
future, missForest, pcaMethods, tidyverse, stats, utils,
methods, SummarizedExperiment, S4Vectors
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, 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, xml2, RCurl, ggplot2, PairedData,
rmarkdown
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
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, dplyr, magrittr
data.table, parallel, ROCR, matrixcalc, mclust, ggplot2,
doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm,
truncnorm, assertthat, BiocStyle, stats, utils
Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2,
ggseqlogo, magrittr, matrixStats, methods, patchwork, processx,
purrr, rlang, readr, stats, tools, tibble, tidyr, utils,
usethis, universalmotif (>= 1.9.3), xml2
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, DOSE, enrichplot, GOSemSim, methods, utils,
AnnotationHub, MeSHDbi, yulab.utils
markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils,
fdrtool, MeSHDbi, 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, tidyr
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,
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
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, utils
rtracklayer, DelayedArray, HDF5Array, BSgenome,
DelayedMatrixStats, parallel, methods, ggplot2, matrixStats,
graphics, stats, utils, GenomicRanges, IRanges
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
Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute,
PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2,
ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr,
preprocessCore, dynamicTreeCut
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
shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings,
Rfast, grDevices, graphics, stats, utils, tools, methods,
shinyFiles, data.table, SummarizedExperiment
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,
GenomicFeatures
methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack,
MCMCglmm, coda, magrittr, tibble, Biobase
methods, stats, utils, MASS, ape, decontam, vegan,
BiocGenerics, S4Vectors, IRanges, Biostrings, DECIPHER,
BiocParallel, DelayedArray, DelayedMatrixStats, scuttle,
scater, DirichletMultinomial, rlang, dplyr, tibble, tidyr
methods, stats, S4Vectors, BiocGenerics, BiocParallel,
DelayedArray, scater, ggtree, ggnewscale, viridis, tibble,
tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape,
DirichletMultinomial
dplyr, reshape2, Rtsne, scales, stats, tibble, tidyr, utils,
vegan
graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply,
stats, phyloseq, metagenomeSeq, Biobase
shinyjs (>= 2.0.0), shinydashboard, shinycssloaders,
shinyWidgets, rmarkdown (>= 1.9.0), DESeq2, RColorBrewer,
dplyr, tidyr, purrr, 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)
dplyr, phyloseq, magrittr, purrr, MASS, utils, ggplot2,
tibble, rlang, stats, coin, ggtree, tidytree, methods, IRanges,
tidyr, patchwork, ggsignif, metagenomeSeq, DESeq2, edgeR,
BiocGenerics, Biostrings, yaml, biomformat, S4Vectors, Biobase,
ComplexHeatmap, ANCOMBC, caret, limma, ALDEx2, multtest,
plotROC
clusterProfiler (>= 4.0.2), config, DT, enrichplot, golem,
magrittr, shiny (>= 1.6.0), shinyWidgets, shinycustomloader,
htmltools, ggplot2, graphics, utils
ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel,
vegan, zoo, ggtree, tidytree (>= 0.3.5), MASS, methods, rlang,
tibble, grDevices, stats, utils, coin, ggsignif, patchwork,
ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>=
1.17.2), pillar, dtplyr, ggtreeExtra
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
BiocNeighbors, SingleCellExperiment, Matrix (>= 1.3-0),
S4Vectors, stats, stringr, methods, igraph, irlba, cowplot,
BiocParallel, BiocSingular, limma, ggplot2, tibble,
matrixStats, ggraph, gtools, SummarizedExperiment, patchwork,
tidyr, dplyr, ggrepel, ggbeeswarm, RColorBrewer, grDevices
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
methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
biganalytics, stringr, Hmisc, utils
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, gplots, glmnet, impute, limma,
pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc,
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
purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap,
reshape2, corrplot, grDevices, graphics, stats, utils,
data.table, R.utils
AnnotationDbi, BiasedUrn, Biobase, BiocGenerics,
GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICmanifest, IRanges, limma, methods,
methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors, statmod,
stringr, SummarizedExperiment
assertthat, caret, deldir, digest, distances, dplyr, filelock,
furrr (>= 0.2.0), ggplot2, MASS, purrr, ranger, readr, rlang,
rlist, R.utils, stats, stringr, tibble, tidyr, withr
stats, grDevices, graphics, utils, MASS, plyr, reshape2,
parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2,
gplots, beeswarm, echarts4r
reshape2, GenomicRanges, pheatmap, deepSNV, grDevices,
graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods,
ggplot2
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, magrittr
AnnotationDbi, gplots, graphics, stats, utils
testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma,
Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq,
xtable
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, ggplot2, wesanderson
S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics,
methods, grDevices, reshape2, NMI, zoo, ClusterR, splines,
matrixStats
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges,
XVector, stringi, stringr, crayon, grDevices
rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods,
RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array,
grDevices, stats, magrittr, forcats, utils, corrplot,
DelayedArray, Rtsne, uwot, basilisk, stringi
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
methods, stats, utils, grDevices, graphics, BiocGenerics,
GenomicRanges, TFBSTools, Biostrings, IRanges, stabs, BSgenome,
glmnet, S4Vectors, SummarizedExperiment, BiocParallel, grid,
circlize, ComplexHeatmap (>= 2.0.0), XVector, GenomeInfoDb,
tools, vioplot
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
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
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
ggplot2, readr, magrittr, dplyr, purrr, reshape2, gridExtra,
utils, stringr, ggpubr, stats, cowplot, RColorBrewer, ggridges,
tidyr, scales, grid, rlang, ggforce, grDevices, gtable, plyr,
knitr, rmarkdown, ggrepel, gghalves, tools
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
BiocParallel, S4Vectors, IRanges, methods, ProtGenerics,
MsCoreUtils, DBI, utils
BiocParallel, S4Vectors, IRanges, MsCoreUtils, methods, stats
MsCoreUtils, S4Vectors, IRanges, rawrr (>= 1.1.14), utils,
BiocParallel
methods, ProtGenerics (>= 1.23.5), MsCoreUtils,
SummarizedExperiment, stats
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, limma, mvtnorm, tidyr,
dplyr
MsCoreUtils, BiocParallel, IRanges (>= 2.13.28), plyr, 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,
missForest
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite,
uuid, jsonlite
stats, methods, lme4, purrr, BiocParallel, Matrix, MASS,
limma, SummarizedExperiment, codetools
MSstatsConvert, data.table, checkmate, MASS, limma, lme4,
preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel,
gplots, marray, stats, grDevices, graphics, methods
data.table, log4r, methods, checkmate, utils, stringi
dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp,
checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse,
scales, stats
minpack.lm, ggplot2, utils, stats, grDevices
dplyr, gridExtra, stringr, stats, ggplot2, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid
ggplot2, BiocParallel, caret, gridExtra, reshape2, stats,
utils, grDevices, graphics, MSstats
limma, lme4, lmerTest, methods, data.table, stats, utils,
ggplot2, grDevices, graphics, MSstats, MSstatsConvert,
checkmate
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, plotrix
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, GenomicRanges, graphics, stats, utils,
pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation
stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 1.2), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, parallel, doParallel, foreach, grDevices, graphics,
utils, SummarizedExperiment, stats
golem, config, R6, shiny, shinydashboard, DT, dplyr, stringr,
anyLib, caret, biosigner, mixOmics, stats, DESeq2,
clusterProfiler, rWikiPathways, ReactomePA, enrichplot, ppcor,
metap, infotheo, igraph, networkD3, easyPubMed, utils,
htmltools, rmarkdown
stats, utils, methods, igraph, Matrix, BiocGenerics,
BiocParallel, IRanges, S4Vectors, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, BiocNeighbors,
BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran,
batchelor, uwot
magrittr, data.table, utils, R.utils, dplyr, stats,
GenomicRanges, GenomeInfoDb, BSgenome, Biostrings,
VariantAnnotation, stringr, googleAuthR, httr, jsonlite,
methods, parallel, rtracklayer, RCurl
BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr,
edgeR, ggplot2, glmmTMB, grDevices, grid, limma, lmerTest,
lme4, Matrix, matrixStats, methods, progress, purrr, S4Vectors,
scales, scater, scuttle, sctransform, stats,
SingleCellExperiment, SummarizedExperiment, variancePartition,
viridis
SummarizedExperiment, VariantAnnotation, cowplot, Biostrings,
base, methods, magrittr, tibble, tidyr, gtools, gridExtra,
MCMCprecision, MASS, matrixTests, 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, factoextra,
cluster, ComplexHeatmap, philentropy, shinydashboard, sortable,
maftools, shiny, shinyjs, shinyalert, shinybusy, shinyBS,
TCGAbiolinks, shinyjqui, stringi
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
cpp11 (>= 0.2.5), readr, S4Vectors, SummarizedExperiment,
BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp,
dplyr, data.table, e1071, fs, GenomicRanges, ggthemes, glue,
limma (>= 3.44.0), patchwork, purrr, rlang, RSQLite, Rsamtools,
scales, scico, stats, stringr, tibble, tidyr, utils, withr,
zlibbioc
BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes,
grDevices, IRanges, methods, pheatmap, RColorBrewer, stats,
utils
hash(>= 2.2.6), openxlsx(>= 4.0.17), rentrez(>= 1.1.0), stats,
rlang, stringr, knitr, testthat, utils, AnnotationDbi, httr,
GenomicRanges, tidyverse, VarfromPDB, org.Hs.eg.db, curl,
dplyr, XML, XML2R
fgsea, limma, methods, reshape, stats, utils
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, ks,
Matrix, stats, methods
e1071, nnet, randomForest, naturalsort, graphics, stats,
utils, matrixStats, epiNEM
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
dplyr, ggplot2, igraph, magrittr, minet, purrr, tibble, tidyr,
AnnotationDbi, GO.db, RandomWalkRestartMH, gprofiler2, methods,
stats
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, SharedObject, stats
Biostrings, checkmate, dplyr (>= 1.0.0), DT, forcats,
ggdendro, grDevices (>= 3.6.0), grid, lifecycle, lubridate,
methods, pander, plotly (>= 4.9.4), readr, reshape2, rmarkdown,
scales, stats, stringr, tidyr, tidyselect (>= 0.2.3), utils,
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
stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang,
S4Vectors, scales, InteractionSet, ggplot2, grDevices,
plyranges, ks, speedglm, data.table, progress, ggridges
methods, stats, utils, tools, parallel, magrittr, Rcpp (>=
1.0.5), data.table, fst, ggplot2, AnnotationHub, BiocFileCache,
BiocGenerics, BiocParallel, Biostrings, BSgenome, DelayedArray,
DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges,
HDF5Array, IRanges, plotly, R.utils, rhdf5, rtracklayer,
SummarizedExperiment, S4Vectors
multtest (>= 1.7.3), graphics, grDevices, stats, akima
BiocGenerics, BiocFileCache, dasper, derfinder, dplyr,
IRanges, GenomeInfoDb, GenomicRanges, ggplot2, ggpubr, ggrepel,
magrittr, rtracklayer, S4Vectors, stringr, data.table,
megadepth, methods, plyr, purrr, tibble, utils
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
checkmate, crayon, curl, digest, dplyr, httr, igraph,
jsonlite, later, logger, magrittr, progress, purrr, rappdirs,
readr(>= 2.0.0), readxl, rlang, stats, stringr, tibble, tidyr,
tidyselect, tools, utils, xml2, yaml
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, stringr
stats, Rcpp, RcppProgress, dplyr, tidyr, ggplot2, progress
Biobase, S4Vectors, methods, AnnotationDbi, stats, utils,
BiocFileCache, shiny, graph, Rgraphviz, ontologyPlot, dplyr,
magrittr, DT, igraph, AnnotationHub
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, methods, graph, XML, png, RCurl
limma, stats, reshape, ggplot2, grDevices, RColorBrewer,
pheatmap, knitr, methods, devtools, parallelDist,
transport, parallel, Rfast, robustbase, dbscan, randomForest,
foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse
Rcpp (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg38, data.table,
stringr, randomForest, xfun, stats, utils, parallel, graphics
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
dplyr, methods, stats, utils, Matrix, jsonlite, homologene,
gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr,
patchwork, DelayedArray, DelayedMatrixStats, Matrix.utils, grr,
repmis, GenomeInfoDbData, tools
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
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
utils, httr, igraph, plyr, rjson, R.utils, jsonlite, readr,
rappdirs
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
data.table, MultiAssayExperiment, ConsensusClusterPlus,
igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro,
CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics,
survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel,
rlang, piano, scales, survcomp, genefu, ggplot2, switchBox,
reportROC, pROC, verification, utils
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
graph, igraph, KEGGgraph, clusterProfiler, ggplot2, plyr,
tidyr, magrittr, stats, methods, utils
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
BiocGenerics, Biobase, S4Vectors, SummarizedExperiment,
MultiAssayExperiment, BiocParallel, ggplot2, magicaxis,
RColorBrewer, parallel, caTools, methods, downloader, stats,
utils, graphics, grDevices, reshape2, jsonlite, data.table,
glue, checkmate
SingleCellExperiment, RColorBrewer, igraph, transport, pracma,
cluster, Rtsne, destiny, RANN, ggplot2, maptree, pheatmap,
scatterplot3d, VGAM, methods, grDevices, graphics, stats,
utils, cowplot, S4Vectors, BiocGenerics, SummarizedExperiment,
Biobase, phateR, reticulate
igraph, Matrix, foreach, doParallel, dplyr, stats, utils,
parallel
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
survival, limma, gplots, Category, AnnotationDbi, hopach,
biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
hgu133a.db, ellipse
SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf,
knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4,
graphics, grDevices, utils, stats
ape, phangorn, tidyr, ggplot2, ggtree, methods
BiocGenerics, methods, GenomicRanges, IRanges, S4Vectors,
edgeR, cli, utils
plyr, stats, graphics, matrixStats, methods
ruv, e1071, dendextend, limma, pcaMethods, stats,
RColorBrewer, circlize, dplyr, igraph, pheatmap,
preprocessCore, tidyr, rlang, graphics, grDevices, utils,
SummarizedExperiment, methods, S4Vectors, BiocGenerics,
ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext
ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table,
DT, energy, ExperimentHub, ggplot2, gridExtra, pbapply,
RColorBrewer, RCurl, shiny, shinyBS, shinyFiles, shinyjs,
OmaDB, plyr, xml2, zoo, yaml
Matrix, GenomicRanges, GenomeInfoDb, supraHex, scales,
grDevices, ggrepel, ROCR, randomForest, glmnet, 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 (>= 4.7), C50 (>= 0.1.2), MASS, matrixStats, partykit,
Rgraphviz, WGCNA, GO.db, impute, preprocessCore, grDevices,
graphics, stats, utils, parallel, pheatmap (>= 1.0.8), dplyr,
gdata, clusterProfiler, ReactomePA, ggplot2, openxlsx, DBI
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, rmarkdown
Streamer, IRanges, reshape2, plyr, RColorBrewer,ggplot2,
Biobase
utils, Biobase (>= 2.5.5), MASS, methods
curl, data.table, dplyr, grDevices, grid, ggplotify, IRanges,
methods, plyranges, purrr, Rcpp, RColorBrewer, rlang, stats,
strawr, tools, utils
methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>=
1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb,
Rsamtools, S4Vectors (>= 0.23.10), utils
stats, impute, pcaMethods, missForest, ggplot2, methods,
SummarizedExperiment, S4Vectors, matrixStats, grDevices,
reshape2, utils
ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT,
LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, 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
broom, caret, clisymbols, ComplexHeatmap, crayon, dplyr,
e1071, ggcorrplot, ggplot2, ggraph, ggrepel, glasso (>= 1.11),
glmnet, impute, knitr, limma, magrittr, mixOmics, MSnbase (>=
2.12), patchwork, qpdf, randomForest, RankProd (>= 3.14),
rmarkdown, tibble, tidyr, vegan
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, truncdist, vegan, VGAM
pheatmap, ggplot2, RColorBrewer, grDevices,
SummarizedExperiment, limma
methods, Rcpp (>= 0.12.0), rstan (>= 2.18.1), rstantools (>=
2.0.0), tibble, dplyr, magrittr, purrr, future, furrr, tidyr
(>= 0.8.3.9000), lifecycle, ggplot2, foreach, tidybayes, edgeR,
benchmarkme, parallel, rlang, stats, utils, graphics
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, utils, cluster, dbscan, doSNOW,
foreach, pbapply, stats, parallel, gtools, rCGH
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
AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2,
IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,
GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang,
scales, S4Vectors, SummarizedExperiment, stats, tibble
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, tiff, Rsamtools
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 (>= 1.26.1), DAPARdata (>= 1.24.0), 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, purrr, Rcpp (>= 0.12.14), recount, Rfast,
R.utils, reshape2, shinyjs, stringr, stats,
SummarizedExperiment, survival, tools, utils, XML, xtable,
methods
stringr, RCurl, igraph, ggplot2, reshape2, grid, parallel,
biomaRt, BgeeDB, topGO, Biobase, labeling, GO.db
Biobase, bit64, chron, data.table, doParallel, DT, enviPat,
foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra,
Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5,
rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats,
utils
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,
Biobase, Biostrings, BiocGenerics, rtracklayer, ggplot2,
gridExtra, futile.logger, VGAM, tools, methods, mclust, 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
Biobase, methods, knitr, tools, xtable, pander, S4Vectors
graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase
(>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0),
GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>=
0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply
(>= 1.8.1)
methods, stats, utils, S4Vectors, IRanges,
SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.19.3),
AnnotationFilter, lazyeval, Biobase, MsCoreUtils (>= 1.1.2),
igraph, plotly
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
SummarizedExperiment, utils, sva, stats, methods, graphics,
Hmisc
Biobase, limSolve, MASS, methods, preprocessCore, stats,
SummarizedExperiment, ggplot2, tidyr, rlang, utils
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
methods, grDevices, graphics, utils, stats, tools,
BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings,
BSgenome, Rsamtools, GenomicFeatures, ShortRead, BiocParallel,
GenomeInfoDb, rtracklayer, GenomicFiles, 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
IRanges, BiocGenerics, ggplot2, reshape2, EnvStats, ExtDist,
matrixStats, S4Vectors
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
Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach,
grDevices, stats, utils
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
AUCell (>= 1.1.6), BiocGenerics, data.table, feather,
graphics, GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr,
tibble, 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)
RcppAnnoy, igraph, NbClust, Rtsne, ggplot2, methods, pracma,
umap, grDevices, graphics, stats
httr, methods, RJSONIO, XML, utils, BiocGenerics, stats,
graph, fs, uuid, uchardet, glue, RCurl, base64url, base64enc,
IRkernel, IRdisplay, RColorBrewer
methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils
graphics, grDevices, methods, stats, MASS, rgl
httr, jsonlite, utils, magick (>= 2.5.1), data.table,
doParallel, foreach, parallel
neo4r, utils, getPass, jsonlite, purrr, magrittr, data.table,
rlang, ReactomeContentService4R, doParallel, parallel, foreach
jsonlite, httr, progress, ggplot2, methods, gplots,
RColorBrewer, dplyr, tidyr
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2, ggraph,
reactome.db, igraph, graphite
utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends,
dir.expiry, filelock, 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, IlluminaHumanMethylation450kmanifest
BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb,
GenomicFeatures, graphics, grDevices, httr, IRanges, 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 (>= 1.25.3), 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
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
httr, rJava, GenomicRanges, rtracklayer, data.table, utils,
plyr, xml2, methods, S4Vectors, dplyr, stats, glue,
BiocGenerics
rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats
gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment,
hash, AnnotationDbi
GenomicFeatures, SGSeq, GenomicRanges, methods, utils
BiocGenerics, BiocParallel, Biostrings, data.table, dplyr,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges,
plotly, rlang
Rcpp (>= 1.0.2), graphics, stats, data.table, elitism,
methods, S4Vectors, IRanges, GenomicRanges, matrixStats,
reldist, doParallel, foreach, parallel, qvalue, DESeq2,
ggplot2, BiocFileCache
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
dplyr, ggplot2, RColorBrewer, grid, regioneR, valr,
caretEnsemble, GenomicFeatures, rtracklayer, GenomicRanges,
GenomeInfoDb, ComplexHeatmap, AnnotationHub, VennDiagram,
callr, circlize, ggplotify, ggprism, methods, stats, RLHub,
aws.s3, pheatmap
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
processx, BiocManager, rtracklayer, stats, tools, methods,
GenomicRanges, stringr
ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats,
SummarizedExperiment, methods
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), abind, locfit, Biobase
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
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
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
annotate (>= 1.21.0), graph (>= 1.21.0), Biobase, RBGL (>=
1.17.0), hypergraph (>= 1.15.2), AnnotationDbi
BiocFileCache, jsonlite, xml2, RCurl, curl, 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
locfdr, SummarizedExperiment, BiocParallel, limma, pbapply,
ggplot2, boot, Matrix, stats, methods, graphics
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
Biostrings, GenomicRanges, IRanges, data.table, BiocParallel,
methods, GenomeInfoDb, S4Vectors, ggplot2, stats, stringi,
utils, graphics, grid, gridExtra, seqLogo
AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel,
Biostrings, data.table, digest, DT, ensembldb, fst,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2,
htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs,
rtracklayer, S4Vectors, scanMiR, scanMiRData, shiny,
shinycssloaders, shinydashboard, stats, utils, waiter
dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats,
e1071, ape, kernlab, AnnotationHub, utils
BiocGenerics, S4Vectors, IRanges, utils, SummarizedExperiment,
SingleCellExperiment, DelayedMatrixStats
stats, utils, methods, grid, gridExtra, Matrix, BiocGenerics,
S4Vectors, SummarizedExperiment, DelayedArray,
DelayedMatrixStats, beachmat, BiocNeighbors, BiocSingular,
BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer,
ggrepel
grid, ggplot2, plyr, spatstat.geom, stats, grDevices
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
dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats,
e1071, ape, kernlab, utils
S4Vectors, limma, ggraph, igraph, methods, cluster,
minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix,
ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo
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, MASS
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, DESeq2, 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
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, MatrixGenerics, SingleCellExperiment
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, MsCoreUtils,
matrixStats, S4Vectors, dplyr, magrittr, rlang
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
cluster, kernlab, origami, RSpectra, coop, Matrix,
DelayedArray, ScaledMatrix, MatrixGenerics
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, edgeR, limma, igraph,
statmod, DelayedArray, DelayedMatrixStats, BiocSingular,
bluster, metapod, dqrng, beachmat
randomForest, e1071, stats, SummarizedExperiment,
SingleCellExperiment, methods
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)
stringdist, dplyr, reshape2, ggalluvial, stringr, vegan,
powerTCR, SummarizedExperiment, plyr, parallel, doParallel,
methods, utils, rlang, igraph, SeuratObject
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
Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
emdbook, magrittr, utils
methods, RSQLite, igraph, S4Vectors, plotly, reactome.db,
AnnotationDbi, SummarizedExperiment, SingleCellExperiment,
nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8),
abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle,
knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics,
stats, utils, outliers, Category, meshr (>= 1.99.1), 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
data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph,
clustree, scran, sys, epivizrData, epivizrServer, ggraph,
scater, Seurat, SingleCellExperiment, ggplot2, stats, utils
methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors,
BiocParallel, GenomicRanges, SummarizedExperiment,
DelayedArray, DelayedMatrixStats, beachmat
S4Vectors, SummarizedExperiment, seriation, ComplexHeatmap,
circlize, methods, randomcoloR, stats, grid, grDevices
ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges,
S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils,
methods, chromhmmData
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, utils, yulab.utils
Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
data.table, eulerr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, ggplotify, grDevices, grid, IRanges, limma,
methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools,
rtracklayer, S4Vectors, stats, UpSetR
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, graphics, KernSmooth,
parallel, matrixStats, DNAcopy, stats, SummarizedExperiment,
e1071, fgsea, ggrepel, reshape2
S4Vectors, SummarizedExperiment, data.table, seriation,
ComplexHeatmap, circlize, methods, BiocParallel, randomcoloR,
edgeR, openxlsx, sva, stats, DESeq2, Matrix, grid
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, tools
BiocGenerics, Biostrings, class, graphics, grDevices,
GenomeInfoDb, GenomicRanges, IRanges, nloptr, methods, stats,
utils, PMCMRplus
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
GOSemSim, ComplexHeatmap (>= 2.7.4), circlize, GetoptLong,
digest, tm, GO.db, org.Hs.eg.db, AnnotationDbi, slam, methods,
clue, grDevices, graphics, stats, utils, proxyC, Matrix,
cluster (>= 1.14.2)
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges,
DelayedArray
BiocManager, circlize, limma, igraph, gplots, grDevices,
edgeR, SIMLR, data.table, pheatmap, stats, Rtsne, graphics,
stringr, foreach, multtest, scran, utils,
ape, batchelor, BiocParallel, celldex, 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, shinyjs, SingleR, sva, reshape2,
AnnotationDbi, shinyalert, circlize, enrichR, celda,
shinycssloaders, DropletUtils, scds (>= 1.2.0), reticulate (>=
1.14), tools, tximport, fishpond, withr, GSEABase, R.utils,
zinbwave, scRNAseq (>= 2.0.2), TENxPBMCData, yaml, rmarkdown,
magrittr, scDblFinder, metap, VAM (>= 0.5.3), tibble, rlang,
stats
BiocGenerics, Biostrings, BSgenome, GenomeInfoDb,
GenomicRanges, data.table, grDevices, plyr, IRanges,
RColorBrewer, stats, QuasR
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocNeighbors, BiocParallel, BiocSingular, stats, utils, Rcpp,
beachmat, parallel
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
Biobase, BiocGenerics, biomaRt, Biostrings, GenomeInfoDb,
GenomicFeatures, GenomicRanges, IRanges, methods, parallel,
Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, utils
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
graphics, grDevices, igraph, matrixStats, methods, S4Vectors,
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
basilisk, reticulate, irlba, stats, assertthat
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
Seurat, SingleCellExperiment, SummarizedExperiment, dplyr,
methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg,
magrittr, utils, S4Vectors, DropletUtils, jsonlite, png
babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet,
checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>=
1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>=
2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix,
methods, plotly (>= 4.9.0), stats, utils, viridis
stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
methods, glmnet, huge, stats, graphics, utils
nnlasso, nnls, parallel, data.table, Biostrings,
GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2,
gridExtra, reshape2
reticulate, basilisk, checkmate, stats, SpatialExperiment,
methods, SummarizedExperiment, Matrix, S4Vectors, ggplot2,
ggrepel, scales, gridExtra
grDevices, stats, utils, graphics, SeuratObject, Biobase,
GeomxTools, repmis, methods, Matrix
BiocFileCache, DropletUtils, rjson, magick, grDevices,
S4Vectors, SummarizedExperiment, BiocGenerics, utils
av, BiocFileCache, data.table, DESeq2, distinct, edgeR, WGCNA,
flashClust, htmlwidgets, genefilter, ggplot2, ggdendro,
grImport, grid, gridExtra, gplots, igraph, HDF5Array, limma,
methods, magick, rsvg, shiny, dynamicTreeCut, grDevices,
graphics, ggplotify, parallel, plotly, rols, rappdirs,
reshape2, stats, SummarizedExperiment, shinydashboard,
S4Vectors, utils, visNetwork, UpSetR, xml2, yaml
BiocGenerics, BSgenome, GenomeInfoDb, GenomicFeatures,
GenomicInteractions, GenomicRanges, ggplot2, IRanges,
matrixStats, motifmatchr, S4Vectors, stats,
SummarizedExperiment, TFBSTools, utils
methods, IRanges, MsCoreUtils (>= 1.3.3), graphics, grDevices,
stats, tools, utils, fs, BiocGenerics
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, scam
httr, igraph, utils, stats, miRNAtap, miRNAtap.db,
AnnotationDbi, org.Hs.eg.db, ggplot2, gridExtra, gplots,
grDevices, lattice, latticeExtra, TCGAbiolinks, gdata,
MAGeCKFlute
stats, scales, bamlss, methods, tools, IRanges, Biostrings,
GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome,
S4Vectors, graphics, ggplot2, utils
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, edgeR, baySeq, Rsamtools, GenomicFeatures,
GenomicAlignments, grDevices, Gviz, BiocParallel, BiocStyle,
BiocManager
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, rmarkdown
methods, graph, RBGL, parallel, BiocGenerics
png, sqldf, plyr, igraph, RCurl, methods, RColorBrewer,
gplots, hash, plotrix
methods,ontologyIndex, datasets, graphics, stats, utils,
knitr, SummarizedExperiment, S4Vectors, rols
methods, BiocGenerics, XVector, stringr, stringi, crayon,
grDevices
ggplot2, ggthemes, grid, gridExtra, methods, scales, sp,
stats, utils
assertthat, Biostrings, stringr, dplyr, methods, rlang,
GenomicFeatures, IRanges, S4Vectors, SummarizedExperiment,
GenomeInfoDb,
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 (>= 0.37.0),
S4Vectors (>= 0.27.12), IRanges (>= 2.23.9), GenomeInfoDb (>=
1.13.1), DelayedArray (>= 0.15.10)
assertthat, caret, dplyr, tidyr, rsample, methods, rlang,
utils, Biostrings, stats, SummarizedExperiment
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
assertthat, Biostrings, stringr, dplyr, methods, rlang,
GenomeInfoDb, S4Vectors, GenomicFeatures
VariantAnnotation, assertthat, Biostrings, stringr, dplyr,
methods, rlang, GenomicFeatures, GenomeInfoDb, S4Vectors, utils
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, SummarizedExperiment, ggplot2, yaml, stringr,
magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
DT, assertthat, bsplus, crayon, dplyr, ggplot2, htmltools,
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, R6, RSQLite,
openssl
DESeq2, GGally, Rtsne, SummarizedExperiment, ape, dplyr,
ggplot2, ggrepel, ggtree, glmpca, pheatmap, plotly, tibble,
magrittr, DT, stats
dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2,
tidyr, ggpubr, RColorBrewer, reshape2, cowplot
ape (>= 5.0), phangorn (>= 2.5), utils, methods
methods, GenomicAlignments, GenomicRanges, IRanges,
BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome,
GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel
BiocGenerics, GenomicRanges, IRanges, matrixStats, methods,
stats, graphics, shiny
ggplot2, ggpubr, methods, mzID, mzR, stats
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
grDevices, stats, utils, S4Vectors, IRanges, BiocGenerics,
reshape2, GenomeInfoDb, BiocParallel, Biostrings, cowplot,
graphics, GenomicAlignments, Hmisc
ASSIGN (>= 1.23.1), GSVA, singscore, methods, ComplexHeatmap,
RColorBrewer, ggplot2, S4Vectors, reshape2, ROCit, DESeq2, DT,
edgeR, gdata, SummarizedExperiment, magrittr, stats, rlang,
BiocParallel, BiocGenerics
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
utils, igraph, methods, graphics, stats, BiocParallel
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, AnnotationDbi,
org.Hs.eg.db, utils
tibble, readr, dplyr, magrittr, tidyr, stringi, stringr,
rlang, purrr, tidyselect, preprocessCore, stats, parallel,
utils, lifecycle, scales, SummarizedExperiment, GenomicRanges,
methods
SummarizedExperiment, 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, plyr
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)
scales, stats, utils, ggplot2, data.table, purrr, dplyr,
VariantAnnotation, GenomicRanges, MatrixGenerics
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
stats, methods, SummarizedExperiment, corpcor, doParallel,
parallel, ggplot2, tidyr, GGally
Rcpp (>= 0.11.2), ALS, alsace, signal, KernSmooth, graphics,
grDevices, stats
methods, stats, grDevices, reshape2, Rtsne, umap,
RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
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, jsonlite
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, rhdf5
mgcv, edgeR, SingleCellExperiment, SummarizedExperiment,
slingshot, magrittr, RColorBrewer, BiocParallel, Biobase,
pbapply, igraph, ggplot2, princurve, methods, S4Vectors,
tibble, Matrix, TrajectoryUtils, viridis, matrixStats, MASS
methods, stats, Matrix, igraph, S4Vectors,
SummarizedExperiment
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
glmGamPoi, DelayedArray, Matrix, MatrixGenerics,
SummarizedExperiment, HDF5Array, methods, 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
hash, ggplot2, stats, methods, igraph, utils, glmnet, vbsr,
grDevices, gplots, gtools, pvclust, R.utils, dqrng,
SummarizedExperiment, BiocParallel, matrixStats
ggplot2, viridis, mgcv, SingleCellExperiment, slingshot,
princurve, Biobase, methods, RColorBrewer,
SummarizedExperiment, grDevices, graphics, rgl
ape, dplyr, jsonlite, magrittr, methods, rlang, tibble,
tidytree (>= 0.3.0), utils
stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2,
hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt,
edgeR, lme4, multcomp
methods, BiocGenerics, utils, ape, rlang, dplyr,
SummarizedExperiment, BiocParallel, IRanges, treeio
RSQLite, RMySQL, lassopv, randomForest, vbsr, xgboost,
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, WGCNA
stats, utils, graphics, grDevices, segmented, gplots,
parallel, magrittr, BiocParallel, DT, S4Vectors,
SummarizedExperiment, methods, shiny, shinyFiles
utils, rtracklayer, Matrix, matrixStats, stats, methods,
graphics, GenomicRanges, GenomicFeatures, IRanges, Rsamtools,
AnnotationDbi
methods, circular, ggplot2, AnnotationDbi, scater,
GenomicRanges, IRanges, S4Vectors, scattermore, dplyr,
RColorBrewer, grDevices, stats, SummarizedExperiment, utils
grDevices, graphics, methods, stats, survival, utils,
siggenes, LogicReg (>= 1.6.1)
shinyjs, shinyFiles, plyr, data.table, DT, stringr,
stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr,
pryr, config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices,
graphics, stats, utils
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,
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
tm, text2vec, tokenizers, textstem, stopwords, data.table,
purrr, DiagrammeR, stats
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
AnnotationDbi, GenomicFeatures, IRanges, GenomicRanges,
BiocGenerics, Biostrings, S4Vectors, rtracklayer, BiocParallel,
stats, methods, utils
SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges,
GenomicRanges, AnnotationDbi, GenomicFeatures, ensembldb,
BiocFileCache, AnnotationHub, Biostrings, tibble, GenomeInfoDb,
tools, utils, methods, Matrix
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, BiocGenerics
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, yaml, IRanges, Rcpp,
Biostrings, BiocGenerics, S4Vectors, rlang, grid
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
SingleCellExperiment, SummarizedExperiment, tensorflow,
scater, gradDescent, CatEncoders, DeepPINCS, purrr, DiagrammeR,
stats
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
methods, stats, IRanges, shiny, shinycssloaders, shinyFiles,
ggplot2
MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix, iterators,
foreach, doParallel, gplots, RhpcBLASctl, progress, reshape2,
aod, scales, Rdpack, rlang, lme4 (>= 1.1-10), grDevices,
graphics, Biobase, methods, 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)
GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), 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
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
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
igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm,
ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb,
ggrepel, textstem, tidygraph, stats, scales, ggraph
cowplot, magrittr, GenomeInfoDb, GenomicAlignments,
RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2,
methods, graphics, stats
wordcloud, csaw, gplots, stats, utils, caTools, graphics,
DESeq2, Biobase
Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, 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
dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>=
2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr
limma, matrixStats, locfit, stats, graphics
mzR (>= 2.25.3), methods, Biobase, BiocGenerics, ProtGenerics
(>= 1.25.1), lattice, RColorBrewer, plyr, RANN, MassSpecWavelet
(>= 1.5.2), S4Vectors, robustbase, IRanges,
SummarizedExperiment, MsCoreUtils, MsFeatures
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
utils, Biostrings, BSgenome, data.table, GenomicRanges,
IRanges, methods, Rcpp, stringi, S4Vectors, future.apply,
stringr, formattable, stats
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, PMCMRplus, 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, cli
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
Rcpp, BH(>= 1.75.0.0), RProtoBufLib(>= 2.3.5),Rhdf5lib,
RcppArmadillo, RcppParallel(>= 4.4.2-1)
Rcpp, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
RcppArmadillo, RcppParallel(>= 4.4.2-1), flowWorkspace
Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
Rcpp, RcppArmadillo, BH(>= 1.65.0.1), cytolib, RProtoBufLib
Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>=
2.3.7),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
BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics,
DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext,
RColorBrewer, pheatmap, viridis
knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0),
gplots
testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown
knitr, testthat, markdown, alpineData, rtracklayer,
ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer
DT (>= 0.5), testthat (>= 2.0.0), plotly (>= 4.7.1),
ChemoSpec, knitr
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
knitr, tidyverse, testthat, DT, magrittr, qwraps2 (>= 0.5.0),
rmarkdown
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, humanCHRLOC, Rgraphviz, RUnit,
hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, RUnit,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, reactome.db,
AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr
BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db, rmarkdown
biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy,
hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db,
markdown, BiocStyle, knitr, BiocManager, BiocFileCache
IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation,
Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge,
rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR,
Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt,
rmarkdown, HubPub
RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData,
rmarkdown, HubPub
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
parallel, knitr, rmarkdown, testthat, withr, readr, BiocStyle
knitr, BiocStyle, BiocManager, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi,
TBX20BamSubset, testthat, pasillaBamSubset
DESeq2, airway, knitr, rmarkdown, testthat
MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata,
hgu133atagcdf
BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR,
knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat
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, rmarkdown
covr, BiocStyle, knitr, rmarkdown, RUnit
Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, rbokeh,
Rtsne, testthat, zoo
affy, AnnotationDbi, BiocManager, diagram, GenomicRanges,
GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS,
mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl,
remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr,
statmod, testthat
airway, ggplot2, testthat, EDASeq, knitr, BiocStyle,
RefManageR, sessioninfo, rmarkdown
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2,
ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3),
DESeq2, NanoporeRNASeq, apeglm, utils, DEXSeq
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
BiocStyle, knitr, magick, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat, magick
knitr, rmarkdown, BiocStyle, testthat, callr
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, HDF5Array
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, rmarkdown, HMP16SData, curatedMetagenomicData,
BiocStyle, testthat
knitr, testthat, rmarkdown, AnnotationHub, httr
knitr, BiocStyle, testthat, rmarkdown, markdown
BiocGenerics, RUnit, BiocStyle, minfiData, parallel,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter
testthat, BiocStyle, knitr, rmarkdown, dplyr,
GenomicAlignments, ComplexHeatmap, GenomeInfoDb, forcats,
scales
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,
rmarkdown, SummarizedExperiment
BiocStyle, prettydoc, 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, rmarkdown, rhdf5client
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
testthat, restfulSE, HDF5Array, BiocStyle, rmarkdown
BiocStyle, covr, devtools, knitr, pkgdown, RefManageR,
rmarkdown, sessioninfo, testthat, utils
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, xml2, git2r
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, igraph, magick, lgr
BiocStyle, lgr, roxygen2, devtools, testthat (>= 2.0.0),
knitr, rmarkdown, covr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr, covr
BiocStyle, knitr, rmarkdown, testthat, mockery
cluster, parallel, GenomicFeatures, dynamicTreeCut,
Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, covr
rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
AnnotationDbi, AnnotationHub, BiocStyle, ExperimentHub,
depmap, knitr, rmarkdown
testthat, knitr, rmarkdown, lattice, latticeExtra,
rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db,
ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer
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, ranger,
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, rmarkdown, markdown, rlang, scmeth,
pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl
xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db,
lumi, knitr
RUnit, devtools, BiocGenerics, knitr, rmarkdown
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans,
kohonen, apcluster
BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 2.1.0), covr
BiocStyle, ComplexHeatmap, fastcluster, heatmaply, knitr,
plotly, rmarkdown
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
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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
testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle,
rmarkdown
BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE,
BiocStyle, knitr, rmarkdown
testthat (>= 3.1), knitr, rmarkdown, BiocStyle
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, KEGGREST, karyoploteR, geneplotter, limma,
lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db
knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db,
limma, affy, genefilter, rmarkdown
BiocStyle, knitr, survival, survminer, rmarkdown, testthat
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
crossmeta, knitr, rmarkdown, testthat, lydata
limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
BiocManager, BiocStyle, TENxPBMCData, singleCellTK,
M3DExampleData
testthat, readr, knitr, rmarkdown, ggplot2, BiocStyle,
ggdendro, broom, lme4, RColorBrewer, SingleCellExperiment,
scater, broom.mixed, cowplot, igraph, ggraph
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation
BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr,
destiny, ggrepel
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics,
BiocManager, kableExtra, rgl
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
BiocStyle, knitr, rmarkdown, testthat, ggplot2
knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater,
scMerge, fgsea, escape, pheatmap, patchwork
airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14),
devtools (>= 2.3.0), BiocStyle, testthat
ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager,
rmarkdown
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs,
png,rmarkdown, BiocManager
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
AnnotationHub, 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, ggimage, ggplotify, ggupset, ReactomePA,
org.Hs.eg.db, knitr, rmarkdown, testthat, tibble
testthat, knitr, markdown, rmarkdown, BiocStyle, Signac,
future
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
BiocStyle, knitr, rmarkdown, testthat, webshot
knitr, testthat, ReactomePA, RUnit, BiocGenerics,
AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db,
biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods,
Biostrings,Homo.sapiens, R.utils
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
BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0)
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown,
BRAIN, UniProt.ws (>= 2.1.4)
RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS,
BiocStyle
knitr, rmarkdown, bookdown, testthat, BiocStyle
BiocGenerics, edgeR, knitr, pvclust, rmarkdown, RUnit, vegan
knitr, rmarkdown, testthat, dplyr, readr, stringr, magrittr,
CluMSIDdata, metaMS, metaMSdata, xcms
BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph,
rmarkdown
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, knitr, rmarkdown, org.Hs.eg.db, prettydoc,
ReactomePA, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel,
BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr
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
VariantAnnotation, DelayedArray, knitr, biomaRt, evobiR,
rmarkdown, devtools, cowplot, usethis, scales, testthat,
GenomicRanges, cn.mops, R.utils
AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked,
BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment,
TCGAutils, curatedTCGAData, ensembldb, grid, knitr, regioneR,
rmarkdown
knitr, parallel, testthat, BiocStyle, rmarkdown,
AnnotationHub, LOLA
BiocStyle, knitr, markdown, testthat (>= 3.0.0)
genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen,
NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE,
AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree,
dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot,
flexclust
covr, testthat, knitr, Rcpp, rmarkdown, markdown
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2, progress
BiocStyle, EBSeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0),
genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), rmarkdown, testthat
testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,
fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,
grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),
gridGraphics, gplots, rmarkdown, Cairo
knitr, rmarkdown, BiocStyle, S4Vectors, matrixStats,
dynamicTreeCut, testthat
knitr, testthat, rmarkdown, covr, viridis, ggplot2,
RColorBrewer, randomForest, tidyr, TSCAN
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra,
magick, Cairo, limma
BiocStyle, knitr, rmarkdown, panelcn.mops,
BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat
RColorBrewer, gplots, BiocStyle, knitr, rmarkdown
pander, markdown, BiocStyle, rmarkdown, knitr, formatR,
testthat
ade4, BiocStyle, CellBench, DuoClustering2018, knitr,
rmarkdown, testthat
Biobase, knitr, rmarkdown, testthat, BiocStyle
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), snpStats, RUnit
knitr, rmarkdown, lydata, org.Hs.eg.db, testthat,
tximportData
AnnotationDbi, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures,
GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr,
igraph, dplyr
BiocStyle, biomaRt, HSMMSingleCell, irlba, knitr, rmarkdown,
VGAM
testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet,
BiocStyle, flowStats
BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat,
shinytest
testthat, flowWorkspaceData , knitr, rmarkdown, parallel
BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat,
BiocStyle
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
BSgenome.Hsapiens.UCSC.hg19
AnnotationFilter, BiocStyle, covr, ensembldb, GenomicState,
knitr, lifecycle, markdown, recount, RefManageR, rmarkdown,
sessioninfo, testthat, tibble
EBcoexpress, testthat, EBarrays, GeneNet, COSINE, mclust,
minqa, SummarizedExperiment, Biobase, knitr, rmarkdown,
BiocStyle, edgeR
knitr, rmarkdown, testthat (>= 2.1.0), BiocStyle, formatR,
cowplot, dagitty, lmtest, sandwich, devtools, curatedTCGAData,
TCGAutils, SummarizedExperiment
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
knitr, curatedTCGAData, MultiAssayExperiment, Homo.sapiens,
rmarkdown
testthat (>= 3.0.0), roxygen2 (>= 7.1.2), doParallel (>=
1.0.16), parallel, knitr (>= 1.34), BiocStyle (>= 2.20.2),
reshape2 (>= 1.4.4), ggplot2 (>= 3.3.5), rmarkdown, devtools
(>= 2.4.2), sessioninfo (>= 1.1.1), covr, granulator,
RefManageR
glmnet (>= 4.1.0), GSVA, viper, fgsea (>= 1.15.4), AUCell,
SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr,
pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo,
pheatmap, testthat, OmnipathR, tidyverse, Seurat
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, lobstr, DelayedMatrixStats,
knitr, rmarkdown, BiocStyle, RUnit
testthat, knitr, rmarkdown, SeqArray, GDSArray
testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark,
profmem, HDF5Array
testthat, knitr, BiocStyle, rmarkdown, Matrix
markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr,
dplyr, reticulate
knitr, rmarkdown, BiocStyle, ggplot2, Rtsne, uwot, testthat
uwot, reshape2, 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, igraph, testthat, FNN, tidyverse,
gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq,
org.Mm.eg.db, scran, repr
knitr, rmarkdown, testthat, BiocStyle, IHW
GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22),
parathyroidSE, BiocStyle, knitr, rmarkdown, testthat
knitr, akima, lattice, scales, gridExtra, latticeExtra,
rmarkdown, BiocStyle, BiocParallel, 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
testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools,
ggplot2, gridExtra, ggpubr, grid
lattice, parallel, MASS, RColorBrewer, xtable
plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR,
ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq,
ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat
prettydoc, clusterProfiler, knitr, rmarkdown, 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
knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment
distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq,
statmod
BiocStyle (>= 2.18.0), BSgenome (>= 1.58.0),
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, rmarkdown
jsonlite, readr, rhdf5, splines, Biobase, AnnotationDbi,
SummarizedExperiment, org.Hs.eg.db
knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie,
Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38,
ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer
BiocStyle, knitr, testthat, data.table, DT,
GenomicInteractions, webshot, R.utils, covr, sesameData
RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway,
org.Hs.eg.db, gridExtra, magrittr, rmarkdown
knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer10,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, MotifDb,
testthat, TFBSTools
SummarizedExperiment, testthat, Biobase, survminer,
affycoretools, knitr, plotROC, prognosticROC, rmarkdown
testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter,
RColorBrewer
ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools,
airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr,
rmarkdown
clusterProfiler, dplyr, europepmc, ggupset, knitr, rmarkdown,
org.Hs.eg.db, prettydoc, tibble, tidyr, ggforce, AnnotationDbi,
ggplotify, ggridges, grDevices, gridExtra, ggnewscale, ggrepel
(>= 0.9.0), ggstar, treeio, scales, tidytree, ggtreeExtra
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
testthat, knitr, rmarkdown, BiocStyle,
BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData
knitr, clusterProfiler, ggfortify, org.Hs.eg.db, rmarkdown
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown,
EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
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, rmarkdown
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, matrixStats
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
devtools, knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0),
data.table, sctransform, readxl, SingleCellExperiment, memoise,
markdown
GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub
BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran,
scater, scds, TENxPBMCData, airway
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, schex, gridExtra, scran, Seurat, knitr, rmarkdown
rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0),
BiocStyle
biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown,
testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi,
GOSemSim
knitr, rmarkdown, GOstats, PerfMeas, GO.db, BiocGenerics
RCurl, 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, knitr, rmarkdown, sessioninfo, testthat (>=
3.0.0), TxDb.Athaliana.BioMart.plantsmart28
testthat, knitr, rmarkdown, macrophage, tximeta,
org.Hs.eg.db, samr, DESeq2, apeglm, tximportData, limma
BiocStyle, knitr, rmarkdown, markdown, BiocFileCache
testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown,
openCyto
Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat,
flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto,
gridExtra
RUnit, BiocGenerics, knitr, markdown, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, DepecheR
xtable, testthat, openCyto, ggcyto, ggridges
knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, stats,
flowClust, openCyto, flowStats, ggcyto
colorspace, flowStats, knitr, rmarkdown, markdown, testthat
testthat, flowWorkspaceData (>= 2.23.2), knitr, rmarkdown,
ggcyto, parallel, CytoML, openCyto
BiocGenerics, testthat, knitr, utils, rmarkdown
BiocStyle, covr, ggrepel, kableExtra, knitr,
metabolomicsWorkbenchR, POMA, rmarkdown, rvest,
SummarizedExperiment, testthat (>= 2.3.2), tidyverse
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, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db,
BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
testthat, knitr, rmarkdown, BiocStyle, GCSConnection
testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown
RUnit, rentrez, knitr, rmarkdown, BiocStyle
assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat
GO.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
apcluster, GEOquery, knitr, rmarkdown, BiocStyle
class, hgu95av2.db, tkWidgets, ALL, ROC, RColorBrewer,
BiocStyle, knitr
GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable, knitr, caret,
survival, BiocStyle, magick, rmarkdown
RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny,
STRINGdb, BiocStyle, magick, rmarkdown
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
BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown,
RUnit
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, BiocParallel,
TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation
AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle,
rmarkdown
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, KEGGREST, 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,
rmarkdown, BiocStyle
RUnit, 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, shinyjs, shinycustomloader, data.table, DT, magrittr,
shinydashboard
knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis,
BiocStyle, testthat, forcats, stats, wordcloud, circlize,
EnrichmentBrowser, clusterProfiler, msigdbr, cluster,
RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr,
utils
testthat, knitr, BiocStyle, rmarkdown, covr
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
rmarkdown, knitr, usethis, testthat (>= 3.0.0)
BiocCheck, roxygen2, knitr, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph
knitr, rmarkdown, BiocGenerics, testthat, covr, markdown
devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat
(>= 3.0.0)
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
ggtreeExtra, ggtree (>= 1.17.1), ape, cowplot, knitr,
BiocStyle, rmarkdown, readxl, ggnewscale, kableExtra, gggenes,
testthat (>= 3.0.0), phangorn
BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix,
scater, scran, uwot, testthat (>= 3.0.0)
emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc,
rmarkdown, stats, testthat, tibble
treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc,
markdown, testthat (>= 3.0.0), pillar, tidytree (>= 0.3.9)
roxygen2, knitr, rmarkdown, testthat, BiocStyle
testthat, knitr, rmarkdown, BiocStyle, IRanges,
GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran
testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, beachmat,
MASS, statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData, muscData, scran
testthat, knitr, rmarkdown, survival, survcomp, pROC,
VennDiagram, BiocStyle, curatedTCGAData, TCGAutils
GO.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
testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle,
BiocManager
Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
rmarkdown, org.Hs.eg.db, prettydoc, testthat, ROCR
hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter,
RColorBrewer, xtable, SparseM, GSEABase, geneplotter,
org.Hs.eg.db, RUnit, BiocGenerics
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
BiocStyle, GSE62944, knitr, rappdirs, rmarkdown
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
BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma,
RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny,
shinydashboard, ggplot2, data.table, plotly, future, promises,
shinybusy, shinyjs
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
rmarkdown, 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, xml2, BiocStyle, knitr,
rmarkdown, testthat
BiocStyle, knitr, rmarkdown, formatR, rrBLUP, qqman
DO.db, DT, knitr, RBGL, testthat, rmarkdown, Gviz, Rsamtools,
IRanges, rtracklayer, 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, rmarkdown
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
futile.logger, LoomExperiment, SummarizedExperiment,
SingleCellExperiment, S4Vectors, methods, testthat (>= 3.0.0),
knitr, rmarkdown, BiocStyle
BiocParallel, GenomicRanges, SummarizedExperiment (>=
1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter,
GenomicFeatures, RUnit, SingleCellExperiment
BiocStyle, testthat, knitr, rmarkdown, seqCNA
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
knitr, doParallel, testthat, BiocGenerics, markdown
parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray,
knitr, markdown, rmarkdown
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
RUnit, BiocGenerics, knitr, rmarkdown, HiTC, DESeq2, Matrix,
BiocFileCache, rappdirs
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown
knitr, annotate, gwascat, testthat, rmarkdown
knitr, rmarkdown, markdown, devtools, BiocStyle
org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat, rmarkdown
knitr, BiocManager, qpdf, hpar, testthat, rmarkdown
rmarkdown, colorspace, e1071, kernlab, ranger,
SummarizedExperiment, Biostrings, randomForest, gprofiler2,
gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools,
knitr
EDASeq, testthat, knitr, rmarkdown, BiocStyle
AnnotationHubData, ExperimentHubData, testthat, knitr,
rmarkdown, BiocStyle,
knitr, BiocStyle, beeswarm, tximportData, DT, tximport,
dplyr, magrittr, BiocFileCache, testthat, rhdf5client,
rmarkdown
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
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown,
testthat
BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071
RUnit, BiocGenerics, BiocManager, rtracklayer, BiocStyle,
knitr, markdown, rmarkdown, EnsDb.Hsapiens.v86,
EnsDb.Mmusculus.v79, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene
knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges,
data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap,
cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3,
GOexpress, SingleCellExperiment, scater, gplots, pheatmap,
airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve
(>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks
RUnit, hgu95av2.db, knitr, GenomicRanges,
SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer,
metagenomeSeq, gplots, vegan, Biobase
testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite,
processx, attempt, BiocStyle, httr
BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db,
org.Hs.eg.db
gProfileR, topGO, 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, sessioninfo, rmarkdown,
roxygen2, vegan, withr, extraDistr, ggalluvial, scales,
gridExtra, R.utils, RefManageR, flexdashboard, DT, circlize,
plotly, gtools, eulerr
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, rmarkdown, org.Mm.eg.db, targetscan.Hs.eg.db,
pheatmap, BiocStyle, testthat
knitr, png, limma, grid, DT, randomForest, digest, testthat,
rmarkdown
BiocStyle, knitr, rmarkdown, markdown, 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
RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db,
SPIA
RUnit, knitr, BiocStyle, gwascat, rmarkdown
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, markdown, gplots, RColorBrewer,
moments, testthat
knitr, rmarkdown, igraph, reshape2, limma,
knitr, rmarkdown, BiocStyle, ggrepel, plotly, iheatmapr,
spelling, testthat
parallel, testthat, knitr, BiocStyle, rmarkdown
testthat, BiocStyle, knitr, rmarkdown, reticulate
LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2,
testthat
beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
ROCR, knitr, M3DExampleData, scater, SingleCellExperiment,
monocle, Seurat, Biobase
knitr, rmarkdown, bookdown, testthat, BiocStyle,
BSgenome.Mmusculus.UCSC.mm10
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors, pheatmap, curl
gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil,
rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools,
BiocGenerics, BiocManager
biomaRt, BiocStyle, DOSE, dendextend, graphics, knitr,
msigdbr, pheatmap, png, pathview, scales, sva, testthat,
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML,
rgl, som
BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit,
BiocGenerics
knitr, rmarkdown, BiocStyle, testthat, covr
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, bluster, knitr, testthat, rmarkdown
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k,
knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
testthat, knitr, rmarkdown, fgsea, BiocManager
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
BiocStyle, rmarkdown, brgedata
knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0)
covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer,
derfinder, GenomeInfoDb, tools, RefManageR, testthat
cowplot, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0),
knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1),
rmarkdown, covr
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, HDF5Array, rmarkdown, structToolbox,
testthat, pmp, grid, png
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
BiocManager, BSgenome, knitr, RMySQL, RUnit
knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s,
testthat, gss, ExperimentHub, tidyr, rmarkdown
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, sesame,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19
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
rmarkdown, 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, TCGAMethylation450k,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr
testthat, knitr, patchwork, BiocStyle, yaml, phyloseq, dada2,
stringr, biomformat, reldist, ade4, microbiomeDataSets,
rmarkdown
knitr, rmarkdown, BiocStyle, testthat, patchwork,
microbiomeDataSets
BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat
testthat, covr, glmnet, Matrix, kernlab, e1071, ranger,
knitr, rmarkdown, BiocStyle
rmarkdown, prettydoc, testthat, knitr, nlme, phangorn, plyr,
DECIPHER, randomForest, biomformat, scales, yaml, withr,
S4Vectors, purrr, seqmagick, glue, corrr, ggupset,
ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats, cli,
phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach
BiocStyle, breastCancerMAINZ, breastCancerNKI,
breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP,
breastCancerVDX, knitr, mGSZ, MIGSAdata, RUnit
testthat, MASS, mvtnorm, scater, scran, covr, knitr,
rmarkdown, uwot, BiocStyle, MouseGastrulationData, magick,
RCurl, curl, graphics
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
scRNAseq, scater, biomaRt, BiocStyle, knitr, rmarkdown
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, rmarkdown
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny
BiocStyle, edgeR, knitr, minfiData, rmarkdown,
tweeDEseqCountData, DMRcate, ExperimentHub
BiocStyle, covr, future, igraph, knitr, Matrix, progeny,
rmarkdown, sctransform, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, testthat (>= 3.0.0)
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, KEGGREST, annotate, Rgraphviz, GOstats, graph,
limma, mouse4302.db, reactome.db
MMDiffBamSubset, MotifDb, knitr, BiocStyle,
BSgenome.Mmusculus.UCSC.mm9
testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan,
phyloseq, curatedMetagenomicData, genefilter
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM
testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown,
markdown, covr, BiocStyle
testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny,
shinyFiles, shinydashboard, shinyjs
knitr, testthat, Seurat, ggpubr, foreach, psych,
MultiAssayExperiment, SummarizedExperiment,
SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown,
data.table, tidyverse, BiocStyle, Matrix
BiocStyle, knitr, rmarkdown, testthat, viper
JASPAR2020, BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene, knitr, rmarkdown, testthat,
BiocStyle, gridExtra
destiny, Hmisc, knitr, Seurat, scater, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
png
knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat
(>= 3.0.0)
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, formatR,
markdown
grImport, grImport2, BiocGenerics, MotifDb, RColorBrewer,
BiocStyle, knitr, RUnit, rmarkdown
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, rmarkdown
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown
BiocStyle (>= 2.5), ExperimentHub, knitr, lattice, mzR,
protViz (>= 0.7), rmarkdown, tartare (>= 1.5), testthat
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, preprocessCore
testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
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)
MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
msPurityData, CAMERA, RPostgres, RMySQL
multcomp, gridExtra, knitr, BiocStyle, RefManageR,
sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata,
MSnbase, matrixStats, MsCoreUtils
BiocStyle, knitr, rmarkdown, MSstatsBioData, tinytest, covr,
markdown
BiocStyle, knitr, rmarkdown, covr, tinytest
BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
BiocStyle, knitr, rmarkdown, tinytest, covr
BiocStyle, HDF5Array (>= 1.19.17), knitr, maftools (>=
2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival,
survminer, testthat
knitr, rmarkdown, 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)
org.Mm.eg.db, rlang, markdown, attempt, processx, testthat,
knitr, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, scater, bluster,
DropletUtils, scRNAseq
SNPlocs.Hsapiens.dbSNP144.GRCh37,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
BSgenome.Hsapiens.1000genomes.hs37d5,
BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, IRanges,
S4Vectors, rmarkdown, markdown, knitr, testthat (>= 3.0.0),
UpSetR, BiocStyle, covr, seqminer, Rsamtools, MatrixGenerics
BiocStyle, countsimQC, cowplot, ExperimentHub, iCOBRA, knitr,
phylogram, RColorBrewer, reshape2, rmarkdown, statmod,
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, rmarkdown
RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
testthat, BiocManager, rmarkdown
DSS, Mus.musculus, Homo.sapiens, knitr, rmarkdown, testthat
(>= 3.0.0), covr
biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf
roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown
grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly,
rlang, rmarkdown, ruv, qusage, shiny, testthat, xlsx
knitr, RUnit, BiocGenerics, BiocStyle, rmarkdown, markdown
knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics
testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran,
DropletUtils, igraph, BiocFileCache, SeuratObject
paxtoolsr, BiocStyle, org.Hs.eg.db, knitr, rmarkdown,
testthat, cgdsr
mixOmics, timeOmics, tidyverse, BiocStyle, testthat, covr,
rmarkdown, 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,markdown
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
testthat, knitr, rmarkdown, DNAcopy, RcppHMM, AnnotationHub,
nullrangesData, excluderanges, EnsDb.Hsapiens.v86,
microbenchmark, patchwork, plotgardener, magrittr, cobalt
knitr, rmarkdown, pheatmap, shiny, openssl, crayon, egg,
DESeq2, limma, DoubleExpSeq, Rsubread, testthat (>= 3.0.0)
BiocStyle, covr, knitr, recount, RefManageR, rmarkdown,
sessioninfo, SummarizedExperiment, testthat (>= 3.0.0),
GenomicFeatures, xfun
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
BiocStyle, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO,
parallelMap, ParamHelpers, Rgraphviz, rmarkdown, smoof,
supraHex, testthat
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, rmarkdown
flowWorkspaceData, knitr, rmarkdown, markdown, 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
remotes, knitr, BiocStyle, covr, markdown, rmarkdown, here,
testthat (>= 3.0.0), piggyback, badger, magick
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
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle, rmarkdown
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
testthat, knitr, BiocStyle, formatR, rmarkdown, RColorBrewer,
foreach, doSNOW, parallel, org.Hs.eg.db, clusterProfiler
testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat, scran, BiocGenerics, knitr, Biobase, GEOquery,
hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2,
airway, org.Hs.eg.db, magrittr, rmarkdown
testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr,
HDF5Array
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, BiocStyle, knitr, rmarkdown, data.table
pander, rmarkdown, knitr, knitcitations, crayon, testthat,
markdown
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq,
SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr,
mia
BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr,
withr
testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown,
org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle,
stringr, calibrate
foreach, doParallel, BiocStyle, knitr, rmarkdown, png,
GGally, gridExtra, ggforce, fgsea, RColorBrewer, ggpubr,
rtracklayer, ggbio, Gviz, data.tree, jsonlite
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, AnnotationDbi, energy, DOSE
ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr,
rmarkdown
AnnotationDbi, AnnotationHub, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures,
GenomeInfoDb, GenomicRanges, ggplot2, InteractionSet, knitr,
org.Hs.eg.db, rtracklayer, plotgardenerData, png, rmarkdown,
scales, showtext, testthat (>= 3.0.0),
TxDb.Hsapiens.UCSC.hg19.knownGene
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
knitr, DT, ontologyPlot, testthat, rmarkdown
Biobase, BiocStyle, covr, plotly, tidyverse, testthat (>=
2.3.2)
BiocStyle, knitr, rmarkdown, colr, metap, repmis
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
BiocStyle, knitr, rmarkdown, Gviz, rtracklayer, ggplot2,
BSgenome.Hsapiens.UCSC.hg38, testthat, stringr, stringi
knitr, rmarkdown, testthat, BiocCheck, BiocManager, BiocStyle
quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
testthat, rmarkdown, knitr, Rtsne, gridExtra
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, Cairo
airway, biomaRt, BiocFileCache, broom, Seurat,
SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl,
pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
BiocStyle, gridExtra, grid, testthat, devtools, knitr,
rmarkdown, ComplexHeatmap
testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, xtable,
rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, akima,
fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals,
reshape, magick
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData,
ropls
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, R.utils,
TxDb.Hsapiens.UCSC.hg19.knownGene, copynumber, covr, knitr,
optparse, org.Hs.eg.db, jsonlite, markdown, 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, mzR, BiocStyle, rmarkdown
SingleCellExperiment, HDF5Array, msdata, ggplot2, gplots,
dplyr, limma, magrittr, DT, shiny, shinydashboard, testthat,
knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats,
imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
gridExtra, knitr, qPLEXdata, rmarkdown, testthat, UniProt.ws,
vdiffr
BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle,
knitr, rmarkdown, BiocManager, MASS
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery,
knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat,
tibble
rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle
Gviz, BiocStyle, GenomicAlignments, Rhisat2, 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
rmarkdown, BiocStyle, knitr, pander, markdown
BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
RUnit, knitr, rmarkdown, gridExtra, annotatr, LOLA,
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Ecoli.NCBI.20080805
knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle,
testthat (>= 2.1.0), limma, sva
BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7),
rmarkdown, tartare (>= 1.5), testthat
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph
testthat, parallel, BiocStyle, knitr, rmarkdown
limma, biomaRt, RUnit, BiocGenerics, BiocStyle
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW,
parallel, rmarkdown
Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach,
gplots, rtracklayer, igraph, knitr,
RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat,
visNetwork
BiocStyle, knitr, rmarkdown, igraph, grDevices
knitr, rmarkdown, testthat, stringr, networkD3, visNetwork,
wesanderson
testthat, knitr, rmarkdown, ReactomeGSA.data, Biobase,
devtools
BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db,
prettydoc, testthat
testthat, igraph, XML, BiocManager, RCurl, bookdown,
rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows
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, DT,
edgeR, ggplot2, RColorBrewer
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
BiocStyle, knitr, rmarkdown,
BSgenome.Hsapiens.UCSC.hg19.masked, testthat
BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot
(>= 1.28.1), 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, rmarkdown, markdown
testthat, BiocStyle, knitr, rmarkdown, BiocSingular
knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db,
BiocStyle, restfulSEData, rmarkdown
mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown
R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics
RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve,
markdown
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, mockery
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), rhdf5 (>=
2.34.0)
BiocStyle, knitr, rmarkdown, tinytest, mockery
testthat, rmarkdown, knitr, BiocStyle, BSgenome,
BSgenome.Hsapiens.UCSC.hg19
knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment
RUnit, BiocStyle, knitr, BSgenome.Drerio.UCSC.danRer10,
edgeR, limma, testthat, rmarkdown
rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0)
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
AnnotationDbi, BiocStyle, covr, lintr, rcmdcheck, DT, httr,
jsonlite, kableExtra, kernlab, knitr, magick, MASS,
org.Hs.eg.db, R.utils, randomForest, readr, rmarkdown, rpart,
testthat (>= 3.0.0), tibble, tidyr,
TxDb.Hsapiens.UCSC.hg19.knownGene, futile.logger
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, sesame
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, Rgraphviz, ppiStats, ScISI, testthat
Biostrings, BiocStyle, testthat, knitr, rmarkdown
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,
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, rmarkdown, 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
knitr, BiocStyle, TPP, testthat, rmarkdown
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,
Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db,
org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, GEOquery, affy, airway, QUBIC
BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
parallel, crayon, RUnit, knitr, markdown, rmarkdown,
BiocGenerics, SNPRelate
BiocGenerics, BioNet, DLBCL, formatR, knitr, msm,
org.Sc.sgd.db, markdown, rmarkdown, RUnit
knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub,
ensembldb, edgeR, DEXSeq, stageR, DelayedArray
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Rnorvegicus.UCSC.rn6
Matrix, scater, uwot, RUnit, knitr, markdown, rmarkdown
BiocStyle, biomaRt, cowplot, destiny, knitr, scRNAseq,
robustbase, rmarkdown, uwot, NMF, testthat, pheatmap, snifter,
Biobase
testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle,
rmarkdown
PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra,
rmarkdown
BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize,
ComplexHeatmap, ggplot2, dplyr, MASS, viridisLite, mbkmeans
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
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, markdown, 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, splatter, scater, kableExtra, mclust,
TENxPBMCData
knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0)
testthat, knitr, BiocStyle, rmarkdown, patchwork, ggplot2,
impute, scater, sva, preprocessCore, vsn, uwot
DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0),
covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter,
SingleCellExperiment, microbenchmark
testthat, BiocStyle, knitr, rmarkdown, HDF5Array, scRNAseq,
dynamicTreeCut, ResidualMatrix, ScaledMatrix, DESeq2, monocle,
Biobase, pheatmap, scater
testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
knitr, rmarkdown, BiocStyle, scater, circlize, scales, Seurat
markdown, BiocGenerics, covr, DuoClustering2018, ggplot2,
knitr, rmarkdown, TENxPBMCData, testthat
testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens
knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s,
metagenomeSeq, epivizrStandalone, GenomeInfoDb
BiocStyle, knitr, scRNAseq, rmarkdown, testthat, scran
testthat, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, markdown, rmarkdown, Rsamtools,
VariantAnnotation
knitr, BiocStyle, rmarkdown, testthat, BiocManager
emojifont, knitr, rmarkdown, prettydoc, tibble
testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
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
BiocStyle, knitr, rmarkdown, ggplot2, pheatmap
testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions,
covr
BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
testthat, parallel, knitr, rmarkdown, BiocStyle
knitr (>= 1.30.0), mCSEA (>= 1.10.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICmanifest, testthat, minfiData
shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
BiocStyle, optparse, testthat, knitr, rmarkdown, tidyverse,
ggpubr
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,
signatureSearchData, DT
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, InteractiveComplexHeatmap (>= 0.99.11), shiny,
shinydashboard, cola, hu6800.db, rmarkdown
BiocStyle, knitr, biomaRt, stringr, monocle
testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq,
Rtsne
testthat, Rsubread, BiocStyle, knitr, lintr, xtable,
spelling, org.Mm.eg.db, stringr, kableExtra, shinythemes,
shinyBS, shinyjqui, shinyWidgets, shinyFiles, BiocGenerics
BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr,
parallel, rmarkdown, readr, SingleMoleculeFootprintingData,
testthat (>= 3.0.0)
testthat, knitr, rmarkdown, BiocStyle, BiocGenerics,
SingleCellExperiment, scuttle, scater, scran, scRNAseq,
ggplot2, pheatmap, grDevices, gridExtra, viridis, celldex
BSgenome, knitr, rmarkdown, RMySQL, RUnit
BiocStyle, devtools, knitr, magick, rmarkdown, testthat
BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat
BiocGenerics, BiocStyle, clusterExperiment,
DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl,
rmarkdown, testthat, uwot, covr
GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2,
Rtsne, Biobase, BiocStyle
BiocManager, bit64, covr, knitcitations, knitr (>= 1.6),
devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat
(>= 2.1.0)
knitr, rmarkdown, scRNAseq, BiocStyle, scater, scran,
scuttle, ggplot2, testthat (>= 3.0.0)
BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
testthat, knitr, parallel,
BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations,
ggdendro, fastICA, sva
BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown,
testthat
AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle,
DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin,
magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr,
PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown,
SummarizedExperiment, statmod, stringr, testthat, webshot
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, testthat, BiocStyle, BumpyMatrix
knitr, rmarkdown, BiocStyle, BiocSingular, RUnit,
BiocGenerics, ExpressionAtlas, DT, Biobase, GEOquery,
shinyWidgets, shinyjs, htmltools, shinyBS, sortable, scater,
scran
BiocManager, Biostrings, knitr, pheatmap, rmarkdown,
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat, covr
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2
covr, testthat, equatiomatic, universalmotif, kebabs,
ComplexHeatmap, rmarkdown, markdown, knitr, devtools,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
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
testthat, knitr, rmarkdown, ggplot2, tidyr
igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI
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
knitr, rmarkdown, testthat, BiocManager, BiocStyle
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, rappdirs
ggplot2, devtools, testthat (>= 2.1.0), roxygen2, rmarkdown,
tidyverse, knitr, ggbio, biovizBase,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
iCOBRA, BiocStyle, rmarkdown, 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
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
Hmisc, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools,
testthat (>= 2.1.0), roxygen2, knitr, plyranges, circlize,
tictoc, IRanges, SummarizedExperiment, rmarkdown
TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools,
testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges,
circlize, tictoc, IRanges, stats, SummarizedExperiment,
rmarkdown
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse,
BiocStyle
synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN,
BiocStyle
BiocStyle, knitr, rtracklayer, igraph, markdown, rmarkdown
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
BiocStyle, knitr, rmarkdown, systemPipeRdata,
GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
GenomicFeatures (>= 1.31.3), VariantAnnotation (>= 1.25.11)
testthat, BiocStyle, knitr, rmarkdown, systemPipeR,
systemPipeRdata, rhandsontable, zip, callr, pushbar, fs, readr,
R.utils, DESeq2, SummarizedExperiment, glmpca, pheatmap, grid,
ape, Rtsne, UpSetR, tidyr, esquisse (>= 1.0.2), cicerone
systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>=
3.0.0), BiocGenerics, Biostrings, methods
BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr,
pheatmap, rGREAT, SpectralTAD
tinytest, BiocStyle, ggimage, knitr, rmarkdown
testthat, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
ggplot2, Seurat, glmnet, cowplot, Matrix, rtracklayer,
BiocStyle
testthat (>= 2.1.0), knitr, rmarkdown, shinytest, shinyBS,
covr
BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra,
testthat (>= 3.0.0), covr
testthat, spelling, lintr, covr, knitr, rmarkdown, BiocStyle,
shiny, circlize, caret, dplyr, plyr, impute, sva, glmnet,
randomForest, MASS, class, e1071, pROC, HGNChelper
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, rmarkdown, 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, AnnotationFilter, Biobase,
GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors,
EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db,
GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR,
ggplot2, png, gwascat, MotifDb, motifStack, RColorBrewer,
rmarkdown
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, survminer, tidySummarizedExperiment,
markdown, uwot
BiocStyle, testthat, knitr, markdown, SingleCellSignalR,
SingleR, scater, scran, tidyHeatmap, igraph, GGally, Matrix,
uwot, celldex, dittoSeq, EnsDb.Hsapiens.v86
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, gplots, matrixStats, Matrix
EBImage, knitr, rmarkdown, testthat, tofsimsData,
BiocParallel, RColorBrewer
limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat,
reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr,
rmarkdown, BiocStyle
topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat,
BiocStyle, xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools,
PharmacoGx, xtable, markdown
biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr,
htmltools, rmarkdown
knitr, rmarkdown, testthat, covr, clusterExperiment
BiocNeighbors, DelayedArray, DelayedMatrixStats,
BiocParallel, testthat, knitr, BiocStyle, rmarkdown
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
testthat, TENxPBMCData, scran, knitr, rmarkdown
testthat, roxygen2, knitr, BiocStyle, rmarkdown
knitr, rmarkdown, BiocGenerics, RUnit, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, inline, parallel
scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors,
rmarkdown, knitr
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer
Biostrings, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, testthat, tidyr, vroom, xml2, yaml
knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0)
ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
RUnit, plyr, knitr, BiocGenerics, rmarkdown, formatR,
markdown, BiocParallel, BSgenome.Scerevisiae.UCSC.sacCer3,
BSgenome.Athaliana.TAIR.TAIR9
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats,
cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
BiocGenerics, shinycssloaders, tidyverse, BiocManager,
Biostrings, xtable, rlist, motifStack, knitr, rmarkdown,
testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis
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, scuttle, scran, metapod, BiocParallel,
BiocNeighbors, batchelor
fgsea, knitr, testthat, reticulate, rmarkdown
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown,
testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
BSgenome.Scerevisiae.UCSC.sacCer3
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, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats,
Matrix, fishpond
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, BiocParallel, seqLogo, motifStack, dplyr, ape,
ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
SC3, knitr, testthat, reticulate, rmarkdown
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, pkgdown, scran,
scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot,
GGally, patchwork, metR
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager
testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore,
knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr
GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
testthat, covr, knitr, rmarkdown, pkgdown
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown,
scater
RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
BiocStyle, knitr, rmarkdown,
IlluminaHumanMethylationEPICmanifest, irlba,
FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore
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
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
0.25.1), ncdf4, testthat, pander, magrittr, rmarkdown,
multtest, MALDIquant, pheatmap, Spectra (>= 1.1.17),
MsBackendMgf, progress
BiocStyle, knitr, rmarkdown, markdown, testthat,
BSgenome.Hsapiens.UCSC.hg38, pander
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
covr, spelling, testthat, knitr, rmarkdown, BiocStyle,
scRNAseq, HDF5Array, rhdf5, BiocFileCache
knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq,
ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2
rgl, XLConnect, edgeR, csaw, BSgenome, GenomeInfoDb,
profileplyr, rtracklayer, grid
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
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