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
methods, stats, zCompositions, lattice, latticeExtra
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 (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings
(>= 2.44.2), pwalign
R (>= 2.5.0), methods, Biobase, BiocManager, GO.db
R (>= 2.7.0), methods, stats4, BiocGenerics (>= 0.29.2),
Biobase (>= 1.17.0), IRanges
BiocGenerics (>= 0.15.10), BiocFileCache (>= 2.99.3)
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
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 (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc
R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
prettydoc, yaml
R (>= 3.5.0), Biostrings, GenomicAlignments, caTools,
GenomicRanges, grDevices, graphics, stats, utils
R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db
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, generics
R (>= 4.0), reticulate, methods, SummarizedExperiment
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
R (>= 3.5.0), igraph (>= 2.0.1.1), poweRlaw, latex2exp,
RSpectra, Rdpack
R (>= 3.5.0), 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 (>= 3.5), GenomicRanges, cowplot, breakpointRdata
R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=
0.17.28), IRanges (>= 2.13.16), Seqinfo, GenomicRanges (>=
1.61.1), Biostrings (>= 2.77.2), BiocIO, rtracklayer (>=
1.69.1)
R (>= 4.3.0), methods, BiocGenerics, IRanges, Seqinfo,
GenomeInfoDb (>= 1.45.5), Biostrings (>= 2.77.2), BSgenome (>=
1.77.1)
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),
Seqinfo, GenomicRanges, foreach, iterators, methods, parallel,
locfit
R (>= 2.10), biovizBase, GenomicRanges, IRanges, ggbio
R (>= 3.5), GenomicRanges (>= 1.61.1), rtracklayer (>=
1.69.1), SummarizedExperiment (>= 1.39.1)
methods, MultiAssayExperiment, R (>= 4.1.0)
R (>= 2.14.0), Biobase, binom, methods, stats
R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics,
S4Vectors, methods, stats, stats4
R (>= 4.4), BiocParallel, matter, ontologyIndex
methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix
R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment
R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase,
utils
R (>= 4.0), SingleCellExperiment, Matrix
R (>= 3.6), SingleCellExperiment, magrittr, methods, stats,
tibble, utils
R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment
R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML,
ggplot2, rmarkdown
R (>= 2.10), methods, Biobase (>= 2.5.5), marray
R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall
R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate,
Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest,
DT, RPMM
R (>= 4.2), ggplot2, SingleCellExperiment
R (>= 4.5.0), SingleCellExperiment, chevreulProcess
R (>= 4.5.0), SingleCellExperiment, scater
R (>= 4.5.0), SingleCellExperiment, shiny (>= 1.6.0),
shinydashboard, chevreulProcess, chevreulPlot
Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors,
ensembldb, AnnotationFilter, data.table
R (>= 3.5.0),GenomicRanges, Biostrings, BSgenome, RcppRoll,
parallel
R (>= 3.5.0), ggplot2, DiffBind, GenomicRanges (>= 1.17.19),
BiocParallel
R (>= 3.5.0), 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 (>= 4.1.0), generics, methods, S4Vectors,
MultiAssayExperiment, BiocParallel, survival
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 (>= 3.5.0), 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 (>= 3.5.0), methods, topGO, GenomicRanges
R (>= 4.0.0), methods, grid, graphics, stats, grDevices
R (>= 4.1), methods, AnnotationFilter, S4Vectors
R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges,
BiocParallel
R (>= 3.5.0), minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylationEPICmanifest
R (>= 4.1), BiocGenerics, SummarizedExperiment
R (>= 4.0.0), SummarizedExperiment, S4Vectors
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
R (>= 2.10), methods, Rsamtools (>= 1.19.17), rtracklayer
R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0)
R (>= 3.5.0), BiocGenerics, Biostrings, GenomicFeatures
R (>= 2.15.0), S4Vectors, IRanges, Seqinfo, GenomicRanges
R (>= 3.5.0), GenomicRanges (>= 1.61.1), SummarizedExperiment
(>= 1.39.1)
SummarizedExperiment, GenomicRanges, IRanges, S4Vectors,
rtracklayer
R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2,
reshape2, fastcluster, rtracklayer, Gviz
R (>= 3.5.0), IRanges, AnnotationDbi, biomaRt (>= 2.17.1)
R (>= 4.0), EBImage, SingleCellExperiment, methods
R (>= 3.5.0), SummarizedExperiment, ggplot2
R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid
R (>= 2.13.0), methods, graphics, parallel, IRanges,
GenomicRanges, SummarizedExperiment, Biostrings, VGAM,
VariantAnnotation (>= 1.27.6),
R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=
0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.27.2),
IRanges (>= 2.17.3), S4Arrays (>= 1.5.4), SparseArray (>=
1.7.5)
MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7)
SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6)
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, DSS, dendextend,
psych, sva
R (>= 4.3.0), SingleCellExperiment, VariantAnnotation,
ensembldb
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 (>= 1.39.6),
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 (>= 4.3.0), variancePartition (>= 1.36.1),
SingleCellExperiment, ggplot2
R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel
R (>= 4.1.0), GenomicRanges, BiocFileCache
blockmodeling, gplots, testthat, R (>= 3.0.0)
R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0),
GenomicRanges
R (>= 3.5.0), BiocGenerics (>= 0.15.10), GenomicRanges (>=
1.61.1), GenomicFeatures (>= 1.61.4), AnnotationFilter (>=
1.5.2)
R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment
R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase
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), RSKC (>= 2.4.2), sparcl (>= 1.0.4)
R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment
Rsubread, GenomicRanges, rtracklayer, matrixStats, IRanges
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.99.3),
BiocFileCache (>= 2.99.3)
utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData
(>= 1.21.3)
R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment,
SpatialExperiment, TreeSummarizedExperiment
R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2, RCurl, jsonlite, BiocStyle
BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0),
ggside (>= 0.3.1), SummarizedExperiment, tibble
methods, LiquidAssociation, parallel, doParallel, stats,
Hmisc, utils
R (>= 4.2.0), 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(>= 3.2), 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 (>= 4.0.0), methods, BiocGenerics (>= 0.37.0), S4Vectors (>=
0.27.12), IRanges (>= 2.23.9), Seqinfo, GenomicRanges (>=
1.61.1), SummarizedExperiment (>= 1.39.1), Biostrings (>=
2.77.2), Rsamtools (>= 2.25.1)
BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics,
methods, Rsamtools (>= 2.25.1), rtracklayer (>= 1.69.1),
SummarizedExperiment (>= 1.39.1)
R (>= 4.0.0), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges,
biomaRt, ggplot2
R (>= 4.0.0), methods, stats4, BiocGenerics (>= 0.53.2),
S4Vectors (>= 0.45.2), IRanges (>= 2.41.1), Seqinfo
R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods,
BiocGenerics (>= 0.13.8)
shiny, limma, Biobase, plotly, enrichR, R (>= 4.1.0)
R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors
methods, BiocGenerics, ggplot2 (>= 1.0.0)
R (>= 4.3.0), ggplot2, ggraph, XML, igraph, tidygraph
R (>= 4.0.0), stats, methods, graphics, GGally, network, sna,
scales, matrixStats
R (>= 3.5), Matrix, MASS, locfdr, stats, utils
circlize, GenomicRanges, graphics, R (>= 4.0)
R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus,
dashboardthemes, shinyWidgets, shinymeta, tidyverse,
operator.tools, maftools
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 (>= 4.1.0), MASS, parallel, S4Vectors (>= 0.17.25), IRanges
(>= 2.13.12), Seqinfo, GenomicRanges (>= 1.31.8),
GenomicAlignments (>= 1.15.6), rtracklayer (>= 1.39.7)
shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5,
R(>= 2.10.0)
R (>= 4.5.0), Biobase, SummarizedExperiment
R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures,
AnnotationDbi
R (>= 3.1.2), grid, IRanges, GenomicRanges
R (>= 3.5.0), GenomicRanges, BiocGenerics
GenomicFeatures, rtracklayer,AnnotationDbi, GenomicRanges,
magrittr, ggplot2, methods, stats,utils ,knitr,dplyr
R (>= 4.5), methods, rhdf5, BiocGenerics, SparseArray
R(>= 4.3), QFeatures, S4Vectors, Spectra
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), Seqinfo, SummarizedExperiment, BiocIO
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
ggfortify, R (>= 4.1), SummarizedExperiment (>= 1.16)
R (>= 4.4.0), SummarizedExperiment (>= 1.1.6), GenomicRanges,
IRanges, S4Vectors
R (>= 3.6), utils, curl, rhdf5, R6, grid
InteractionSet, GenomicRanges, SummarizedExperiment, R (>=
4.1.0)
R (>= 4.1), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5),
MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
R (>= 3.5.0), Biostrings, pwalign, GenomicAlignments,
BiocParallel, hiAnnotator
R (>= 2.15.0), methods, IRanges, GenomicRanges
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
R (>= 3.5.0), Biobase, IRanges, GenomicRanges, RColorBrewer,
rtracklayer, graphics, GenomeInfoDb
R (>= 2.10), methods, Biobase, annotate, plotrix
R (>= 3.5.0), GenomicRanges, GenomicAlignments, BrowserViz (>=
2.17.1)
R (>= 3.5.0), GenomicRanges, methods, shiny
R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
R (>= 3.6), methods, Biobase, BiocParallel
R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges,
MultiAssayExperiment, SummarizedExperiment,stats
R (>= 2.14.0), plyr, ggbio, GenomicRanges
R (>= 3.5.0), methods, BiocGenerics, grid
R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment,
edgeR, S4Vectors, GenomicFiles
R (>= 4.1), mclust, BiocParallel, survival
R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1),
AnnotationHub
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2),
S4Vectors (>= 0.45.4)
R(>= 4.2.0), Matrix, parallel, BiocParallel,
SummarizedExperiment, BiocGenerics, lme4, nnls
R (>= 4.2), limma, DEXSeq, satuRn (>= 1.7.0), sva, ggplot2 (>=
3.3.5), pfamAnalyzeR
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 (>= 4.0), ggplot2, parallel, stats, S4Vectors
R (>= 3.5.0), S4Vectors, SingleCellExperiment,
SummarizedExperiment, methods, rhdf5, BiocIO
R (>= 4.1), ExperimentHub, AnnotationHub
R (>= 4.3.0), stats, methods, utils, SummarizedExperiment,
SingleCellExperiment, BiocGenerics
S4Vectors, adabag, GenomicRanges, R (>= 4.1)
R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
R (>= 4.4), BiocParallel, Matrix, methods
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 (>= 4.0), Rsolnp, snowfall, deSolve, CNORode
R (>= 4.0), R6 (>= 2.0), GenomicRanges, BiocParallel
R(>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer
R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea,
ggplot2, ggrepel
R (>= 4.0.0), DESeq2, limma, locfit, splines
GenomicRanges, ggplot2, R (>= 4.0), SummarizedExperiment
R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign
R (>= 4.1.0), methylclockData, devtools, quadprog
R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods
R (>= 3.5.0), methods, grDevices, graphics, stats, utils,
GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools
Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment,
SummarizedExperiment, BiocGenerics
R (>= 4.1.0), MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3)
R (>= 4.1.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0),
SummarizedExperiment, TreeSummarizedExperiment
R (>= 4.3.0), SummarizedExperiment, stats
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 (>= 1.61.1),
SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2),
bumphunter (>= 1.1.9)
R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICv2anno.20a1.hg38
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
Biostrings, GenomicRanges, ggplot2 (>= 4.0.0), R (>= 4.5.0),
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
limma
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.2.1), GenomicFeatures, txdbmaker
R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors,
SummarizedExperiment
R (>= 3.6), SummarizedExperiment, S4Vectors
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
R (>= 4.2.0), magrittr, dplyr, ggplot2, edgeR, RUVSeq, DESeq2,
limma, rhdf5, foreach, Rfast, octad.db, stats, httr, qpdf,
ExperimentHub, AnnotationHub, Biobase, S4Vectors
dplyr, optimalFlowData, rlang (>= 0.4.0)
R (>= 2.14.0), BiocGenerics (>= 0.15.10), AnnotationDbi (>=
1.33.15), Seqinfo, GenomicFeatures (>= 1.61.4)
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 (>= 3.0.0), methods, Biobase, BiocGenerics,
R (>= 3.5), cn.mops, methods, utils, stats, graphics
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
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 (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges
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), oligo (>= 1.32.0),graphics,grDevices, methods,
stats, utils, mclust, oligoClasses
R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1)
BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)
R (>= 3.5.0), methods, BiocGenerics, Biostrings
R (>= 4.1), MultiAssayExperiment (>= 1.33.6)
R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
R (>= 4.4), parallel, GenomicRanges, Rbowtie
GenomicRanges, Rsamtools, rtracklayer, VGAM, qvalue
R (>= 2.12.0), methods, VariantAnnotation (>= 1.25.11),
Biostrings (>= 2.47.6), pwalign, Biobase
R (>= 4.2.0), gdsfmt, SNPRelate, stats, utils, GENESIS, dplyr,
Rsamtools
R (>= 3.2.1), stats, methods, Rmpfr, gmp
R (>= 4.1.0), DelayedArray, BiocGenerics
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 (>= 4.4.0), SummarizedExperiment, methods
R (>= 4.0.0), S4Vectors, dplyr, tibble, BiocSet,
SummarizedExperiment
R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
R (>= 2.6.0), methods, utils, graph, grid
R (>= 4.0.0), GenomicRanges, IRanges, methods
R (>= 4.1), Rsamtools, GenomicFeatures, GenomicAlignments
R (>= 3.0.2), methods, GenomicRanges, abind
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, grid, gridExtra, limma, matrixStats, methods,
illuminaio, methylumi, plyr, reshape2
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
R (>= 3.5.0), methods, Seqinfo, GenomicRanges (>= 1.61.1),
Biostrings (>= 2.77.2)
foreach, doParallel, parallel, Biostrings, methods, utils
R (>= 3.5), methods, GenomicRanges (>= 1.37.2)
R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>=
0.45.2), S4Vectors, IRanges
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.53.2)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER,
parallel, reshape2, 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 (>= 3.5.0), Biostrings, pwalign, stringr
R (>= 4.3), RaggedExperiment, GenomicRanges
R (>= 3.5.0), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment
methods, SCArray (>= 1.13.1), SeuratObject (>= 5.0), Seurat
(>= 5.0)
R (>= 4.0), S4Vectors, SingleCellExperiment,
R (>= 3.6), SummarizedExperiment, dynamicTreeCut,
SingleCellExperiment
SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1)
R (>= 3.4), methods, SummarizedExperiment
R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb,
BSgenome.Hsapiens.UCSC.hg19
R (>= 4.0), methods, epivizr, SummarizedExperiment
R (>= 4.3), basilisk, shiny, SingleCellExperiment
R (>= 4.0), SummarizedExperiment, ComplexHeatmap
R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
GenomicRanges, ShortRead, stats
R (>= 3.1), AnnotationDbi, GO.db, annotate
R (>= 4.2), GenomicRanges, IRanges, S4Vectors
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
BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db
R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
R (>= 3.5.0), GenomicRanges, Rsamtools, data.table, checkmate
R (>= 3.5.0), BiocGenerics, SummarizedExperiment
R (>= 4.1.0), methods, SingleCellExperiment
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 4.3.0), SummarizedExperiment, CATALYST
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 (>= 3.5.0), methods, Rsamtools, Biostrings, reshape,
ggplot2, RColorBrewer, stats
ggplot2 (>= 3.5.0), Rsamtools, S4Vectors
GenomicRanges, rtracklayer, VariantAnnotation, BiocGenerics, R
(>= 4.1.0)
R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3),
GenomicRanges (>= 1.61.4), Biobase
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
GenomicRanges, rtracklayer, VariantAnnotation,
StructuralVariantAnnotation, BiocGenerics, Biostrings, R (>=
4.0)
GenomicRanges, rtracklayer, BiocGenerics,
StructuralVariantAnnotation, R (>= 4.0)
Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1),
methods
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment
R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0)
SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7)
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.6), EpiDISH, limma, nnls, quadprog
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R (>= 3.5.0), grDevices, methods, GenomicRanges, grid
R (>= 2.15.0), methods, limma, anota, DESeq2, edgeR, RankProd,
topGO, org.Hs.eg.db, GOSemSim, Heatplus, gplots, plotrix,
Biobase
R (>= 3.5.0), GenomicRanges, IRanges,
BSgenome.Hsapiens.UCSC.hg19
R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18),
Biostrings
R (>= 3.5), GenomicRanges, Structstrings
R (>= 3.6), GenomicRanges, Modstrings, Structstrings, tRNA
R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils
BiocGenerics, S4Vectors, Seqinfo, GenomicRanges (>= 1.61.1),
GenomicFeatures (>= 1.61.4)
R (>= 2.15.2), methods, BiocGenerics, Biobase
R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors
R (>= 3.5.0), BiocGenerics (>= 0.13.6), GenomicRanges (>=
1.27.6), SummarizedExperiment (>= 1.5.3)
Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
R (>= 4.3.0), ggplot2, limma (>= 3.62.2), BiocParallel
R (>= 4.0.0), methods, BiocGenerics (>= 0.37.0),
MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1),
SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1)
R (>= 3.5.0), methods, BiocGenerics (>= 0.25.1),
VariantAnnotation (>= 1.13.29)
R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28)
R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3)
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 (>= 4.3.0), methods, BiocGenerics (>= 0.15.3),
SummarizedExperiment
R (>= 4.0.0), 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, DNAcopy, tilingArray, waveslim, cluster, aCGH
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
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
alabaster.matrix, alabaster.ranges, alabaster.se,
alabaster.sce, alabaster.spatial, alabaster.string,
alabaster.vcf, alabaster.bumpy, alabaster.mae
alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>=
2.47.6), jsonlite, jsonvalidate, Rcpp
methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges
methods, alabaster.se, S4Vectors, jsonlite, rhdf5
methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.33.3),
S4Arrays, SparseArray (>= 1.5.22), rhdf5 (>= 2.47.1),
HDF5Array, Matrix, Rcpp
methods, S4Vectors, BiocGenerics, IRanges, Seqinfo, rhdf5
methods, alabaster.ranges, alabaster.matrix, BiocGenerics,
S4Vectors, IRanges, GenomicRanges, jsonlite
methods, utils, grDevices, S4Vectors, alabaster.sce, rhdf5
methods, S4Vectors, alabaster.se, alabaster.string, Rsamtools
Rfast, BiocParallel, GenomicRanges, IRanges, S4Vectors,
SummarizedExperiment, multtest, directlabels
rmarkdown (>= 2.5), tools, methods, ggplot2 (>= 3.4.0),
GGally, dplyr, rjson, shiny, shinydashboard, DT, stats, utils,
tximport (>= 1.17.4), cowplot, rlang, Rcpp
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
rjsoncons (>= 1.0.1), DBI, duckdb (>= 1.3.1), rlang, curl,
BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats,
tools, methods, whisker, ggplot2
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, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack,
doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest,
multcomp, nloptr, parallel, utils
igraph, Biobase, survival, MASS, stats, RColorBrewer
ape, assertthat, caret, covr, DESeq2, dplyr, DT, forcats,
ggforce, ggplot2, GUniFrac, lattice, limma, magrittr, Matrix,
methods, MultiAssayExperiment, plotly, rentrez, reshape2,
ROCit, S4Vectors (>= 0.23.19), scales, shiny, shinyjs, stats,
SummarizedExperiment, tibble, tidyr, tsne, umap, utils, vegan,
XML
DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice,
Rsamtools, genefilter, IRanges, BiocGenerics
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), httr
DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr2,
yaml, dplyr
GenomicFeatures, Rsamtools, rtracklayer, BiocGenerics,
jsonlite, BiocManager, biocViews, BiocCheck, graph,
AnnotationDbi, Biobase, Biostrings, DBI, Seqinfo, GenomeInfoDb
(>= 1.45.5), OrganismDbi, RSQLite, AnnotationForge,
futile.logger (>= 1.3.0), XML, RCurl
AnnotationDbi, AnnotationHub, dplyr, GenomicFeatures (>=
1.61.4), GenomicRanges (>= 1.61.1), Seqinfo, ggplot2, IRanges,
methods, readr, regioneR, reshape2, rtracklayer (>= 1.69.1),
S4Vectors (>= 0.23.10), stats, utils
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
stats, utils, methods, futile.logger, GCPtools, jsonlite,
httr, rapiclient, yaml, tibble, shiny, DT, miniUI, htmltools,
BiocBaseUtils
AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods,
rjsoncons, tibble, utils
httr, httr2, dplyr, jsonlite, methods, tibble
methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr,
dplyr, lubridate, plotly, ggplot2
AnVILBase, BiocBaseUtils, dplyr, GCPtools (>= 0.99.2), httr,
jsonlite, methods, rlang, stats, tibble, tidyr, utils
AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite,
rmarkdown, yaml, readr, whisker, tools, utils, stats
AnVIL, dplyr, jsonlite, rlang, tibble, tidyr, utils, methods,
plyr, stringr
GenomicRanges, GenomicFeatures, GenomicAlignments, DESeq2,
ggrepel, SummarizedExperiment, Rsubread, stats, ggplot2,
methods, rtracklayer, VariantAnnotation, dplyr, tidyr, repmis,
Rsamtools, HybridMTest
emdbook, SummarizedExperiment, GenomicRanges, methods, stats,
utils, Rcpp
Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly,
SeuratObject, SingleCellExperiment, magrittr,
SummarizedExperiment, topGO, methods, stats, utils,
org.Hs.eg.db, org.Mm.eg.db, rlang
shiny, shinyjs, DT, VariantAnnotation, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
Homo.sapiens, SNPlocs.Hsapiens.dbSNP144.GRCh37,
XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, 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, stats, GenomicRanges, S4Vectors,
GenomicFeatures, IRanges, GenomicScores, SummarizedExperiment
oligo, limma, httr, utils, jsonlite, rlang, tools, methods
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
GenomicRanges, GenomicFeatures, BiocGenerics, IRanges,
GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle,
igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid,
graphics, pbmcapply, txdbmaker
Biostrings, GenomicRanges, IRanges, graphics, grDevices,
methods, stats, utils
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
ggplot2, yaml
SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp
(>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize,
grid, grDevices, graphics
BSgenome, Biostrings, ChIPpeakAnno, IRanges, GenomicRanges,
GenomicAlignments, GenomeInfoDb, GenomicScores, graphics, grid,
limma, Rsamtools (>= 1.31.2), randomForest, rtracklayer, stats,
motifStack, preseqR, utils, KernSmooth, edgeR, BiocParallel
BiocGenerics, S4Vectors, IRanges, Matrix, GenomicRanges,
GenomicAlignments, Seqinfo, SummarizedExperiment, Rsamtools,
motifmatchr, TFBSTools, stats, pracma, ggplot2, ggrepel, dplyr,
limma, methods, rtracklayer
methods, stats, Matrix, BiocGenerics, MatrixGenerics,
BiocParallel, S4Vectors, IRanges, Seqinfo, GenomicFeatures,
GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb,
SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli
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
DelayedArray, DelayedMatrixStats, data.table, graphics,
grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats,
SummarizedExperiment, BiocGenerics, utils
abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster,
codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce,
ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma,
lme4, magrittr, matrixStats, methods, MultiAssayExperiment,
parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors,
scales, stats, stringi, SummarizedExperiment, survival, tidyr,
tidyselect, tools, utils, vsn
dplyr, Peptides, progress, purrr, ranger, rlang, stats,
stringr, tidyr, toOrdinal, 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), Seqinfo
BiocGenerics, BiocParallel, data.table, dplyr, tidyr,
GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr,
knitr, methods, BiocParallel, robustbase, BiocStyle,
ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils,
grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>=
0.19-4)
aricode, BiocParallel, data.table, dbscan, SpatialExperiment,
SingleCellExperiment, SummarizedExperiment, S4Vectors, stats,
Matrix, MatrixGenerics, mclust, igraph, irlba, leidenAlg (>=
1.1.0), utils, uwot, RcppHungarian
magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap,
ggplot2, logistf, limma, stats, igraph, utils, data.table,
S4Vectors, SummarizedExperiment
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 (>= 1.5.0), matrixStats, assertthat,
reshape2, BiocParallel, posterior, hexbin
methods, glmGamPoi, scran, scuttle, stats, utils,
SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), rstantools (>= 2.1.1)
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats,
BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat
data.table, DESeq2, dplyr, EBSeq, ggdendro, ggnewscale,
ggplot2, limma, matrixStats, pheatmap, RColorBrewer, reader,
reshape2, scran, shiny, shinyjs, shinythemes, stats,
SummarizedExperiment, sva, S4Vectors, tibble, tidyr, tidyverse,
umap, utils
scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2,
RColorBrewer, scales, SummarizedExperiment
Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran,
SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, magrittr,
assertthat, arrow, mclust, RCurl, DirichletReg, xgboost (<
2.0.0), utils, dplyr, rlang, ggplot2, tibble, rjson, tidyr,
scales, microbenchmark, BiocFileCache, BiocSingular,
BiocParallel
Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix,
parallel, MASS, locfit, fitdistrplus, stats, methods, graphics,
grDevices, SingleCellExperiment, SummarizedExperiment,
BiocParallel, utils
edgeR, GenomicRanges, abind, parallel, graphics, stats, utils
SummarizedExperiment, VariantAnnotation, Rsamtools, grDevices,
GenomicRanges, IRanges, Biostrings
methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics,
Matrix, Rcpp
methods, beachmat, HDF5Array, DelayedArray, Rcpp
methods, beachmat, tiledb, TileDBArray, DelayedArray, Rcpp
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio, methods, ggplot2
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
abind, stats, graphics, utils, methods, dixonTest, ids
AnVIL (>= 1.16.0), BiocFileCache, dplyr, GenomeInfoDb,
GenomicRanges, httr, methods, purrr, rtracklayer, rlang,
R.utils, stats, stringr, tibble, tidyr, tools, utils
cli, edgeR, BiocParallel, methods, progressr, stats,
SummarizedExperiment, utils
cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators
(>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>=
0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods,
BiocParallel
stats, ggplot2, scales, methods, pROC, foreach, doParallel,
parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils
dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6),
tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid,
methods, cowplot, Hmisc, sortable, shinyjqui, grDevices,
scales, DT, SummarizedExperiment, S4Vectors
GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt,
jsonlite, methods, dplyr, data.table, sjmisc, grDevices,
graphics, stats, utils, rslurm, rhdf5, txdbmaker
R.utils, data.table, curl, RCurl, digest, methods, stats,
utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata,
HDF5Array, bread
stats, utils, GEOquery, graphics, BiocGenerics, illuminaio
tidyr, tibble, plyr, matrixStats, stats, ggplot2, methods,
rtracklayer, S4Vectors, ggforce, GenomeInfoDb, ComplexHeatmap,
RColorBrewer, lifecycle, rlang, forcats, dplyr,
GenomicFeatures, IRanges, kableExtra, ggdist
BiocBaseUtils, BiocGenerics, BiocIO, curl, GenomicRanges,
IRanges, methods, Rsamtools, S4Vectors, Seqinfo, stats, utils,
XVector
R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, 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
BiocGenerics, available, cli, glue, gert, gh, gitcreds, httr,
usethis, dplyr, purrr, tibble, methods, rprojroot, stringr,
yaml, tools, utils, rlang, quarto, renv
BiocBaseUtils, BiocFileCache, BiocManager, biocViews, callr,
cli, codetools, graph, httr2, knitr, methods, rvest,
stringdist, tools, utils
DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils,
methods, BiocBaseUtils
methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl,
httr2
Rgraphviz, geneplotter, graph, BiocGenerics, methods
AnnotationHub, ExperimentHub, DT, htmlwidgets, rclipboard,
S4Vectors, shinyAce, shinybiocloader, shinyjs, shinythemes,
utils
stats, utils, futile.logger, parallel, snow, codetools
BiocFileCache, BiocManager, biocViews, tibble, methods, rlang,
stringr, stats, rvest, dplyr, xml2, readr, httr, httr2,
htmltools, DT, tools, utils, igraph (>= 2.0.0), jsonlite, gh,
RBGL, graph, curl, glue, lubridate, purrr, tidyr, yaml
methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO,
AnnotationDbi, KEGGREST, ontologyIndex, tidyr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>=
2.21.1)
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
R6, RSQLite, Rcpp, XML, chk, fscache (>= 1.0.2), git2r,
jsonlite, lgr, lifecycle, methods, openssl, plyr, progress,
rappdirs, sched (>= 1.0.1), stats, stringr, tools, withr, yaml
ggplot2, graphics, Rcpp, SummarizedExperiment, animation,
rlang, biocViews, sessioninfo, BiocStyle
AnnotationDbi, BiocFileCache, curl, httr2, progress, stringr,
utils, xml2
stringr, viridis, fgsea, grid, methods, AnnotationDbi, dplyr,
GO.db, org.Hs.eg.db (>= 3.19.1), rSpectral, WGCNA, ggplot2,
ggrepel, minpack.lm, cowplot, data.table, scales, stats, Matrix
WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva,
RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel,
patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep,
stats, grDevices, utils, methods, BiocParallel, minet, GENIE3,
SummarizedExperiment
igraph (>= 1.0.1), AnnotationDbi, Biobase
methods, utils, grDevices, stats, crayon
igraph, cluster, psych, stringr, GenomicRanges, MASS, scran,
methods, stats, utils, grDevices, graphics, foreach, doParallel
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),
Seqinfo, GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1),
SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2),
Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1),
GenomicFeatures (>= 1.61.4), AnnotationDbi, VariantAnnotation
(>= 1.55.1), ensembldb (>= 2.33.1), AnnotationFilter (>=
0.99.8), rlang
readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools,
data.table, Biobase, GenomicRanges, IRanges, BiocGenerics,
VariantAnnotation, DelayedMatrixStats, SummarizedExperiment,
GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats,
rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools,
BiocParallel
methods, BiocGenerics, Biobase, S4Vectors, IRanges, Seqinfo,
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, Seqinfo,
S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage,
utils, HiCBricks
CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr,
GenomicRanges, ggforce, stringr, plyranges, methods, utils,
magrittr
doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist,
bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot,
dplyr, rlang, GenomicRanges
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
plyr, kernlab, gbm, stringr, cowplot, ggplot2, biomaRt,
Biostrings, parallel, utils, stats,
BSgenome.Hsapiens.UCSC.hg38, rtracklayer, GenomicRanges,
Seqinfo, IRanges, S4Vectors, data.table
methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>=
1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2,
BiocGenerics, gtools, doParallel, foreach
methods, Biobase, tidyselect, dplyr, ggplot2, magrittr, rlang,
stringr, withr, edgeR, ComplexHeatmap, impute (>= 1.80.0),
data.table (>= 1.16.0), RColorBrewer (>= 1.1-3), circlize (>=
0.4.16), ggrepel (>= 0.9.6), e1071 (>= 1.7-8),
SummarizedExperiment
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
GenomicRanges, methods, rlang, S4Vectors, utils
BiocStyle, DELocal, EBSeq (>= 1.38.0), DESeq2 (>= 1.38.2),
NOISeq, forcats (>= 1.0.0), genefilter, ggplot2, ggplotify,
plyr, clusterProfiler (>= 4.8.2), pheatmap, sechm (>= 1.6.0),
stringr, purrr (>= 0.3.5), edgeR (>= 3.40.1)
utils, stats, matrixStats, XVector, Rsamtools (>= 2.25.1)
utils, stats, Biobase, S4Vectors, GenomicRanges (>= 1.61.1),
BiocIO, rtracklayer (>= 1.69.1)
IRanges (>= 2.23.9), Seqinfo, scales, stats, parallel, tools,
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, beachmat (>= 2.23.2)
BiocGenerics (>= 0.31.6), BiocStyle, Biobase, ggplot2,
WriteXLS, gtools, RColorBrewer, limma, grid, gtable, gridExtra,
biovizBase, e1071, methods, grDevices, stats, utils
BiocFileCache, httr2, RCurl, cli, curl, rlang, jsonlite,
matrixStats, methods, doParallel, glmnet, ggalluvial, ggplot2,
gridExtra, grid, Rtsne, ggrepel, foreach, multtest, igraph,
orthogene, stabledist, circlize (>= 0.4.14), ComplexHeatmap (>=
2.0.0), stats, scales, RANN, SpatialExperiment,
SummarizedExperiment, tools
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
SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
grDevices, methods, stats, utils
doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi,
MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats,
SummarizedExperiment
affy, ggplot2, annotate, grid, gridExtra, tcltk, Biobase
pryr(>= 0.1.3), assertthat(>= 0.2.0), methods(>= 3.6.3),
Matrix(>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>=
0.16.0), IRanges(>= 2.12.0), Seqinfo, GenomicFeatures(>=
1.61.4), GenomicAlignments(>= 1.45.1), BiocParallel(>= 1.12.0),
GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>=
1.9.4), GenomicInteractions(>= 1.15.1)
ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges,
IRanges, reshape2, methods, BioNERO
BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR,
data.table, formula.tools, Seqinfo, GenomicAlignments (>=
1.45.1), GenomicFeatures (>= 1.61.4), GenomicRanges (>=
1.61.1), ggplot2 (>= 2.2.0), gtools, IRanges (>= 2.18.0),
KernSmooth, memoise, plyr, rlang, Rsamtools (>= 2.25.1),
reshape2, rtracklayer (>= 1.69.1), S4Vectors (>= 0.27.5),
scales, som, stringdist, stringi, SummarizedExperiment (>=
1.39.1), utils, vegan, VGAM
ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr,
DT, MesKit, maftools, data.table, utils, stats, methods, tidyr
GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart,
survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr,
graphics, stats, utils, grDevices, R.oo, R.methodsS3
combinat, GenomeInfoDb, GenomicRanges, ggplot2, ggtree,
Matrix, matrixStats, methods, pheatmap, snpStats, S4Vectors,
utils, VariantAnnotation, vcfR
CardinalIO, Biobase, EBImage, graphics, grDevices, irlba,
Matrix, matter (>= 2.7.10), nlme, parallel, utils
Rcpp (>= 1.0.7),RcppArmadillo, SummarizedExperiment, methods,
MCMCpack, fields, wrMisc, concaveman, sp, dplyr, sf, Matrix,
RANN, ggplot2, reshape2, RColorBrewer, S4Vectors, scatterpie,
grDevices,ggcorrplot, stats, nnls, BiocParallel, RcppML, NMF,
spatstat.random, gtools, SingleCellExperiment,
SpatialExperiment
readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson,
rmarkdown
circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel,
ggridges, graphics, grDevices, grid, gridExtra, 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
Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma,
reshape2, rdist, igraph, geometry, Rfast, data.table, abind,
pheatmap, EBImage, S4Vectors, SeuratObject,
SingleCellExperiment, SpatialExperiment, Matrix, methods,
SummarizedExperiment, msigdbr
BiocFileCache, RColorBrewer, cBioPortalData, genefilter,
gplots, grDevices, stats, utils, openxlsx, zip
BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr,
Seqinfo, GenomicRanges, httr, IRanges, methods, readr,
RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors,
SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>=
1.9.4), utils
ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7),
patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot,
reshape2, ggforce, dplyr, tidyr, stringr, depmap,
ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist,
purrr, pvclust, stats, rlang
utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite,
rapportools, basilisk, reticulate, shinyBS, shinycssloaders,
rintrojs, rlang, markdown
Rcpp, sparseMatrixStats, stats, BiocParallel, irlba,
SingleCellExperiment, Matrix, SummarizedExperiment
plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph,
scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump,
stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales,
viridis, grDevices, graphics, stats, methods
matrixStats, Seurat, SeuratObject, stats, BiocParallel,
ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment,
SummarizedExperiment, methods
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, dbscan, DelayedArray,
stringr, ComplexHeatmap, gridExtra, circlize, dendextend,
ggdendro, pROC
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, seqinr,
Rsamtools
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
assertthat, 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
base, ggplot2, ggforce, ggtree, patchwork, ape, methods, Rcpp
(>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
2.18.1), rstantools (>= 2.4.0), stats, utils, scales
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
httr, curl, utils, tools, cli, shiny, DT, rjsoncons
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,
dplyr, purrr
furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr,
future, stats
circlize, ComplexHeatmap, clusterProfiler, DESeq2, dplyr,
GenomicTools.fileHandler, GGally, ggnetwork, ggplot2, ggpubr,
ggrepel, graphics, grid, igraph, Matrix, network, Rcpp, RCy3,
stats, SummarizedExperiment, S4Vectors, utils, methods
Rsamtools, Seqinfo, GenomicRanges, rtracklayer, idr,
RColorBrewer, genomation
Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges,
magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats,
rlang
tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb,
GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3),
stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1),
Rsamtools (>= 2.4.0), rlang (>= 0.4.0),
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.NCBI.GRCh38
Rcpp, utils, GenomicRanges, basilisk, R.utils, stats,
cfToolsData, grDevices, graphics
Biobase, CGHbase, CGHcall, methods, stats, utils
prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
limma, DNAcopy, preprocessCore,impute, marray, wateRmelon,
plyr,goseq,missMethyl,ggplot2,
GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly
(>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
shiny, plotly, pheatmap, bioDist, dendextend, cowplot,
corrplot, grDevices, stats, graphics, reshape2, S4Vectors,
SummarizedExperiment
base, cluster, clustree, ComplexHeatmap (>= 2.5.4), circlize,
dplyr, EnsDb.Hsapiens.v86, forcats, fs, ggplot2, grid, plotly,
purrr, S4Vectors, scales, scater, scran, scuttle, stats,
stringr, tibble, tidyr, utils, wiggleplotr (>= 1.13.1),
tidyselect, patchwork
batchelor, bluster, circlize, cluster, DBI, dplyr,
EnsDb.Hsapiens.v86, ensembldb, fs, GenomicFeatures, glue,
megadepth, methods, purrr, RSQLite, S4Vectors, scran, scuttle,
stringr, tibble, tidyr, tidyselect, utils
alabaster.base, clustree, ComplexHeatmap, DataEditR (>=
0.0.9), DBI, dplyr, DT, EnhancedVolcano, fs, future, ggplot2,
ggplotify, grDevices, methods, patchwork, plotly, purrr,
rappdirs, readr, RSQLite, S4Vectors, scales, shinyFiles,
shinyhelper, shinyjs, shinyWidgets, stats, stringr, tibble,
tidyr, tidyselect, utils, waiter, wiggleplotr
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, Seqinfo,
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, Seqinfo, stats, BiocParallel, GenomicRanges
(>= 1.61.1), ggplot2 (>= 1.0), data.table (>= 1.9.6), Rsamtools
(>= 2.25.1), 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), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments,
GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment,
VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics,
grid, InteractionSet, KEGGREST, matrixStats, multtest,
regioneR, rtracklayer, stats, utils, universalmotif, stringr,
tibble, tidyr, data.table, scales, ensembldb
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, 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, aplot, BiocGenerics, boot, dplyr, enrichplot,
IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2,
gplots, graphics, grDevices, gtools, magrittr, methods,
plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors,
scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene,
utils, yulab.utils (>= 0.1.5)
methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges,
ShortRead
Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14),
graphics, grDevices, HilbertVis, ShortRead, stats, timsac,
utils
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
Biobase, GEOquery, frma, affy, bigmemory, biganalytics
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,
ggrepel, gggenes, gridExtra, qualV, stringdist, stringr, 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,
forcats, Rcpp, coop, matrixTests, DelayedArray
IRanges, Seqinfo, GenomicRanges, ggplot2, nabor, BiocParallel,
BiocGenerics, Biostrings, TFBSTools, Rsamtools, S4Vectors,
methods, Rcpp, grid, plotly, shiny, miniUI, stats, utils,
graphics, DT, Rtsne, Matrix, SummarizedExperiment,
RColorBrewer, BSgenome
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,
Seqinfo,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,
stats, tools, utils, R.utils, methods, S4Vectors, rlang,
magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings,
IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny,
shinyFiles, shinyjs, plotly, parallel, htmltools
SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>=
1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid,
dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales,
scran (>= 1.14.6), graphics, methods, stats, utils, reshape2,
ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5,
rlang, Rcpp, compositions
grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2
(>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr
BSgenome, GenomicRanges, seqinr, e1071, Biostrings, Seqinfo,
IRanges, utils, stringr, stats, S4Vectors
AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2,
edgeR, ensembldb, Seqinfo, GenomicRanges, ggplot2, ggrepel,
graphics, grDevices, KernSmooth, limma, methods, pheatmap,
qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2,
SummarizedExperiment, stats, tximport, utils
shiny, ggraph, igraph, ggiraph, cowplot, htmlwidgets, readxl,
dplyr, readr, purrr, tibble, patchwork, R.utils, shinyWidgets,
colorspace, shinyhelper, shinycssloaders, ggnewscale,
shinydashboard, DT, colourpicker, grDevices, methods, utils,
stats, ggplot2, magrittr, tools
methods, Biobase, Rcpp, igraph, gRbase (>= 1.6.6), qpgraph,
KEGGgraph, corpcor
dplyr, rtracklayer, GenomicRanges, ggplot2, BSgenome,
Biostrings, utils
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop,
slam, matrixStats, methods
FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach,
dplyr, fpc, mice, modeest, flock, networkD3, methods,
ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices,
ggplot2, grid, stats, utils, pbapply
methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats,
limma, 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
methods, igraph, ggplot2, scales, BiocParallel, graphics,
stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat,
SeuratObject, SingleCellExperiment, ggdendro
AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3),
GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph,
magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils,
yulab.utils (>= 0.1.6)
methods, pracma, princurve (>= 2.0.5), scatterplot3d,
RColorBrewer, grDevices, graphics, utils, stats
cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang,
scales, stringr, tibble, tidyr, stats, methods,
SingleCellExperiment, SummarizedExperiment, SeuratObject,
matrixStats, S4Vectors, proxy, httr, utils
blaster, future, future.apply, grDevices, igraph, methods,
Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils,
posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales
BiocParallel, BiocNeighbors, bluster (>= 1.16.0), scater,
harmony, SingleCellExperiment, SummarizedExperiment, methods,
Matrix, reshape2
methods, rhdf5, data.table, flowCore, SummarizedExperiment,
matrixStats
DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
BiocGenerics, Biobase, IRanges, Rsamtools, Seqinfo, S4Vectors
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
GenomicRanges, IRanges, S4Vectors, BiocParallel, methods,
magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009
BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq,
IRanges, Rsamtools, 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, dplyr, fgsea,
forcats, ggplot2
methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, stringr, tibble, tidyr, dplyr, devtools
utils, graphics, stats, methods, reshape2, ggplot2, scales,
ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite,
Biostrings
BiocManager, rmarkdown, Seqinfo, S4Vectors, AnnotationDbi,
graphics, stats, utils, methods, magrittr, ggplot2,
TxDb.Mmusculus.UCSC.mm9.knownGene
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.5.4), matrixStats (>= 1.2.0), GetoptLong, circlize (>=
0.4.7), GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer,
cluster, skmeans, png, mclust, crayon, methods, xml2,
microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6),
digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr,
foreach, doParallel, doRNG, irlba
methods, ggplot2, reshape2, dplyr, gridExtra, plotly,
circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel,
GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils,
Matrix, grid, stats, SummarizedExperiment, plyr, Gviz
ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>=
1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices,
graphics, methods, SummarizedExperiment
AnnotationHub, BiocParallel, bumphunter, ExperimentHub,
GenomicRanges, IRanges, lmerTest, methods, stats, utils
methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach,
coda
knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots,
gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr,
modeest, edgeR, limma, vioplot, methods, stats, utils, ape,
phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny,
shinydashboard
AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel,
grDevices, gplots, IRanges, GenomicFeatures, XVector,
methylPipe, GO.db, S4Vectors, Seqinfo
circlize (>= 0.4.14), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,
matrixStats, foreach, doParallel, codetools
BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr,
RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges,
Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils,
BiocParallel, stringi
data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr,
rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio,
scales, shinydashboard, shinyjs, stats, tibble, grid
stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra,
utils, data.table
BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli,
DelayedArray, Matrix, methods, purrr, rlang,
SingleCellExperiment, sparseMatrixStats, SpatialExperiment,
SummarizedExperiment
slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment,
SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume
(>= 0.9.1), methods, pbapply, matrixStats, BiocParallel,
TrajectoryUtils, igraph, distinct
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 (>= 1.50.0), gdata, genefu, limma, matrixStats,
randomForest, stats, utils, methods, BiocParallel
Seqinfo, rtracklayer, stringr, S4Vectors, methods
fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats,
SummarizedExperiment, BiocParallel, graph, ggplot2, methods,
Rfast, pheatmap, survival, topGO, graphics, grDevices
methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges,
Seqinfo
regioneR, IRanges, Rsamtools, SummarizedExperiment,
VariantAnnotation, methods, stats, GenomeInfoDb, GenomicRanges,
cn.mops, rhdf5, utils
Matrix, aricode, LiblineaR, SparseM, ggplot2, umap, Rtsne,
pheatmap, reshape2, dplyr, SingleCellExperiment,
SummarizedExperiment, S4Vectors, methods, stats, utils, RANN,
sparseMatrixStats, irlba, flexclust, scran, class, matrixStats,
tidyr, cowplot, uwot, scatterpie, RColorBrewer, ggrastr,
ggrepel, RSpectra, BiocParallel, withr
methods, stats, utils, Biostrings, Biobase, dplyr, stringr,
purrr, ggplot2, data.table
Biobase, S4Vectors, MultiAssayExperiment, MatrixGenerics,
piano, BiocParallel, parallel, BumpyMatrix, checkmate, methods,
stats, utils, graphics, grDevices, lsa, data.table, crayon,
glue, rlang, bench
ggplot2, ggthemes, grDevices, gridExtra, irlba, Matrix,
methods, MultiAssayExperiment, pals, reshape2,
SingleCellExperiment, SummarizedExperiment, transport
edgeR, DESeq2, capushe, Rmixmod, e1071, BiocParallel, ggplot2,
scales, HTSFilter, corrplot, HTSCluster, grDevices, graphics,
stats, methods, compositions, mvtnorm
CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr,
rlang, stringr, utils, visNetwork, decoupleR
stats, methods, grDevices, Matrix, ggplot2, ggrepel, gghalves,
ggthemes, graphics, parallel, parallelly, tibble, tidyr, dplyr,
BiocSingular, parallelDist, ComplexHeatmap, circlize, grid,
scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat,
dendextend, zeallot, assertthat, withr, SingleCellExperiment,
proxy, RSpectra
rmarkdown (>= 2.5), edgeR, DESeq2 (>= 1.16.0), dplyr, tidyr,
ggplot2, grDevices, tools, SummarizedExperiment, genefilter,
DT, GenomeInfoDbData, caTools, randtests, stats, utils,
methods, ragg
S4Vectors (>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges,
GenomicAlignments, parallel, tools
parallel, genefilter, grDevices, stats, graphics
SummarizedExperiment, grDevices, reshape2 , survival ,
survminer , ggplot2 , MTLR , glmnet , rms , preprocessCore ,
Matrix , stats, Hmisc, ggfortify, randomForestSRC, caret,
SurvMetrics, MASS,
methods, corpcor, BiocParallel, ggplot2, plyr
splines, graphics, nor1mix, stats, quantreg
DT, shiny, grid, ComplexHeatmap, InteractiveComplexHeatmap,
graphics, stats, ggplot2, plotly, shinyWidgets,
shinycssloaders, shinyjqui, dittoSeq, matrixStats,
colourpicker, shinyjs, circlize, PCAtools, utils, grDevices,
htmlwidgets, methods
BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges,
S4Vectors, stringr
BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15),
Seqinfo, GenomicRanges, IRanges, Rbowtie, readr, stats,
stringr, utils
BiocGenerics, BSgenome, crisprBase (>= 0.99.15), Seqinfo,
Rbwa, readr, stats, stringr, utils
AnnotationDbi, BiocGenerics, Biostrings (>= 2.77.2), BSgenome
(>= 1.77.1), crisprBowtie (>= 0.99.8), crisprScore (>= 1.1.6),
GenomeInfoDb (>= 1.45.7), GenomicFeatures (>= 1.61.4),
GenomicRanges (>= 1.61.1), IRanges, Matrix, MatrixGenerics,
methods, rtracklayer (>= 1.69.1), S4Vectors, Seqinfo, stats,
txdbmaker (>= 1.5.6), utils, VariantAnnotation (>= 1.55.1)
basilisk (>= 1.9.2), BiocGenerics, Biostrings, IRanges,
methods, randomForest, reticulate, stringr, utils, XVector
parallel, data.table, seqinr, S4Vectors (>= 0.9.25), IRanges,
BSgenome, hash, methods,reticulate,rhdf5,XVector, DelayedArray,
Seqinfo, GenomicRanges, dplyr, keras, mltools, gtools,
openxlsx, rio, rlang, stringr
BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign,
crisprScore, crisprViz, DT, Seqinfo, htmlwidgets, methods,
pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter
AnnotationDbi, BiocParallel, Biostrings, methods,
GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices,
grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>=
0.9.38), utils
BiocManager, cli, crisprBase, crisprBowtie, crisprScore,
crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils
BiocGenerics, Biostrings, BSgenome, Seqinfo, GenomicFeatures,
GenomicRanges, grDevices, Gviz, IRanges, methods, S4Vectors,
txdbmaker
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
Rdpack, viridis, tidytree, variancePartition (>= 1.36.3),
SingleCellExperiment, ggtree, dplyr, stats, MASS, Rfast
bamsignals, Rsamtools, GenomicRanges, preprocessCore,
randomForest, rtracklayer, Seqinfo, S4Vectors, ggplot2,
matrixStats, dplyr, IRanges, GenomicAlignments,
GenomicFeatures, TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, reshape2, magrittr, stats,
utils, grDevices, SummarizedExperiment, BiocParallel, fs,
methods
Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods,
S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod,
utils
WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
bayesbio, dplyr, ggeasy, ggforce, ggnewscale, ggplot2, ggraph,
ggrepel, graphics, grDevices, kerntools, methods, qs, reshape2,
Seurat, SeuratObject, SingleCellExperiment,
SummarizedExperiment, sgof, spatstat.utils, stats, textshape,
tidygraph, viridis, wesanderson
GenomicAlignments, GenomicFeatures, Rsamtools, ggplot2,
grDevices, stats, utils
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache
BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment,
GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang,
grDevices, stats, circlize, ggrepel, SingleCellExperiment,
MatrixGenerics
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
stats, pscl, qvalue, BiocParallel, methods, knitr,
SpatialExperiment, SummarizedExperiment
methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>=
1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli,
assertthat, SeuratObject, Seurat, methods, rlang, stats,
S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr
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,
txdbmaker, 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
stats, abind, sirt, MASS,TOAST, tibble, parallel,
preprocessCore, SummarizedExperiment, TCA, PROPER,
methods,dplyr, utils, RColorBrewer, graphics, edgeR,
BiocParallel, checkmate, mvtnorm, DESeq2, rlang, e1071
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
CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes,
matrixStats, randomForest, rmarkdown, SingleCellExperiment,
stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods
stats, methods, BiocParallel, RColorBrewer, cowplot,
doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr,
mbest, pheatmap, 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
SpatialExperiment, S4Vectors, BiocParallel, HDF5Array,
DelayedArray, RColorBrewer, viridis, utils,
SummarizedExperiment, tools, graphics, raster, grDevices,
stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny,
shinydashboard, matrixStats, rhdf5, nnls
methods, stats, rlang, pracma, withr, flowCore, reshape2,
ggplot2, ggrepel, ggforce, patchwork, transport, smacof,
BiocParallel, CytoPipeline
gplots, tools, flowCore, grDevices, stats, utils, matrixStats,
methods
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, jsonlite,
dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats,
tibble
methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1),
ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI,
diagram, jsonlite, scales
shiny, shinydashboard, utils, colourpicker, shinycssloaders,
svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite,
EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors,
SummarizedExperiment
pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils,
biomaRt, motifStack, httr
stats, Seqinfo, 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
AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2,
goseq, magrittr, patchwork, plyranges, reshape2, rlang,
Rsamtools, Rsubread, stats, stringr, tidyr, utils
BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods,
miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam,
stats, SummarizedExperiment, uwot, RANN
Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter,
foreach
cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue,
gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr,
readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr,
UpSetR, waldo
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
MCMCpack, matrixStats, robustbase, aod, e1071
Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice,
BiocGenerics
plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore,
flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks
CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr,
matrixStats, methods, patchwork, parallel, pbapply, reshape2,
rlang, scattermore, stats, statmod, survey, tibble, 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
celda, dbscan, DelayedArray, ggplot2, Matrix (>= 1.5.3),
MCMCprecision, methods, patchwork, plyr, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1),
rstantools (>= 2.2.0), S4Vectors, scater, Seurat,
SingleCellExperiment, SummarizedExperiment, withr
AnnotationHub, BiocFileCache, DelayedMatrixStats, dplyr,
ExperimentHub, ggplot2, graphics, grDevices, MatrixGenerics,
methods, purrr, rafalib, reshape2, S4Vectors, scran,
SingleCellExperiment, spatialLIBD, stats, stringr,
SummarizedExperiment, tibble, utils
SummarizedExperiment, methods, S4Vectors, utils, DESeq2,
edgeR, limma, cli
tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers,
webchem, purrr, ttgsea, PRROC, reticulate, stats
fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats,
grDevices, graphics, depmap, readr, dplyr
checkmate, data.table, DESeq2, edgeR (>= 3.13.4),
GenomicRanges, methods, S4Vectors, stats, SummarizedExperiment
GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats,
graphics, grDevices, BiocGenerics, Seqinfo, IRanges,
BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Hs.eg.db, utils
Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, 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,
dendextend, DESeq2, dplyr, edgeR, ggplot2, ggdendro, grid,
ggrepel, grDevices, knitr, logging, magrittr, psych,
RColorBrewer, reshape, rlang, scales, stats, stringr, stringi,
S4Vectors, SummarizedExperiment, tidyr, tibble
graphics, grDevices, methods, stats, utils
methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0),
S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>=
1.5.19)
methods, utils, S4Arrays, SparseArray, DelayedArray (>=
0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray
(>= 1.13.1), irlba, Matrix, einsum,
DESeq2, dplyr, reshape2, limma, SummarizedExperiment, ggplot2,
matrixStats, stats
IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2,
tictoc
matrixStats, stats, truncdist, base64enc, ggplot2
stats, MASS, Matrix, ggplot2, gridExtra, methods
MatrixGenerics, BiocGenerics, class, Seqinfo, IRanges, Matrix,
SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr
Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba
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), Seqinfo (>= 0.99.2), GenomeInfoDb
(>= 1.45.9), GenomicAlignments, GenomicFeatures, GenomicFiles,
GenomicRanges (>= 1.61.1), Hmisc, IRanges (>= 2.3.23), methods,
qvalue (>= 1.99.0), Rsamtools (>= 2.25.1), rtracklayer,
S4Vectors (>= 0.23.19), stats, utils
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
derfinder (>= 1.1.0), Seqinfo, GenomeInfoDb (>= 1.45.9),
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, Seqinfo, GenomeInfoDb, GenomicAlignments, glue,
IRanges, plyr, Rcpp (>= 0.12.13), rtracklayer, S4Vectors (>=
0.23.19), SummarizedExperiment, tools, utils
BiocGenerics (>= 0.7.5), Biobase, BiocParallel, matrixStats,
methods, stats4, locfit, ggplot2 (>= 3.4.0), Rcpp (>= 0.11.0),
MatrixGenerics
edgeR, limma, dplyr, stats, Matrix, SpatialExperiment,
ggplot2, SummarizedExperiment, S4Vectors, BiocGenerics,
data.table, assertthat, terra, sf, spatstat.explore,
spatstat.geom, ggforce, ggnewscale, patchwork, BiocParallel,
methods, scales, scuttle
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, rlang, 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), Seqinfo, GenomicRanges,
methods, S4Vectors, SummarizedExperiment, stats, utils
Biobase, GEOquery, impute, limma, pheatmap, plyr, scales,
snpStats, sva, swamp, stats, methods, utils, bnstruct,
RColorBrewer, grDevices
BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools,
statmod, geneplotter, genefilter
BiocGenerics, methods, rlang, S4Vectors, tidyselect
RColorBrewer, amap, gplots, grDevices, limma,
GenomicAlignments, locfit, stats, utils, IRanges, lattice,
systemPipeR, tools, Rcpp, dplyr, ggplot2, BiocParallel,
parallel, S4Vectors, Rsamtools (>= 2.13.1), 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
methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel,
foreach, stats, BANDITS, Matrix, SingleCellExperiment,
SummarizedExperiment, ggplot2, tximport, gridExtra
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
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
BiocGenerics, circlize, ComplexHeatmap, cowplot, dplyr, edgeR,
GenomicRanges, ggplot2, Matrix, methods, rlang, stats, stringr,
tibble, tidyr, tidyselect
Rcpp, Biobase, stats, biwt, gtools, MASS, tools, dplyr,
methods, utils
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
AnnotationHub, ExperimentHub, bsseq, Seqinfo, limma, edgeR,
minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges, stats,
utils, S4Vectors, methods, graphics, SummarizedExperiment,
biomaRt, grDevices
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, Seqinfo,
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,
Seqinfo, splines
dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods,
Rcpp (>= 0.11.2), BH
GenomicRanges, IRanges, Rsamtools, GenomicAlignments,
BiocBaseUtils, S4Vectors, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics
BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3),
janitor, Matrix, methods, netgsa, stats, stringr, utils,
SummarizedExperiment
biomaRt, data.table, utils, stats, Biostrings, pwalign,
SummarizedExperiment, VariantAnnotation, AnnotationDbi,
GenomeInfoDb, IRanges, GenomicRanges, methods
biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid,
igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr,
dplyr
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, fgsea, ggplot2, GOSemSim (>=
2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils
(>= 0.1.6)
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>=
1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi,
GenomicFeatures
edgeR, SummarizedExperiment, DelayedMatrixStats,
sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr,
GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52),
ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges,
irlba, limma, metafor, remaCor, broom, tidyr, rlang,
BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools,
reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS,
Rdpack, utils, stats
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors,
IRanges, GenomicRanges, SummarizedExperiment, BiocParallel,
SparseArray (>= 1.5.18), DelayedArray (>= 0.31.9),
DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng,
beachmat, scuttle
utils, RSQLite, UniProt.ws, biomaRt,ensembldb,
BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors
zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors,
rlang, grDevices, stats, utils
Gviz, Biostrings, rtracklayer, GenomicAlignments,
GenomicRanges, ggsci, igraph, rlang, scales, stringr, dplyr,
tibble, tidyr, purrr, methods, grDevices, stats, utils
progeny, easierData, dorothea (>= 1.6.0), decoupleR,
quantiseqr, ROCR, grDevices, stats, graphics, ggplot2, ggpubr,
DESeq2, utils, dplyr, tidyr, tibble, matrixStats, rlang,
BiocParallel, reshape2, rstatix, ggrepel, magrittr, coin
clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang,
stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, vctrs (>=
0.6.4), BiocStyle
rtracklayer, GenomeInfoDb, R.utils, tools, methods
Biobase (>= 2.64.0), BiocFileCache (>= 2.12.0), BiocGenerics
(>= 0.50.0), BiocParallel (>= 1.38.0), biomaRt (>= 2.60.1),
Biostrings (>= 2.77.2), edgeR (>= 4.2.1), Seqinfo,
genomeIntervals (>= 1.60.0), GenomicAlignments (>= 1.45.1),
GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1),
graphics, IRanges (>= 2.38.1), LSD (>= 4.1-0), methods,
parallel, rappdirs (>= 0.3.3), Rsamtools (>= 2.25.1), S4Vectors
(>= 0.42.1), ShortRead (>= 1.62.0), 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, qvalue(>= 1.99.0), MASS
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 (>= 4.0), methods, SummarizedExperiment, BiocGenerics,
utils
GenomicRanges, ggplot2, reshape, grid, grDevices, graphics,
methods, parallel, stats, utils, IRanges, Seqinfo, S4Vectors,
GenomicFeatures, TCGAbiolinks (>= 2.23.7), 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 (>= 1.61.2), DelayedArray
reticulate, BiocGenerics, circlize, ComplexHeatmap,
data.table, dplyr, GenomicFeatures, GenomicRanges, ggplot2,
glue, graphics, grDevices, igraph, IRanges, magrittr, memoise,
methods, parallel, patchwork, scales, segclust2d, stats,
stringr, txdbmaker, utils, uuid, zoo
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
BiocGenerics, Biostrings, BSgenome, BiocParallel,
BiocFileCache, GenomeInfoDb, GenomicRanges, httr, IRanges,
jsonlite, motifmatchr, Matrix, pwalign, rtracklayer, Rcpp,
S4Vectors, stats, utils
survivalROC, glmnet, rms, mboost, Matrix, igraph, methods,
survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache
BiocGenerics, Rgraphviz, clusterProfiler, hash, S4Vectors,
dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics,
utils, purrr, tidyr, stats
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 (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7),
ggnewscale, ggplot2 (>= 3.5.0), ggrepel (>= 0.9.0), ggtangle
(>= 0.0.5), graphics, grid, igraph, methods, plyr, purrr,
RColorBrewer, reshape2, rlang, stats, utils, scatterpie,
GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6)
gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE,
methods
methods, RSQLite (>= 1.1), DBI, Biobase, Seqinfo, GenomeInfoDb
(>= 1.45.5), AnnotationDbi (>= 1.31.19), rtracklayer (>=
1.69.1), S4Vectors (>= 0.23.10), Rsamtools, IRanges (>=
2.13.24), ProtGenerics, Biostrings (>= 2.77.2), curl
stats, methods, utils, data.table, BiocGenerics,
GenomicRanges, Rcpp
AnnotationHub, ChIPseeker, data.table, genomation,
GenomicRanges, IRanges (>= 2.41.3), Seqinfo (>= 0.99.2),
GenomeInfoDb (>= 1.45.7), ggplot2 (>= 3.5.0), htmltools,
methods, plotly, reshape2, rmarkdown, rtracklayer, stats,
stringr, utils, BiocGenerics, downloadthis, parallel
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,
Seqinfo, GenomicRanges, rtracklayer, IRanges, Rsamtools,
bamsignals, csaw, S4Vectors, limma, stats, Rhdf5lib, rhdf5,
Matrix, MASS, scales, ggpubr, ggplot2, GreyListChIP, pheatmap,
grDevices
AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table,
doParallel, doSNOW, downloader, dplyr, ELMER.data,
ExperimentHub, foreach, Seqinfo, GenomicFeatures,
GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges,
limma, methods, parallel, plyr, progress, R.matlab,
RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats,
SummarizedExperiment, tibble, tidyr, utils
minfi, bumphunter, isotree, robustbase, ggplot2,
GenomicRanges, GenomicFeatures, IRanges, SummarizedExperiment,
stats, matrixStats, BiocGenerics, S4Vectors, utils, biomaRt,
BiocParallel, GenomeInfoDb, Homo.sapiens, purrr, tibble, Gviz,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, rtracklayer, AnnotationDbi,
AnnotationHub, ExperimentHub, reshape2, grid, ensembldb,
gridExtra, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19, ggrepel
BoutrosLab.plotting.general, BoolNet, e1071, gtools, stats,
igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg,
minet, grDevices, graph, mnem, latex2exp
EpipwR.data, ExperimentHub (>= 2.10.0), ggplot2
AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp,
S4Vectors, SummarizedExperiment, bluster, checkmate, entropy,
lifecycle, methods, scran, scuttle, stats, utils, scMultiome,
GenomeInfoDb, GenomicRanges, AUCell,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat
scran, ComplexHeatmap, Matrix, SummarizedExperiment,
checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph,
patchwork, reshape2, scales, scater
GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors,
IRanges, graphics, plotrix, grDevices, stats, methods
BiocParallel, data.table, matrixStats, stats, survival,
igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid,
bigmemory, graphics, utils
methods, utils, httr, xml2, curl, rex, GenomicFeatures,
txdbmaker, GenomicRanges, Seqinfo, 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 (>= 1.61.1), SummarizedExperiment (>=
1.39.1), OrganismDbi, GenomicFeatures (>= 1.61.4), Seqinfo,
IRanges, ensembldb (>= 2.33.1)
git2r, epivizrServer, Seqinfo, BiocGenerics, GenomicFeatures,
S4Vectors
edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr,
qvalue, reshape2, ROCR, scales, stringr, knitr
Rcpp (>= 0.12.11), methods, knitr, Rbowtie2, rtracklayer,
ggplot2, Biostrings, ChIPseeker, clusterProfiler, igraph,
rJava, magrittr, digest, BSgenome, AnnotationDbi,
GenomicAlignments, GenomicFeatures, R.utils, Seqinfo,
BiocGenerics, S4Vectors, IRanges, rmarkdown, tools,
VennDiagram, grid, JASPAR2018, TFBSTools, grDevices, graphics,
stats, utils, parallel, corrplot, BiocManager, motifmatchr
ggdist, ggplot2 (>= 3.5.0), grDevices, Matrix, MatrixGenerics,
methods, stats, SummarizedExperiment, utils
SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang,
SummarizedExperiment
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, dplyr, dendextend (>= 1.16.0)
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,
fgsea
stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2,
reshape2, limma, stringr, HGNChelper, Matrix, parallel,
SingleCellExperiment, SummarizedExperiment, DelayedArray,
BiocParallel, orthogene (>= 0.99.8), data.table
stats, methods, grDevices, graphics, utils
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
csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb,
glue, ggrepel, InteractionSet, IRanges, matrixStats, methods,
patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer,
S4Vectors, Seqinfo, scales, stats, stringr, tidyr, tidyselect,
vctrs
methods, graphics, grDevices, stats, utils
BiocParallel, brio, cli, curl (>= 6.0.0), data.table, httr2
(>= 1.0.0), MCMCpack, methods, openEBGM, rlang, rvest, tools,
utils, vroom, xml2
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2,
rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex,
tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT,
clusterProfiler, org.Hs.eg.db
methods, shiny, stats, IRanges, Biostrings, ShortRead, DT,
S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
ape, data.table, dynamicTreeCut, methods, R.utils, rJava,
stats, stringr, utils
methods, graphics, grDevices, stats, BiocGenerics, S4Vectors,
IRanges
fda, RColorBrewer, genomation, ggplot2, ComplexHeatmap,
grDevices, stats, utils
stats, plyr, VariantAnnotation, SummarizedExperiment,
rtracklayer, GenomicRanges, methods, IRanges, foreach,
doParallel, parallel
tcltk, graphics, grDevices, stats, utils
SingleCellExperiment, methods, stats, utils, irlba, TSCAN,
SC3, matrixStats
pheatmap, MASS, pracma, stats, SummarizedExperiment, methods
openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes,
forcats, RColorBrewer, RCy3, utils, stats
tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect,
tibble, purrr, readr, stringr, httr2, rvest, progress,
BiocFileCache, shiny, ggplot2
Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache,
curl, igraph
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),
cowplot, grid, fastmatch, Matrix, scales, utils
foreach, doParallel, GenomicRanges, IRanges, Rsamtools,
parallel, S4Vectors
Biobase, BiocParallel, parallel, stats, SummarizedExperiment,
survival, utils
withr, BiocGenerics, Seqinfo, 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, IRanges, SummarizedExperiment, GenomicRanges,
matrixStats, svMisc, Matrix, SingleCellExperiment, jsonlite
data.table, fdrtool, grDevices, graphics, Rcpp, stats, utils
abind, basilisk, bambu, BiocParallel, Biostrings,
BiocGenerics, crew, circlize, ComplexHeatmap, cowplot, cli,
dplyr, GenomicRanges, GenomicFeatures, GenomicAlignments,
Seqinfo, ggplot2, ggbio, grid, gridExtra, igraph, jsonlite,
magrittr, magick, Matrix, MatrixGenerics, readr, reticulate,
Rsamtools, rtracklayer, RColorBrewer, R.utils, S4Arrays,
ShortRead, SingleCellExperiment, SummarizedExperiment,
SpatialExperiment, scater, scatterpie, S4Vectors, scuttle,
stats, scran, stringr, tidyr, utils, withr, methods, tibble,
tidyselect, IRanges
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, flowCore, parallel
Biobase, BiocGenerics (>= 0.29.2), grDevices, graphics,
methods, stats, utils, stats4, Rcpp, matrixStats, cytolib (>=
2.13.1), S4Vectors
flowDensity (>= 1.13.1), Cairo, e1071, grDevices, graphics,
stats,methods
flowCore, graphics, flowViz (>= 1.42), car, polyclip, gplots,
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
stats, utils, colorRamps, ConsensusClusterPlus, dplyr,
flowCore, ggforce, ggnewscale, ggplot2, ggpubr, grDevices,
magrittr, methods, rlang, Rtsne, tidyr, BiocGenerics, XML
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, corpcor, mnormt, clue
utils, dplyr (>= 1.0.0), tibble, magrittr, plyr, rlang
flowCore, methods, flowViz, stats, flowClust
stats4, Biobase, flowCore, graphics, grDevices, grid,
KernSmooth, lattice, latticeExtra, MASS, methods, RColorBrewer,
stats, utils, hexbin,IDPmisc
Biobase, BiocGenerics, cytolib (>= 2.13.1), XML, ggplot2,
graph, graphics, grDevices, methods, stats, stats4, utils,
RBGL, tools, Rgraphviz, data.table, dplyr, scales(>= 1.3.0),
matrixStats, RProtoBufLib, 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, RMTstat, pracma
Biobase, MASS, DBI, affy, methods, oligo, oligoClasses,
preprocessCore, utils, BiocGenerics
Biobase, DBI, methods, preprocessCore, stats, utils
NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db,
dplyr, stringr
pls, matrixStats, minfi, methods,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb,
grDevices, graphics, stats
psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster,
fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest,
methods, SummarizedExperiment, stats, S4Vectors
Biostrings, stats, GenomicRanges, IRanges, Rcpp, RcppRoll,
data.table, Seqinfo, S4Vectors, ggplot2, cowplot, progress,
ggseqlogo, viridis, ggpointdensity, tools,
SummarizedExperiment, VariantAnnotation, dplyr, openxlsx,
tidyr, magrittr, ggdensity
BiocGenerics, Biostrings, dplyr, Seqinfo, GenomicRanges, httr,
IRanges, jsonlite, methods, VariantAnnotation
AnnotationDbi, BiocGenerics, dplyr, DT, Seqinfo, GenomeInfoDb,
openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny,
shinyjs, tidyr, shinythemes
DaMiRseq, MLSeq, stats, methods, SummarizedExperiment
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
data.table, igraph, BioNet, plyr, methods, XML, sna,
intergraph, network, GGally, grid, ggplot2, mwcsr, pryr,
htmlwidgets, htmltools, shinyCyJS (>= 1.0.0)
stats, utils, methods, ggplot2, tidyr, expm, Rcpp,
RcppParallel, gdsfmt
BiocGenerics, Seqinfo, S4Vectors, IRanges, Biostrings,
BSgenome, GenomicRanges, Rsamtools, GenomicAlignments,
matrixStats, MASS, splines, grDevices, graphics, stats, methods
AnVILBase, BiocBaseUtils, dplyr, httr, rlang, tibble, tidyr,
utils
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
shiny, jsonlite, rjson, XML, limma, edgeR, DESeq2,
clusterProfiler, DOSE, org.Hs.eg.db, biomaRt, survival,
survminer, pathview, ggplot2, gplots, DT, GenomicDataCommons,
BiocParallel
methods, BiocGenerics, BiocParallel, matrixStats, Biostrings,
S4Vectors, IRanges, Seqinfo, GenomeInfoDb, GenomicRanges,
GenomicFiles, GenomicAlignments, GenomicFeatures, Rsamtools,
AnnotationHub, RColorBrewer, AnnotationDbi, bitops, plotrix,
SummarizedExperiment, grDevices, graphics, stats, utils, cli
BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils
(>= 1.7.1), MultiAssayExperiment, purrr, stringr, S4Vectors,
SummarizedExperiment, data.table
assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx,
data.table, futile.logger, gDRutils (>= 1.7.1), magrittr,
methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats,
stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml,
openxlsx
BiocCheck, BiocManager, BiocStyle, checkmate, desc, git2r,
lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild,
withr
BiocParallel, BumpyMatrix, checkmate, data.table, digest, drc,
jsonlite, jsonvalidate, methods, MultiAssayExperiment,
S4Vectors, stats, stringr, SummarizedExperiment, qs, utils
tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray
GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs,
utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork,
shinycssloaders, fontawesome, grDevices, parallel, stats,
ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl,
ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools,
BiocParallel, BiocFileCache, cluster, circlize
tcltk, ggplot2, methods, stats, grDevices, graphics, utils
dplyr, grDevices, ggplot2, magrittr, mixtools, scales,
pbmcapply, parallel, stats, utils
magrittr, glue, memoise, jsonlite, data.table, rlang,
lubridate, utils, stringr, SummarizedExperiment, Biobase,
tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat,
digest, R.utils, kableExtra, base64enc
graphics, grDevices, methods, stats, tcltk, utils, xtable
utils, GenomicRanges, org.Hs.eg.db, BiocGenerics, Seqinfo,
GenomicFeatures, IRanges, rtracklayer
utils, methods, stats, Biobase, BiocGenerics
MatrixGenerics (>= 1.11.1), AnnotationDbi, annotate, Biobase,
graphics, methods, stats, survival, grDevices
amap, impute, mclust, limma, graphics, stats, utils,
iC10TrainingData
plyr, graph, htmlwidgets, Rgraphviz, RCy3, 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, ComplexUpset,
dendextend, DESeq2, dplyr, DT, dynamicTreeCut, expm, ggforce,
ggplot2 (>= 3.5.0), ggrepel, ggridges, GO.db, graphics,
grDevices, grid, igraph, matrixStats, methods, mosdef (>=
1.1.0), 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,
Seqinfo, 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)
Biostrings, BiocGenerics, BiocParallel, Seqinfo,
GenomicRanges, IRanges, matrixStats, XVector, dplyr,
data.table, parallel, doParallel, foreach, methods, S4Vectors,
stats, numbers, utils
Seqinfo, GenomicRanges (>= 1.21.16), IRanges(>= 2.3.14),
S4Vectors (>= 0.7.10)
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
stats, httr, xml2, jsonlite, utils, rlang, readr,
GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr
data.table, ggplot2, reshape2, methods, utils, Biostrings,
plyr, dplyr, scales, broom, GenomeInfoDb, stats
methods, utils, stats, DBI, XVector, Biostrings (>= 2.77.2),
rtracklayer (>= 1.69.1)
BiocBaseUtils, GenomeInfoDb (>= 1.45.7), GenomicAlignments (>=
1.45.1), IRanges, S4Vectors, Seqinfo, VariantAnnotation (>=
1.55.1)
AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures,
Seqinfo, methods, IRanges, RBGL, S4Vectors
Rsamtools, rtracklayer, GenomicRanges (>= 1.29.6), IRanges,
BiocGenerics (>= 0.15.3), data.table, stringr, Seqinfo,
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, Seqinfo, Rdpack
methods, Rsamtools, parallel, tidyr, rtracklayer (>= 1.54.0),
plyranges (>= 1.14.0), cowplot (>= 1.1.1), VennDiagram,
ggplotify, Seqinfo, IRanges, ComplexHeatmap, RCAS (>= 1.20.0),
scales (>= 1.2.0), GenomicAlignments (>= 1.30.0), edgeR,
circlize, viridis, ggsignif (>= 0.6.3), ggsci (>= 2.9), ggpubr,
grDevices, graphics, stats, utils, GenomicFeatures, genomation
(>= 1.36.0), txdbmaker, ggplot2 (>= 3.3.5), BiocGenerics,
dplyr, grid
stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache,
IRanges (>= 2.3.23), Biostrings, Seqinfo, GenomeInfoDb (>=
1.45.5), AnnotationHub, rhdf5, DelayedArray, HDF5Array
ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr,
dplyr, plotly, BiocFileCache, grid, flextable, irlba
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders,
reticulate, stats
AnnotationDbi, biomaRt (>= 2.45.8), BiocGenerics, Biostrings,
DBI, 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, Seqinfo, VariantAnnotation
Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods,
graphics, stats, testthat, GeomxTools, NanoStringNCTools
DT, XML, httr, sva, xfun, edgeR, htmltools, factoextra,
heatmaply, pheatmap, scales, shinyHeatmaply, shinybusy,
ggplot2, stringr, umap, GEOquery, impute, grDevices, stats,
graphics, markdown, knitr, utils, xml2, R.utils, readxl,
shinycssloaders, car
xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
aricode, BiocGenerics, Biostrings, clue, cluster, dbscan,
future.apply, Seqinfo, GenomicRanges, graphics, grDevices,
grid, htmlwidgets, igraph, InteractionSet, IRanges, MASS,
Matrix, methods, plotrix, progressr, RANN, rgl, rjson,
S4Vectors, scales, stats, trackViewer
BiocGenerics, rjson, readxl, EnvStats, reshape2, methods,
utils, stats, data.table, lmerTest, dplyr, stringr, grDevices,
graphics, GGally, rlang, ggplot2, SeuratObject
readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr,
limma, curl, rentrez, R.utils, stringr, SummarizedExperiment,
S4Vectors, rvest, httr2
utils, data.table, plyr, cqn, topconfects, stats,
SummarizedExperiment, methods
repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods,
Biobase, XML, rhdf5, digest, iterators
grDevices, graphics, methods, stats, utils, dbscan,
fastcluster, matrixStats
bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, dplyr, DT,
ggbeeswarm, ggplot2, htmltools, magrittr, shiny,
SummarizedExperiment, tibble, tidyselect, tidyr
DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr,
methods, purrr, rlang, scales, stats, stringr, tibble, tidyr
grid, grDevices, graphics, stats, utils, gridExtra, scales,
reshape2, gtable, Hmisc, biovizBase (>= 1.29.2), Biobase,
S4Vectors (>= 0.13.13), IRanges (>= 2.11.16), Seqinfo,
GenomeInfoDb (>= 1.45.5), GenomicRanges (>= 1.61.1),
SummarizedExperiment (>= 1.39.1), Biostrings (>= 2.77.2),
Rsamtools (>= 2.25.1), GenomicAlignments (>= 1.45.1), BSgenome
(>= 1.77.1), VariantAnnotation (>= 1.55.1), rtracklayer (>=
1.69.1), GenomicFeatures (>= 1.61.4), OrganismDbi, GGally,
ensembldb (>= 2.33.1), AnnotationDbi, AnnotationFilter, rlang
plyr, scales, hexbin, data.table, RColorBrewer, gridExtra,
rlang
BiocFileCache, data.table, dplyr, magick, patchwork,
shadowtext, stringr, tibble, methods, utils, stats, grDevices,
gtable
gdsfmt, ggrepel, grDevices, paletteer, RColorBrewer, rlang,
scales, SeqArray (>= 1.32.0), stats, tidyr, dplyr, pals,
magrittr
Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot,
RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA,
grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1)
Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2,
grDevices, grid, methods, rlang, scattermore, stats, Seurat,
SingleCellExperiment, SummarizedExperiment, tidydr, tidyr,
tibble, utils, RColorBrewer, yulab.utils, scales
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
ggside, grid, ggrepel, RColorBrewer, scales, grDevices,
methods, stats
ape, aplot, dplyr, ggplot2 (>= 4.0.0), grid, magrittr,
methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>=
0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils,
scales, stats, cli, ggiraph (>= 0.9.1)
ggplot2 (>= 4.0.0), utils, rlang, ggnewscale, stats, ggtree,
tidytree (>= 0.3.9), cli, magrittr
interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools,
rlang, tibble, tidyr, tidyselect, stats
KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise,
cachem, jsonlite, rvest
BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges,
gtools, MultiAssayExperiment, plyr, stringi, stringr,
SummarizedExperiment, methods, stats, reshape2, randomForest,
limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics,
GenomicFeatures, ReactomePA, clusterProfiler, dplyr,
AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges,
ggtree, shinydashboard, plotly, DT, MASS,
InteractiveComplexHeatmap, ComplexHeatmap, visNetwork,
shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr,
circlize, MethylMix, shinyjs
DBI, RMariaDB, 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, beachmat, DelayedMatrixStats, matrixStats,
MatrixGenerics, SparseArray (>= 1.5.21), S4Vectors,
DelayedArray, HDF5Array, Matrix, SummarizedExperiment,
SingleCellExperiment, BiocGenerics, methods, stats, utils,
splines, rlang, vctrs
biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2,
glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet,
Matrix, MultiAssayExperiment, SummarizedExperiment, survminer,
TCGAutils, utils
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel,
mvnfast, SingleCellExperiment, rlang
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, Seqinfo, methods, GenomicAlignments,
GenomicFeatures, IRanges, rtracklayer, pracma, colorspace,
S4Vectors
DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs,
reshape2, RColorBrewer, survival, survminer, stats,
compareGroups, rpart, partykit, DescTools, car, rstatix,
fabricatr, shinylogs, magrittr
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
AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils,
stats, utils, yulab.utils (>= 0.1.6)
mgcv, graphics, stats, utils, AnnotationDbi, GO.db,
BiocGenerics, methods, rtracklayer, GenomicFeatures, Seqinfo
clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats,
stringr
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
BiocGenerics, S4Vectors (>= 0.9.38), IRanges, Rsamtools,
ShortRead, rtracklayer, ggplot2, BiocManager, grDevices, utils,
stats, Seqinfo
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
stats, utils, graphics, ggplot2, plotly, scales, RColorBrewer,
dplyr, grDevices, GenomicRanges, shiny, cowplot, ggpubr,
stringr, rlang
futile.logger, checkmate, patchwork (>= 1.2.0), reshape2,
data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer,
ComplexHeatmap, DESeq2, circlize, progress, utils, methods,
stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang,
Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment,
forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>=
1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble,
viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb
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, graph (>= 1.67.1), httr, rappdirs, stats,
utils, graphics, rlang, purrr
graphics, grDevices, reshape2, stats, utils
GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS,
parallel, Seqinfo, 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 (>= 1.5-0), parallel,
BiocParallel, SingleCellExperiment, SpatialExperiment,
sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array,
BiocSingular, cli
circlize (>= 0.4.8), GetoptLong, grDevices, utils
Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table,
matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors
(>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3),
GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures,
rio, tidyr, tools, methods, purrr, ggplot2, openxlsx,
patchwork, rlang
ComplexHeatmap, eulerr, GenomicRanges, IRanges, lubridate,
methods, stringr, writexl
XVector (>= 0.5.7), rtracklayer (>= 1.69.1), lattice,
RColorBrewer, biomaRt (>= 2.11.0), AnnotationDbi (>= 1.27.5),
Biobase (>= 2.15.3), GenomicFeatures (>= 1.61.4), ensembldb (>=
2.11.3), BSgenome (>= 1.77.1), Biostrings (>= 2.77.2),
biovizBase (>= 1.13.8), Rsamtools (>= 2.25.1), latticeExtra (>=
0.6-26), matrixStats (>= 0.8.14), GenomicAlignments (>=
1.45.1), Seqinfo, GenomeInfoDb, BiocGenerics (>= 0.11.3),
digest(>= 0.6.8), graphics, grDevices, stats, utils
S4Vectors (>= 0.9.25), IRanges, Seqinfo, GenomeInfoDb,
GenomicRanges (>= 1.29.6), GenomicFeatures, readr, Biostrings,
AnnotationDbi, BiocFileCache, snpStats, VariantAnnotation,
AnnotationHub, data.table, tibble
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
utils, httr2, jsonlite, parallel, filelock, rappdirs
stats, tools, rhdf5filters, S4Vectors, IRanges, S4Arrays
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
2.13.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel,
methods, matrixStats
httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache,
tools, utils, digest, shiny, miniUI, DT
utils, stats, tools, Matrix, BiocGenerics (>= 0.51.2),
S4Vectors, IRanges, S4Arrays (>= 1.1.1), rhdf5
dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices,
stats, MsCoreUtils
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, Seqinfo
assertthat, Biobase, BiocGenerics, biomaRt, checkmate (>=
2.1), circlize, ComplexHeatmap, DESeq2, dplyr, edgeR, EnvStats,
forcats (>= 1.0.0), GenomicRanges, ggplot2, ggrepel (>= 0.9),
IRanges, limma, magrittr, matrixStats (>= 1.5.0), methods,
MultiAssayExperiment, purrr, R6, Rdpack (>= 2.6.2), rlang,
S4Vectors, stats, tidyr, utils
matrixStats, stats, data.table, harmonicmeanp, metap, cluster,
spdep, Matrix, limma, methods
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
InteractionSet, BiocGenerics, BiocParallel, dplyr, Seqinfo,
GenomicRanges, ggplot2, grDevices, IRanges, Matrix, methods,
rhdf5, rlang, rtracklayer, S4Vectors, stats, utils, strawr,
tibble, stringr, tidyr, gridExtra, data.table, reshape,
checkmate, purrr, withr
Biostrings, BSgenome, cli, data.table, dplyr, GenomeInfoDb,
GenomicInteractions, GenomicRanges, InteractionSet, ggplot2,
ggpubr, ggVennDiagram, gplots, igraph, IRanges, memoise,
methods, S4Vectors, stringr, tibble, tidyr, UpSetR, utils
ggplot2, viridis, RColorBrewer, scales, reshape2, stringr,
data.table, Seqinfo, GenomicRanges, stats, IRanges, grDevices,
S4Vectors, digest, tibble, jsonlite, BiocParallel, R.utils,
readr, methods
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth,
methods, utils, graphics, pheatmap, gtools, rhdf5
methods, ggplot2, Rcpp (>= 0.12.8), stats, S4Vectors, gtools,
pbapply, BiocParallel, BiocGenerics, grid, cowplot, gridExtra,
data.table, multiHiCcompare, Seqinfo
InteractionSet, strawr, Seqinfo, GenomicRanges, IRanges,
S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5,
Matrix, vroom, dplyr, stats
InteractionSet, SummarizedExperiment, GenomicRanges, IRanges,
GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO,
BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr,
stringr, ggplot2, ggrastr, scales, stats, utils
BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet,
vroom, basilisk.utils, basilisk, reticulate, rmarkdown,
rmdformats, plotly, dplyr, stringr, sessioninfo, utils
data.table, InteractionSet, GenomicRanges,
SummarizedExperiment, Rcpp (>= 1.0.12), S4Vectors, gtools,
pbapply, BiocGenerics, Seqinfo
Rcpp(>= 0.11.0), parallel, stats, Biostrings, GenomicRanges,
rtracklayer, strawr, rhdf5, BSgenome,IRanges, S4Vectors,
BSgenome.Dmelanogaster.UCSC.dm6
Seqinfo, GenomicRanges, IRanges, InteractionSet, rtracklayer,
ggplot2, ComplexUpset, reshape2, eulerr, S4Vectors, methods,
utils, htmlwidgets, svglite
methods, utils, png, grDevices, circlize (>= 0.3.3), IRanges,
GenomicRanges, polylabelr, Rcpp
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, ggpubr, dplyr, tibble, visNetwork,
reshape2, MetBrewer
ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap,
dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment,
ggrepel
sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl,
methods
Biostrings, graphics, grDevices, rtracklayer, RColorBrewer,
Matrix, parallel, Seqinfo
dplyr, httr2, jsonlite, S4Vectors, stringi, stats,
SummarizedExperiment, utils
knitr, rmarkdown, SpatialExperiment, SummarizedExperiment,
circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid,
methods, stats, RANN, Rcpp (>= 1.0.9)
graphics, grDevices, stats, utils, BiocGenerics
dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils,
gridExtra
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, MCL
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
edgeR, DESeq2, BiocParallel, Biobase, utils, stats, grDevices,
graphics, methods
httr2, dplyr, tidyr, tibble, rjsoncons, rlang, utils, stringr,
whisker, purrr
available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager,
utils
Rcpp, graphics, GenomicRanges, SummarizedExperiment, IRanges
ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment,
stats, methods, RColorBrewer, ComplexHeatmap, grDevices,
BiocParallel
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 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods,
UpSetR, utils, rlang
DESeq2, SummarizedExperiment, mosdef (>= 1.1.0),
GenomicRanges, IRanges, S4Vectors, ggplot2 (>= 2.0.0),
heatmaply, plotly, pheatmap, 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,
graphics, base64enc, methods, utils, stats
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
mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI
(>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11),
parallelly , glmnet, stats, utils, SummarizedExperiment,
stringr, S4Vectors, DescTools, MatrixExtra, methods
methods, utils, stats, tools, R.utils, curl, httr, xml2,
rvest, xtable, jsonlite, S4Vectors, IRanges, GenomeInfoDb
methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel
(>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0),
SummarizedExperiment, tidyr
methods, BiocGenerics, httpuv, utils, rtracklayer,
VariantAnnotation, RColorBrewer, httr
BiocGenerics, checkmate, futile.logger, GenomeInfoDbData,
htmlwidgets, httr, jsonlite, randomcoloR, utils
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
DT, dplyr, bslib, bsicons, ggplot2, viridis, tidyr, leaflet,
clipr, rlang
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, Seqinfo, stats, ggfortify,
grDevices, methods, Matrix, utils, graphics, gridExtra, grid,
lattice, Rsamtools, survival, BiocParallel, GenomicAlignments,
parallel
STRINGdb, pwalign, igraph, graphics, utils, seqinr
hash, httr, Matrix, matrixStats, methods, Rcpp, rvest,
SingleCellExperiment, stats, stringr, utils
methods, stats, graphics, grid, lattice, grDevices
ggplot2, httr, jsonlite, patchwork, UniProt.ws
stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
xml2, maps, rlang
SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA,
grDevices, graphics, survival, igraph, Pigengene (>= 1.19.26),
Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast,
tidyr, tidyselect, utils
graphics, grDevices, RColorBrewer, gplots, futile.logger,
stats, utils, methods, ape, phyclust, Matrix, fastcluster,
parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin,
caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus,
future, foreach, doParallel, Seurat, 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,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq,
depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges,
GenomicFeatures, ggplot2, IRanges, limma,
magrittr,methods,parallelly, plyranges, preprocessCore,
readr,reshape2, RSQLite, Seqinfo, stats, S4Vectors, utils
pROC, deSolve, rootSolve, KernSmooth, readxl, GenomicFeatures,
GenomicRanges, IRanges, BiocGenerics, GenomicAlignments,
Rsamtools, S4Vectors, Seqinfo, DESeq2, plgem, rtracklayer,
SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny
SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2
methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12),
IRanges, Seqinfo
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), txdbmaker,
IRanges, seqinr, graphics, grDevices, stats, utils, grid,
methods, DBI, RMariaDB, GenomicAlignments, BiocParallel,
BiocGenerics, DEXSeq, DESeq2
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2,
methods, BiocGenerics, XVector, tibble, stats, BiocParallel,
bit64, stringr, utils
Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer,
stats
Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats,
assertthat
utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs,
lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools,
grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib,
vegan, data.table, DT
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2,
ggrepel, colourpicker, igraph, vipor, mgcv, graphics,
grDevices, viridisLite, shinyWidgets, listviewer,
ComplexHeatmap, circlize, grid
DESeq2, edgeR, methods, S4Vectors, shiny, SummarizedExperiment
iSEE, iSEEu, methods, ggplot2, igraph, rlang, stats,
SummarizedExperiment, SingleCellExperiment, visNetwork,
BiocBaseUtils
AnnotationHub, BiocManager, DT, iSEE, methods, rintrojs,
S4Vectors, shiny, shinydashboard, shinyjs, utils
BiocFileCache, DT, iSEE, methods, paws.storage, rintrojs,
shiny, shinydashboard, shinyjs, stringr, urltools, utils
ggplot2, methods, S4Vectors, shiny, shinyWidgets, stats,
SummarizedExperiment
ape, ggplot2, ggtree, grDevices, methods, miaViz, purrr,
S4Vectors, shiny, mia, shinyWidgets, SingleCellExperiment,
SummarizedExperiment, tidygraph, TreeSummarizedExperiment,
utils
methods, S4Vectors, IRanges, shiny, SummarizedExperiment,
SingleCellExperiment, ggplot2 (>= 3.4.0), DT, stats,
colourpicker, shinyAce
methods, Rcpp, data.table, glue, stats, doParallel, parallel,
doRNG, foreach, iterators, ggplot2, HDInterval,
SummarizedExperiment, S4Vectors
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, RColorBrewer, rtracklayer,
VennDiagram, DBI, grDevices, graphics, stats, utils, Seqinfo,
grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), edgeR,
futile.logger, stringr, dplyr, magrittr, readr, tibble,
XVector, BiocGenerics, RCurl, Biobase, SummarizedExperiment,
tidyr, S4Vectors, BiocParallel, pwalign
AnnotationDbi, 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
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, Seqinfo, ggfortify,
grDevices, methods, Matrix, BiocParallel,utils, stats
shiny, survival, survminer, hwriter, plotly, ggplot2,
S4Vectors, graphics, stats, utils, UpSetR
spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr,
doParallel, BiocParallel, methods,
BumpyMatrix,SpatialExperiment
regioneR, GenomicRanges, IRanges, Rsamtools, stats, graphics,
memoise, rtracklayer, Seqinfo, GenomeInfoDb, S4Vectors,
biovizBase, digest, bezier, GenomicFeatures, bamsignals,
AnnotationDbi, grDevices, VariantAnnotation
methods, stats, Rcpp (>= 0.11.2), Matrix (>= 1.5-0), XVector
(>= 0.7.3), S4Vectors (>= 0.27.3), e1071, LiblineaR, graphics,
grDevices, utils, apcluster
methods, XML (>= 2.3-0), graph, utils, RCurl, Rgraphviz
AnnotationDbi, DBI, grDevices, methods, tools, utils
data.table, BiocParallel, sqldf, stats, grid, grDevices
aods3, Biobase, DESeq2, DSS, ggplot2, gplots, graphics,
grDevices, matrixStats, stats, utils, foreach, doParallel,
parallel, shiny, shinycssloaders, ade4, factoextra, DT
survival, tools, methods, pracma, doParallel, foreach,
parallel, SummarizedExperiment, S4Vectors
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
sesameData, dplyr, methods, rlang, GenomicRanges, IRanges,
reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel,
tibble, wheatmap, magrittr
curl, igraph, foreach, doParallel, sortable, dplyr, forcats,
data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast,
stats, SummarizedExperiment, utils, purrr, stringi, stringr,
Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs,
data.table, htmltools, htmlwidgets, bsplus, shinyvalidate,
shiny, shinythemes, shinyFiles, shinyjs, shinyBS,
shinydashboard, biomaRt, callr, logr, ggplot2, svglite
BiocGenerics (>= 0.25.1), Seqinfo, httr, Matrix
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr,
testthat, tibble, tidyr, forcats, stringr, ggtree,
BiocGenerics, ape, ggrepel, mia, purrr, tidyselect, treeio
stats, utils, irlba, methods, SingleCellExperiment,
SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0),
glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix,
DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats,
Rcpp, harmony (>= 1.2.0), limma, BiocNeighbors
Hmisc, stats, energy, grDevices, graphics, utils,
MultiAssayExperiment, ggplot2, ggpubr
grDevices, graphics, stats, utils, methods, statmod
methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot,
xtable, utils
ggplot2, stringr, plyr, ggrepel, reshape2, grDevices,
graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci,
tidyverse, methods, stats, SummarizedExperiment, S4Vectors
limma, stringr, qvalue, utils, stats, BiocParallel, S4Vectors,
dplyr
VariantAnnotation, MatrixGenerics, SummarizedExperiment,
data.table, stringr, httr, 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
data.tree, reshape2, networkD3, stringdist, purrr, ape,
cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap,
Biostrings, pwalign, IRanges, BiocGenerics(>= 0.36.1), ggtree
methods, stats, utils, data.table, S4Vectors, rlang, dplyr,
tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD,
magrittr
dplyr, ggnewscale, ggplot2, magrittr, methods, rlang,
SummarizedExperiment, MKmisc, matrixTests
Biobase, graphics, grDevices, methods, stats
ggplot2, class, concaveman, grid, BiocParallel,
spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors,
methods, spicyR, purrr, stats, data.table, dplyr, tidyr,
SingleCellExperiment, SpatialExperiment, SummarizedExperiment,
pheatmap, spatstat.random, lifecycle, simpleSeg, rlang,
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
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
S4Vectors, Biobase, scran, dplyr, ggplot2
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,
scater
dplyr, rtracklayer, BSgenome, Biostrings, utils, methods,
IRanges, ExperimentHub
robustbase, biglm, pcaPP, edgeR, metagenomeSeq, pbapply, car,
dplyr, vegan, chemometrics, ggplot2, pheatmap, logging,
data.table, lmerTest, hash, optparse, grDevices, stats, utils,
glmmTMB, MASS, cplm, pscl, lme4, tibble
dplyr, plyr, pbapply, lmerTest, parallel, lme4, optparse,
logging, multcomp, ggplot2, RColorBrewer, patchwork, scales,
rlang, tibble, ggnewscale, survival, methods, BiocGenerics,
SummarizedExperiment, TreeSummarizedExperiment
BiocParallel, DelayedArray, WGCNA, ff, data.table,
dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, httr,
RJSONIO, logging, methods, utils
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
utils, reticulate, S4Vectors, methods, basilisk,
ExperimentHub, AnnotationHub
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy, pheatmap
doParallel, igraph, bigstatsr, rjson, plyr, data.table,
UpSetR, reshape2, jsonlite, methods, ff, argparse, impute,
RnBeads.hg19, RnBeads.hg38, utils, stats
utils, rtracklayer, Matrix, matrixStats, stats, S4Vectors,
methods, graphics, GenomicRanges, GenomicFeatures, IRanges,
Rsamtools, AnnotationDbi, aod, BiocParallel, DESeq2, openxlsx,
RColorBrewer, reshape2, TRESS
caret, parallel, doParallel, foreach, e1071, future.apply,
future, missForest, pcaMethods, tidyverse, stats, utils,
methods, SummarizedExperiment, S4Vectors
flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2,
RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils,
e1071, xgboost, parallel, pbapply, reshape2, gtools, utils,
stats, cowplot, methods, grDevices, graphics
methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges,
InteractionSet, data.table, stats, rlang, glue, assertthat,
plyranges, magrittr, dbscan, purrr, progress, Seqinfo, strawr
(>= 0.0.91), DelayedArray, HDF5Array, abind, BiocParallel,
IRanges, SummarizedExperiment, rhdf5, plotgardener,
RColorBrewer, colourvalues, utils, grDevices, graphics, grid
Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr,
magrittr, rlang, S4Vectors
dplyr, rtracklayer, reshape2, Gviz, DT, Seqinfo, stats, utils,
IRanges, methods, BiocGenerics, parallel, data.table
Biobase, graphics, grDevices, venn, mclust, stats, MASS
AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr,
graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb,
org.Hs.eg.db, patchwork, SeuratObject, SingleCellExperiment,
stats, SummarizedExperiment, tidyr, utils
methods, TFBSTools, IRanges, XVector, Biostrings
BiocGenerics, ProtGenerics, digest, irlba, stats, stats4,
graphics, grDevices, parallel, utils
methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap,
rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva,
tibble, tidyr, vegan, stats, utils, Matrix
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
MatrixEQTL, dplyr, ggplot2, readxl, stringr, tidyr,
metagenomeSeq, pheatmap, broom, graphics, stats, methods
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
e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment,
SingleCellExperiment
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 (>= 2.31.2),
methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5)
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
dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils,
rlang, graphics, matrixStats, tidyr
BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics,
methods, S4Vectors, Spectra (>= 1.17.6), BiocParallel,
SummarizedExperiment, QFeatures, AnnotationHub, graphics,
CompoundDb
utils, MsCoreUtils, BiocParallel, methods, stats
dplyr, ggplot2, KEGGREST, methods, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>=
2.4.0), S4Vectors, stringr, SummarizedExperiment, tidyr,
dynamicTreeCut, rlang, ape, ggtree, patchwork
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
stats, RANN, igraph, vegan, edgeR, ecodist, ggplot2, viridis,
ggpubr, ape, cluster, matrixStats
rtracklayer, tools, GenomicAlignments, GenomeInfoDb, IRanges,
ggplot2, Rsamtools, purrr, data.table, methods, dplyr,
magrittr, reshape2
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench
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
utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats,
clusterProfiler, RecordLinkage, RCy3
ABSSeq, Biobase, BiocGenerics, BiocParallel, biomaRt,
Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter,
Seqinfo, 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,
txdbmaker, utils, VennDiagram, vsn, yaml, zoo
Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats,
GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm,
data.table
methylKit, GenomicRanges, Seqinfo, parallel, BiocGenerics,
S4Vectors, methods, stats, IRanges, msm
AnnotationHub, annotatr, BiocCheck, BiocManager, BiocParallel,
BiocStyle, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, cowplot, data.table, DelayedArray,
devtools, dplyr, ExperimentHub, foreach, GenomeInfoDb,
HDF5Array, IRanges, knitr, MatrixGenerics, R.utils, rcmdcheck,
RcppRoll, remotes, rhdf5, rtracklayer, S4Vectors, scales,
tibble, tidyr, tools, TumourMethData, usethis
dplyr, plyr, GenomicRanges, SummarizedExperiment,
DelayedArray, ggplot2, ggpubr, tibble, tidyr, S4Vectors,
sesameData, sesame, AnnotationHub, ExperimentHub, stringr,
readr, methods, stats, Matrix, MASS, rlang, pscl, IRanges,
sfsmisc, progress, utils, openxlsx, JASPAR2024, RSQLite,
TFBSTools
rtracklayer, DelayedArray, HDF5Array, BSgenome,
DelayedMatrixStats, parallel, methods, ggplot2, S4Vectors,
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, gridExtra,
preprocessCore, dynamicTreeCut, planet
RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler,
missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db,
AnnotationDbi, shiny,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
BiocParallel, parallel, stats, methods, corpcor,
SummarizedExperiment, utils
methylKit, BiocParallel, GenomicRanges, IRanges, S4Vectors,
methods, parallel, ggplot2, gridExtra, rebus
IRanges, data.table (>= 1.9.6), parallel, S4Vectors (>=
0.13.13), Seqinfo, KernSmooth, qvalue, emdbook, Rsamtools,
gtools, fastseg, rtracklayer, mclust, mgcv, Rcpp, R.utils,
limma, grDevices, graphics, stats, utils
foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute,
data.table, limma, R.matlab, digest
marray, gplots, IRanges, BiocGenerics, Gviz,
GenomicAlignments, Biostrings, parallel, data.table, Seqinfo,
S4Vectors
shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings,
pwalign, Rfast, grDevices, graphics, stats, utils, tools,
methods, shinyFiles, data.table, SummarizedExperiment
bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges,
Seqinfo, 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
mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors,
urltools, utils, tidyjson
ape, BiocGenerics, BiocParallel, Biostrings, bluster,
DECIPHER, decontam, DelayedArray, DelayedMatrixStats,
DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics,
methods, rbiom, rlang, S4Vectors, scater, scuttle, stats,
stringr, tibble, tidyr, utils, vegan, Rcpp
ape, bluster, htmltools, iSEEtree (>= 1.1.4), mia, rintrojs,
scater, scuttle, shinydashboard, shinyjs, shinyWidgets,
S4Vectors, SingleCellExperiment, SummarizedExperiment,
TreeSummarizedExperiment, utils, vegan
SummarizedExperiment, deSolve, stats, poweRlaw,
MatrixGenerics, S4Vectors
dplyr, methods, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tidyr, TreeSummarizedExperiment
ape, BiocGenerics, BiocParallel, DelayedArray,
DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggtree,
methods, rlang, S4Vectors, scales, scater,
SingleCellExperiment, stats, tibble, tidygraph, tidyr,
tidytext, tidytree, viridis
Biostrings, compositions, 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)
clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem,
gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets,
shinycustomloader, htmltools, ggplot2, graphics, stats, utils,
yulab.utils
ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel,
vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang,
tibble, grDevices, stats, utils, coin, ggsignif, patchwork,
ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>=
1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table,
ggfun (>= 0.1.1)
BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr,
TreeSummarizedExperiment
TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2,
ggpubr, ggridges, glue, S4Vectors, dirmult
BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>=
1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods,
igraph, irlba, utils, cowplot, BiocParallel, BiocSingular,
limma, ggplot2, tibble, matrixStats, ggraph, gtools,
SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel,
ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv
BiocGenerics, S4Vectors, preprocessCore, grDevices, methods,
grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses
methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
biganalytics, stringr, Hmisc, utils
S4Vectors, Seqinfo, 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, Seqinfo, 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
AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR,
fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics,
graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>=
2.44.0), rlang, stats, utils
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, RColorBrewer,
grid, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, methods,
rJava, BiBitR, rqubic, Biobase, PMA, stats, dbscan, mclust,
SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase,
org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE,
MatrixCorrelation, energy
corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler,
ReactomePA, DOSE, survival, grDevices, graphics, stats, utils,
Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel
purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap,
reshape2, corrplot, grDevices, graphics, stats, utils,
data.table, R.utils, viridis
AnnotationDbi, BiasedUrn, Biobase, BiocGenerics, GenomeInfoDb,
GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICv2manifest, IRanges, limma,
methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors,
statmod, stringr, SummarizedExperiment
BiocParallel, MCMCpack, Matrix, S4Vectors, methods,
rtracklayer, car, mvtnorm, SummarizedExperiment,
SingleCellExperiment, BiocGenerics, stats, rlang
stats, grDevices, graphics, utils, MASS, plyr, reshape2,
parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2,
gplots, beeswarm, echarts4r, kableExtra, dplyr, network
reshape2, GenomicRanges, pheatmap, deepSNV, grDevices,
graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods,
ggplot2
AnnotationDbi, ape, circlize, ComplexHeatmap, ggplot2, ggtree,
magrittr, org.Hs.eg.db, scales
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, ggrepel, BiocParallel, utils,
gsignal, rgl
gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats, magrittr,
SummarizedExperiment
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,
stringr, 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
dplyr, tidyr, ggplot2, BiocGenerics, DESeq2, edgeR, ggrepel,
grDevices, pheatmap, utils, tidyselect, progress, RColorBrewer,
GenomicRanges, rtracklayer, data.table, SimDesign, scales,
IRanges, stats, methods, Biostrings, reticulate, S4Vectors,
Seqinfo, SummarizedExperiment, rlang, bioseq, grid
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges,
XVector, stringi, stringr, crayon, grDevices
stats, utils, RCy3, stringr, graphics, grDevices, RUnit,
BiocParallel, igraph
methods, graphite, genefilter, BiocGenerics, gplots, GSEABase,
Biobase, parallel, corpcor, svd, cluster, grDevices, graphics,
stats, utils
SpatialExperiment, Matrix, purrr, data.table, dplyr (>=
1.1.1), magrittr, rjson, utils, methods, terra, ggplot2, rlang,
cli, EBImage, rhdf5, BiocParallel, S4Vectors, stats
circlize, cluster, ComplexHeatmap, dplyr, ggplot2, graphics,
grid, grDevices, magrittr, methods, MKmisc,
MultiAssayExperiment, parallel, qvalue, RColorBrewer, readr,
reshape2, rlang, stats, stringr, tibble, tidyr, utils
BiocGenerics, BiocParallel, Biostrings, BSgenome, circlize,
ComplexHeatmap (>= 2.11.1), Seqinfo, GenomicRanges, cli,
ggplot2 (>= 4.0.0), glmnet, grDevices, grid, IRanges, methods,
rlang, RSQLite, stabs, stats, SummarizedExperiment, S4Vectors,
TFBSTools, tidyr, tools, utils, XVector
parallel, igraph (>= 1.0.1), BiocGenerics, HSMMSingleCell (>=
0.101.5), plyr, cluster, combinat, fastICA, grid, irlba (>=
2.0.0), matrixStats, Rtsne, MASS, reshape2, leidenbase (>=
0.1.9), limma, tibble, dplyr, pheatmap, stringr, proxy, slam,
viridis, stats, biocViews, RANN(>= 2.5), Rcpp (>= 0.12.0)
parmigene, randomForest, gplots, circlize, RColorBrewer,
HiveR, clusterProfiler, DOSE, Biobase, grDevices, graphics,
GEOquery, stats, purrr, RISmed, grid, utils, ComplexHeatmap,
GenomicRanges, dplyr, fuzzyjoin, rtracklayer, magrittr, qpdf,
readr, seqminer, stringr, tibble, tidyHeatmap, tidyr,
AnnotationHub, easyPubMed, org.Hs.eg.db, EpiMix, BiocGenerics,
ggplot2, ExperimentHub, rlang, withr, data.table
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, Seqinfo, S4Vectors
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
MultiAssayExperiment, methods, survminer, graph, graphite,
AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap,
survival, RColorBrewer, SuperExactTest, reshape, NbClust,
S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap,
FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase,
ggplotify, qpgraph, org.Hs.eg.db, Matrix
DT, ggplot2, ggforce, ggrepel, graphics, grDevices, htmltools,
methods, AnnotationDbi, topGO, GO.db, clusterProfiler, goseq,
utils, RColorBrewer, rlang, DESeq2, scales,
SummarizedExperiment, S4Vectors, stats
HiddenMarkov, zoo, IRanges, S4Vectors, dplyr, ggplot2,
lazyeval, matrixStats, methods, rlang, stringi, stringr, scran,
Seurat, Signac, edgeR, Rcpp
S4Vectors, stats, utils, methods, grDevices, graphics,
BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges,
GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools
methods, grDevices, stringr, parallel, BiocGenerics, S4Vectors
(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings,
BSgenome, rtracklayer, VariantAnnotation, BiocParallel,
motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment,
pwalign, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny,
vroom
Matrix, Rcpp, methods, TFBSTools, Biostrings, BSgenome,
S4Vectors, SummarizedExperiment, GenomicRanges, IRanges,
Rsamtools, Seqinfo
BiocFileCache, BiocParallel, DT, ggplot2, plotly,
universalmotif, GenomicRanges, IRanges, rtracklayer, tools,
htmltools, rmarkdown, viridis, SummarizedExperiment,
htmlwidgets, Rsamtools, GenomicAlignments, Seqinfo, Biostrings,
BSgenome, memes, S4Vectors, dplyr, purrr, tidyr, heatmaply,
stats, utils
ade4, Biostrings, ggplot2, grDevices, graphics, htmlwidgets,
stats, stats4, utils, XML, TFBSTools
Seqinfo, graphics, harmonicmeanp, IRanges, matrixStats,
methods, parallel, patchwork, rlang, S4Vectors, stats,
universalmotif,
httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales,
gtools, tidyr, data.table, jsonlite, rlist, Seqinfo, methods,
biomaRt, stats, IRanges
S4Vectors, scales, stats, graphics, statmod
BiocParallel, methods, progress, stats, SummarizedExperiment
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
Rcpp, Biostrings, GenomicRanges, IRanges, ape, doParallel,
dplyr, foreach, methods, parallel, pwalign, rlang, seqinr,
stats, stringi, stringr, tibble, tidyr, utils
BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>=
1.35.3), MsCoreUtils, DBI, utils
curl, ProtGenerics, BiocFileCache, S4Vectors, methods,
progress
ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges,
MsCoreUtils, methods, stats
ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges,
rawrr (>= 1.17.2), utils, BiocParallel
BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3),
DBI, MsCoreUtils, IRanges, data.table, progress, stringi,
fastmatch, BiocGenerics
methods, S4Vectors, IRanges, Spectra, SummarizedExperiment,
QFeatures, DBI, BiocGenerics
methods, ProtGenerics (>= 1.23.5), MsCoreUtils,
SummarizedExperiment, stats
BSgenome, easyRNASeq, edgeR, GenomicAlignments,
GenomicFeatures, Seqinfo, ggbio, ggplot2, IRanges, parallel,
plyr, Rsamtools, R.utils, stats, SummarizedExperiment,
S4Vectors, utils
softImpute, methods, stats, graphics, pdist, reticulate,
scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr,
dplyr
MsCoreUtils, PSMatch (>= 1.13.2), BiocParallel, IRanges (>=
2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods,
MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice,
ggplot2, scales, MASS, Rcpp
QFeatures, limma, SummarizedExperiment, magrittr, rlang,
dplyr, purrr, stats, tidyr, stringr, ggplot2, ggseqlogo,
heatmaply, readr, rstatix, tibble, ggpubr
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
stats, methods, lme4, purrr, BiocParallel, Matrix, MASS,
limma, SummarizedExperiment, MultiAssayExperiment, codetools
MSstatsConvert, data.table, checkmate, MASS, htmltools, limma,
lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel,
gplots, plotly, marray, stats, grDevices, graphics, methods,
statmod, parallel
arrow, DBI, dplyr, MSstats, MSstatsConvert, readr, sparklyr,
utils
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, plotly, htmltools
minpack.lm, ggplot2, utils, stats, grDevices
dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel, plotly, htmltools
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid
shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly,
data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM,
MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid,
utils, stats, htmltools, methods, tidyr, grDevices, graphics,
mockery, MSstatsBioNet, shinydashboard, arrow, tools
limma, lme4, lmerTest, methods, data.table, stats, utils,
ggplot2, grDevices, graphics, MSstats, MSstatsConvert,
checkmate, plotly, htmltools
methods, stats, MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, DelayedArray, S4Vectors
graphics, grDevices, stats, methods, fields
Biobase, BiocBaseUtils, BiocGenerics, DelayedArray,
GenomicRanges, IRanges, MatrixGenerics, methods, S4Vectors,
tidyr, utils
Matrix, ggplot2, MultiAssayExperiment, ropls, graphics,
methods, plotrix, grDevices, pcaMethods
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
BiocGenerics, Biostrings, BSgenome, CRISPRseek, data.table,
Seqinfo, 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, metaboliteIDmapping, 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 (>= 2.0), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, S4Vectors, data.table, grid, dplyr, tidyr,
matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize,
mashr, grDevices
stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork,
scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel,
methods, SummarizedExperiment
stats, utils, methods, igraph, Matrix, BiocGenerics,
BiocParallel, IRanges, S4Vectors, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, BiocNeighbors,
BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran,
batchelor, uwot
data.table, utils, R.utils, dplyr, stats, GenomicRanges,
GenomeInfoDb, IRanges, ieugwasr(>= 1.0.1), BSgenome,
Biostrings, stringr, VariantAnnotation, methods, parallel,
rtracklayer(>= 1.59.1), RCurl
BiocParallel, blme, ComplexHeatmap, data.table, DESeq2, dplyr,
edgeR, ggplot2, glmmTMB, grDevices, grid, IHW, limma, lmerTest,
lme4, Matrix, matrixStats, methods, progress, purrr, rlang,
S4Vectors, scales, scater, scuttle, sctransform, stats,
SingleCellExperiment, SummarizedExperiment, variancePartition
SummarizedExperiment, VariantAnnotation, 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, decompTumor2Sig, topicmodels,
ggrepel, plotly, utils, factoextra, cluster, ComplexHeatmap,
philentropy, maftools, shiny, stringi, tidyverse, ggpubr,
Matrix (>= 1.6.1), scales
BiocGenerics, S4Vectors, methods, SummarizedExperiment, Rcpp,
edgeR (>= 3.42.0), dplyr, Matrix, limma, tidyr, stats, GGally,
ggplot2, tidyselect (>= 1.2.0), tibble, rlang, grDevices, csaw,
rmarkdown, xfun, DT, ggrepel, IRanges, utils, DelayedArray,
tools
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST,
ComplexHeatmap, stats, utils
methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7),
Hmisc, sqldf, plyr, S4Vectors
httr, jsonlite, S4Vectors, Hmisc, plyr, magrittr, Seqinfo,
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, cli, S4Vectors, SummarizedExperiment,
BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp,
dplyr, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr,
glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr,
rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr,
tibble, tidyr, utils, withr
BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes,
grDevices, IRanges, methods, pheatmap, RColorBrewer, stats,
utils
DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods,
stats,
httr, xml2, utils, methods, grDevices, ggplot2, IRanges,
GenomicRanges, S4Vectors
R.utils, matrixStats, plyranges, transport, Rsamtools,
S4Vectors, grDevices, graphics, rtracklayer, dplyr, Seqinfo,
methods, GenomicRanges, utils, stats, magrittr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, ggplot2, gplots,
BiocGenerics, rlang
SingleCellExperiment, SummarizedExperiment, SeuratObject, ks,
Matrix, stats, methods, ggrastr
e1071, nnet, randomForest, naturalsort, graphics, stats,
utils, matrixStats, epiNEM
airway, DelayedArray, DelayedMatrixStats, DESeq2, methods,
methods, NetActivityData, SummarizedExperiment, utils
Rcpp, RcppParallel, parallel, grDevices, graphics, stats,
utils, dynamicTreeCut, WGCNA, impute, colorspace, methods,
BiocStyle, R.utils
glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust,
parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
stats, Matrix, dplyr, doParallel, foreach, parallel,
sparseMVN, ggplot2, gridExtra, pROC
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 (>= 1.1.0), forcats, ggdendro,
grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate,
methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats,
stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics,
grid, methods, MultiAssayExperiment, SummarizedExperiment,
pracma, rlang, RSpectra, scales, stats
graphics, grDevices, marray, methods, nnet, stats
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
BRISC, BiocParallel, Matrix, matrixStats, stats, methods
limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0)
KEGGREST,png,dplyr,graphics,RSQLite,DBI,tidyr,grDevices,stringr,Seqinfo,
S4Vectors,SummarizedExperiment,reactome.db,rWikiPathways,RCurl,
dbplyr,utils,ggplot2,igraph,stats,reshape2,readr, GO.db,
biomaRt,rtracklayer,IRanges,GenomicRanges,GenomicFeatures,AnnotationDbi,methods
vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods,
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, Seqinfo, GenomicRanges,
IRanges, Rsamtools, S4Vectors, ShortRead, dplyr, ggplot2,
magrittr, parallel, stats, utils, grDevices
stats, IRanges, GenomicRanges, Seqinfo, methods, rlang,
S4Vectors, scales, InteractionSet, ggplot2, grDevices,
plyranges, data.table, progress, ggridges
multtest (>= 1.7.3), graphics, grDevices, stats, interp
EDASeq, GSVA, data.table, htmlwidgets, plotly, reshape2,
grDevices, utils
GenomicRanges, methods, data.table, assertthat, ggplot2, Gviz,
IRanges, AnnotationHub, grDevices, stats, Seqinfo,
GenomeInfoDb, shiny, shinyFiles, DT, rtracklayer,
shinydashboard, shinyBS,tidyr
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, bit
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
dplyr, stringr, rols, tidyr, methods, stats, tibble,
data.tree, jsonlite, plyr, BiocFileCache, readr, DiagrammeR,
rlang, lubridate
HelloRanges, fpc, stats, MultiAssayExperiment, pdftools,
methods, grDevices, utils,clValid, NbClust, cowplot, rmarkdown,
kableExtra, rtracklayer, IRanges, Seqinfo, reshape2, ggplot2,
factoextra, rgl, corrplot, MASS, graphics, FactoMineR,
PerformanceAnalytics, tidyr, data.table, cluster, magick
methods, matrixStats, graphics, stats, SummarizedExperiment,
MultiAssayExperiment, RaggedExperiment
survminer, survival, fastmatch, reshape2, stringr, beeswarm,
grDevices, DT, shiny, shinythemes, shinyWidgets, plotly,
networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea,
openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics,
grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2,
S4Vectors, SummarizedExperiment, RSQLite, Matrix,
shinycssloaders, ROCR, drc
dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr,
tidyselect, grid, stats, stringr
checkmate, crayon, curl, digest, dplyr(>= 1.1.0), fs, httr2,
igraph, jsonlite, later, logger, lubridate, magrittr, progress,
purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown,
RSQLite, R.utils, rvest, sessioninfo, stats, stringi, stringr,
tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML,
xml2, yaml, zip
DT, shiny, bs4Dash, waiter, thematic, MSnbase, PSMatch,
SummarizedExperiment, MultiAssayExperiment, shinyBS, shinyjs,
shinyjqui, RColorBrewer, gplots, highcharter, visNetwork,
tibble, grDevices, stats, utils, htmlwidgets, vioplot,
graphics, FactoMineR, dendextend, dplyr, factoextra, tidyr,
nipals
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
biomaRt, grDevices, graphics, utils, methods,
Biobase, S4Vectors, methods, stats, utils, BiocFileCache,
shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT,
igraph, AnnotationHub, SummarizedExperiment, reticulate,
R.utils, httr, basilisk, jsonlite, RBGL, ellmer
methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz,
ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>=
3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices
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
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
AnnotationDbi (>= 1.45.0), Biostrings (>= 2.51.1), biomaRt,
biomartr (>= 1.0.7), BiocFileCache, BiocGenerics (>= 0.29.1),
BiocParallel (>= 1.19.0), BSgenome, cowplot (>= 1.0.0),
data.table (>= 1.11.8), DESeq2 (>= 1.24.0), fst (>= 0.9.2),
GenomeInfoDb (>= 1.15.5), GenomicFeatures (>= 1.31.10), ggplot2
(>= 2.2.1), gridExtra (>= 2.3), httr (>= 1.3.0), jsonlite,
methods (>= 3.6.0), qs, R.utils, Rcpp (>= 1.0.0), Rsamtools (>=
1.35.0), rtracklayer (>= 1.43.0), stats, SummarizedExperiment
(>= 1.14.0), S4Vectors (>= 0.21.3), tools, txdbmaker, utils,
XML, xml2 (>= 1.2.0), withr
RSQLite, S4Vectors, Seqinfo, IRanges, GenomicRanges (>=
1.61.1), GenomicFeatures (>= 1.61.4), AnnotationDbi, rlang,
methods, tools, utils, BiocFileCache, DBI, dbplyr, tibble
methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL,
S4Vectors, IRanges, GenomicRanges (>= 1.61.1)
dplyr, methods, stats, utils, Matrix, jsonlite, homologene,
gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr,
patchwork, DelayedArray, grr, repmis, ggtree, tools
AnnotationHub, basilisk, BiocParallel, colorspace, cowplot,
DelayedArray, dplyr, ExperimentHub, ggplot2 (>= 3.4.0), ggpubr,
ggrepel, ggsci, grDevices, grid, HDF5Array, keras, methods,
orthosData, parallel, plyr, reticulate, rlang, S4Vectors,
stats, tensorflow, tidyr
BBmisc, BiocGenerics, DESeq2 (>= 1.16.1), generics,
GenomicRanges, ggplot2, ggrepel, graphics, grDevices,
heatmaply, IRanges, matrixStats, pcaMethods, pheatmap, plotly,
plyr, pracma, PRROC, RColorBrewer, reshape2, RMTstat,
S4Vectors, scales, splines, stats, txdbmaker, utils
AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0),
GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db
(>= 3.16.0), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2),
TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>=
0.36.0)
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
DESeq2, DEXSeq, limma, fgsea, msigdbr, sva,
SummarizedExperiment, S4Vectors, BiocParallel, ggplot2,
aggregation, stats, utils, methods, showtext
SummarizedExperiment, KEGGREST, igraph, data.table, methods,
stats, magrittr, CompQuadForm, tibble
matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit,
hexbin
GenomicRanges, Rsamtools, IRanges, S4Vectors, Seqinfo,
grDevices
clusterProfiler, dplyr, forcats, GSEABase, igraph, limma,
metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer,
rlang, tibble, withr, utils
graphics, grDevices, MASS, methods, pvclust, stats, utils,
RedeR
stats, data.table, depmixS4, Seurat, SingleCellExperiment,
AnnotationHub, magrittr, GenomicRanges, BiocStyle
stats, utils, dplyr, rlang, iterators, parallel, foreach,
doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges,
S4Vectors
circlize, clusterProfiler, ComplexHeatmap, dplyr, fgsea,
ggforce, ggplot2, ggpubr, ggraph, ggrepel, grid, igraph, purrr,
sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork
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
KEGGgraph, XML, Rgraphviz, graph, png, AnnotationDbi,
org.Hs.eg.db, KEGGREST, methods, utils
lars, methods, parallel, stats, survival, utils
DESeq2, SummarizedExperiment, mosdef (>= 1.1.0),
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
graphics, stats, methods, ggplot2, utils, grDevices, stringr,
plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl,
DT, igraph, shinycssloaders, shinyhelper, shinyjs, shinyjqui,
shinyWidgets, htmlwidgets, plotly, colourpicker, shinytoastr
dplyr, limma, lme4, MASS, matrixStats, reshape2, stats,
tibble, SummarizedExperiment, methods
Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2,
methods, graphics, stats
limma, fields, GenomicRanges, ggplot2, plyr, tools, methods,
data.table
S4Vectors, rtracklayer, stats, Seqinfo, magrittr, zoo,
ggplot2, methods, parallel, cowplot
utils, methods, grDevices, graphics, circlize, httr, dplyr,
attempt, lubridate, survival, survminer, ggplot2,
GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel,
future, future.apply
ggplot2, protolite, Biobase, GEOquery, Rook, htmltools,
httpuv, jsonlite, limma, edgeR, opencpu, assertthat, methods,
httr, rhdf5, utils, parallel, stringr, fgsea (>= 1.9.4),
svglite, gtable, stats, Matrix, pheatmap, scales, ccaPP, grid,
grDevices, AnnotationDbi, DESeq2, data.table, curl, apeglm,
tidyr, config (>= 0.3.2), rhdf5client (>= 1.25.1), yaml, fs,
phantasusLite, XML
data.table, rhdf5client(>= 1.25.1), httr, stringr, stats,
utils, Biobase, methods
BiocGenerics, Biobase, S4Vectors, SummarizedExperiment,
MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer,
magicaxis, parallel, caTools, methods, downloader, stats,
utils, graphics, grDevices, reshape2, jsonlite, data.table,
checkmate, boot, coop
igraph, Matrix, foreach, doParallel, dplyr, stats, utils,
parallel
Biobase, biodb, biodbChebi, data.table, futile.logger,
ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets,
igraph, limma, methods, MultiAssayExperiment, MultiDataSet,
PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble,
tidyr, utils, VennDiagram
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
BiocFileCache, 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,
stringi
ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table,
dplyr, DT, energy, extrafont, fastcluster, ggplot2, gridExtra,
htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast,
scattermore, shiny, shinyBS, shinycssloaders, shinyFiles,
shinyjs, stringr, tsne, svglite, umap, xml2, zoo, yaml
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods
utils, Seqinfo, GenomicRanges, GenomicAlignments, Biostrings,
Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr,
S4Vectors, methods
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,
DOSE
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,
Seqinfo, parallel, stats, utils, rmarkdown
dplyr, utils, stats, GenomicRanges, BiocGenerics, methods
basilisk, reticulate, progress, ggplot2, MASS, invgamma,
grDevices, stats, graphics, SummarizedExperiment, S4Vectors
cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales,
Hmisc, patchwork, grDevices, stats, methods,
SummarizedExperiment
utils, Biobase (>= 2.5.5), MASS, methods
curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue,
grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr,
Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils,
withr
mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr,
lmerTest, performance, grid, stats, pheatmap, vegan, Biobase,
BiocStyle, TreeSummarizedExperiment
InteractionSet, Seqinfo, BiocGenerics, GenomicRanges,
plyranges, IRanges, S4Vectors, rlang, dplyr, tibble,
tidyselect, methods, utils
dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect,
vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods
ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT,
LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils
Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics,
grDevices, utils, Biobase, BiocGenerics, Matrix, Seqinfo,
IRanges, Biostrings, BSgenome (>= 1.32.0)
aricode, BiocNeighbors, BiocParallel, bluster, clevr, clue,
cluster, elsa, fclust, igraph, Matrix, matrixStats, mclustcomp,
methods, pdist, sp, spdep, stats, utils, SpatialExperiment,
SummarizedExperiment
methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics
stats, utils, grDevices, mvtnorm, sn, dplyr, flowPeaks,
ggplot2, tidyverse, cowplot, mlrMBO, DiceKriging, smoof,
ParamHelpers, lhs, rgenoud, BiocManager
broom, caret, ComplexHeatmap, dbscan, dplyr, DESeq2, fgsea,
FSA, ggcorrplot, ggplot2, ggrepel, glmnet, grid, impute,
janitor, limma, lme4, magrittr, MASS, mixOmics, multcomp,
msigdbr, purrr, randomForest, RankProd (>= 3.14), rlang,
SummarizedExperiment, sva, tibble, tidyr, utils, uwot, vegan
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, truncdist, vegan, VGAM
benchmarkme, dplyr, edgeR, foreach, ggplot2, graphics,
lifecycle, magrittr, methods, parallel, purrr, Rcpp (>=
0.12.0), RcppParallel (>= 5.0.1), rlang, rstantools (>= 2.1.1),
stats, tibble, tidybayes, tidyr (>= 0.8.3.9000), utils
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), Seqinfo, 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, Seqinfo, S4Vectors
S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics,
e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW,
foreach, pbapply, stats, parallel, gtools, rCGH
AnnotationDbi, BiocParallel, data.table, dplyr, DESeq2,
IRanges, GenomicRanges, GenomicFeatures, GenomicAlignments,
GenomeInfoDb, ggplot2, gplots, graphics, methods, rlang,
scales, S4Vectors, SummarizedExperiment, stats, tibble,
txdbmaker
GenomicRanges, Biostrings, GenomicFeatures, txdbmaker,
rtracklayer
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, utils, methods, BiocGenerics, SummarizedExperiment,
S4Vectors, extraDistr
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, Seqinfo, grDevices, rlang,
tiff, Rsamtools
Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra,
decoupleR, reshape2
SingleCellExperiment, methods, cluster, stats, limma, NMF,
ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2,
viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2,
cowplot, ggrepel, umap, tsne
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, colorspace
shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics,
utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker,
shinyhelper, shinyWidgets, shinyjs, colorspace, stats,
grDevices, grid, BiocGenerics, shinydashboard
dplyr, magrittr, data.table, RColorBrewer, ggplot2, S4Vectors,
ComplexHeatmap, stringr, NormalyzerDE, tibble, limma, MASS,
edgeR, matrixStats, preprocessCore, stats, gtools, methods,
ROTS, ComplexUpset, tidyr, purrr, circlize, gprofiler2,
plotROC, MSnbase, UpSetR, dendsort, vsn, Biobase, reshape2,
POMA, ggtext, scales, DEqMS, vegan
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.35.1), DAPARdata (>= 1.30.0), rhandsontable,
data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets,
webshot, shinythemes, later, shinycssloaders, future, promises,
shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase,
DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown,
rclipboard, sass, shinyTree, shinyWidgets
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
utils, stats, igraph, methods, Spectra (>= 1.17.10), Matrix,
BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1),
QFeatures, MsCoreUtils, IRanges
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
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, Seqinfo, GenomeInfoDb, GenomicFeatures,
Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer,
ggplot2, gridExtra, futile.logger, VGAM, tools, methods,
mclust, rhdf5, Matrix
biovizBase, Biostrings, GenomicRanges, IRanges, data.table,
methods
Biobase, methods, knitr, tools, xtable, pander, S4Vectors
graphics, methods, stats, utils, BiocGenerics, Biobase (>=
2.18.0), CGHbase (>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>=
1.32.0), Seqinfo, 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 (>= 0.53.4), ProtGenerics
(>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils
(>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect,
reshape2
rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils,
stats, igraph, VIM, scales, grDevices, graphics, limma
methods, parallel, Matrix (>= 1.5-0), grid, annotate, graph
(>= 1.45.1), Biobase, S4Vectors, BiocParallel, AnnotationDbi,
IRanges, Seqinfo, 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
MASS, pscl, arrangements, hitandrun, assertthat, dplyr,
BiocParallel
SummarizedExperiment, utils, sva, stats, methods, graphics,
Hmisc
dplyr, sva, stats, ggplot2, rlang, methods
methods, rlang, checkmate, dplyr, collapse, vroom, tidyr,
tibble, utils, stats, ashr, S4Vectors, BiocGenerics
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 (>= 2.13.1), GenomicFeatures, txdbmaker,
ShortRead, BiocParallel, Seqinfo, rtracklayer, GenomicFiles,
AnnotationDbi
methods, Seqinfo, 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, BiocGenerics, data.table, S4Vectors,
Biobase, parallel, BiocParallel, RColorBrewer, caTools,
magicaxis, methods, reshape2, scales, grDevices, graphics,
stats, utils, assertthat, matrixStats, downloader
stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome,
Biostrings, SummarizedExperiment, SingleCellExperiment,
S4Vectors, Seqinfo, GenomeInfoDb, GenomicAlignments,
GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer,
Matrix, cli
BiocBaseUtils, BiocGenerics, Seqinfo, IRanges, Matrix,
MatrixGenerics, methods, S4Vectors, stats, SummarizedExperiment
(>= 1.39.1), utils
S4Vectors, GenomicRanges, ensembldb, BSgenome, AnnotationDbi,
methods, class, pROC, IRanges, AnnotationFilter, rlang,
VariantAnnotation, MatrixGenerics, ggplot2, stringr
methods, data.table, Seqinfo, GenomicRanges, IRanges,
BiocGenerics, S4Vectors, Rcpp
graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
BiocGenerics
S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, gtools,
BSgenome, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
SummarizedExperiment, GenomicScores
curl, jsonlite, R.utils, utils, paws.storage, methods
dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools,
BiocManager, BiocParallel, rawrr (>= 1.15.5), rlang, reshape2,
scales, shiny (>= 1.5), stats, utils
EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats
GenomicRanges, IRanges, BSgenome, BSgenome.Hsapiens.UCSC.hg19,
GenomeInfoDb (>= 1.12.0), Biostrings, rtracklayer,
GenomicFeatures, txdbmaker, rmarkdown (>= 0.9.5), genomation
(>= 1.5.5), knitr (>= 1.12.3), BiocGenerics, S4Vectors,
plotrix, pbapply, RSQLite, proxy, pheatmap, ggplot2, cowplot,
seqLogo, 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,Seqinfo,GenomicRanges,AnnotationDbi,
parallel,IRanges,grDevices,aCGH
AUCell (>= 1.1.6), BiocGenerics, data.table, graphics,
GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble,
GSEABase, methods, R.utils, stats, SummarizedExperiment,
S4Vectors, utils, zoo
RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM,
ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS,
grDevices, graphics, methods
Biostrings, GOSemSim, curl, doParallel, foreach, httr2,
jsonlite, methods, rlang, stats, utils
RcppAnnoy, igraph, NbClust, Rtsne, ggplot2(>= 3.4.0), methods,
pracma, umap, grDevices, graphics, stats, Rcpp (>= 0.11.0),
MatrixGenerics, SingleCellExperiment
utils, stats, BiocParallel, batchtools, DiagrammeR, shiny,
R.utils, codetools, basilisk
rappdirs, methods, utils, git2r, httr, S4Vectors
httr, methods, RJSONIO, XML, utils, BiocGenerics, stats,
graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc,
IRkernel, IRdisplay, RColorBrewer, gplots
methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils
graphics, grDevices, methods, stats, MASS, rgl
Biobase, BiocSingular, dplyr, ggplot2, gplots, httr, igraph,
jsonlite, methods, progress, RColorBrewer,
SummarizedExperiment, tidyr
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>=
3.3.5), ggraph, reactome.db, igraph, graphite, gson,
yulab.utils (>= 0.1.5)
utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends,
dir.expiry, filelock, BiocStyle
dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment
phyloseq, ks, reshape2, ggplot2, stats, methods, graphics,
grDevices, matrixStats, Matrix
BiocParallel, derfinder, downloader, GEOquery, GenomeInfoDb,
GenomicRanges, IRanges, methods, RCurl, rentrez, rtracklayer
(>= 1.35.3), S4Vectors, stats, utils
BiocFileCache, methods, rtracklayer, S4Vectors, utils, httr,
data.table, R.utils, Matrix, GenomicRanges, sessioninfo, tools
minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl,
R.utils, BiocFileCache, basilisk, reticulate,
DelayedMatrixStats
BiocGenerics, biomaRt, Biostrings, circlize, Seqinfo,
GenomicFeatures, graphics, grDevices, httr, IRanges, methods,
parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats,
stringr, txdbmaker, utils
AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils
WGCNA, ica, moments, clusterProfiler, msigdbr, RColorBrewer,
car, lme4, lmerTest, pheatmap, biomaRt, stats, grDevices,
BiocParallel, ggplot2, patchwork, BiocGenerics, S4Vectors
randomForest, fgsea, DOSE, BiocParallel, DESeq2, limma, WGCNA,
ggplot2 (>= 2.2.0), methods, reshape2, magrittr, BiocStyle
stats, grDevices, utils, ggplot2, dplyr, scater, gridExtra,
BiocStyle, BayesSpace, fgsea, magrittr, SingleCellExperiment,
RColorBrewer, Seurat, S4Vectors, tibble, TOAST, assertthat,
colorspace, shiny, SummarizedExperiment
memoise, GenomicRanges, IRanges, BSgenome, Biostrings,
rtracklayer, parallel, graphics, stats, utils, methods,
Seqinfo, GenomeInfoDb, S4Vectors, tools
stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2,
methods, scales, cluster, grid, grDevices
BiocStyle (>= 2.5.19), derfinder (>= 1.25.3), DEFormats,
DESeq2, Seqinfo, 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,
Seqinfo, BiocParallel, doParallel, parallel, foreach, caret,
kernlab, ranger, BSgenome, AnnotationHub, org.Hs.eg.db, impute,
iterators
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
Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5,
cluster, data.table, Seqinfo, GenomicRanges, glmnet, ggplot2,
gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel,
reshape2, S4Vectors, RhpcBLASctl, survival
Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools,
utils, methods, jsonlite, yaml, basilisk
methods, utils, stats, lsr, FactoMineR, stringr, circlize,
corrplot, ggplot2, ggridges, 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, jsonlite
utils, Seqinfo, data.table, IRanges, GenomicRanges, parallel,
Rsamtools
Biostrings, GenomicRanges, methods, graphics, seqLogo
Seqinfo, GenomicFeatures, GenomicRanges, ggplot2, graphics,
IRanges, methods, regioneR, S4Vectors, stats,
TxDb.Hsapiens.UCSC.hg19.knownGene
graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats,
GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db,
progress, circlize, AnnotationDbi,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer,
S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment,
AnnotationDbi
txdbmaker, SGSeq, GenomicRanges, methods, utils
bslib, BiocGenerics, BiocParallel, Biostrings, ComplexHeatmap,
cowplot, crosstalk, data.table, dplyr, DT, fst, Seqinfo,
GenomicFeatures, GenomicRanges, ggplot2, grid, htmlwidgets,
httr, IRanges, jsonlite, knitr, markdown, NGLVieweR, plotly,
rlang, rclipboard, RCurl, rtracklayer, shiny, shinycssloaders,
shinyhelper, shinyjs, shinyjqui, shinyWidgets, stringr, writexl
Rcpp (>= 1.0.2), graphics, stats, data.table, elitism,
methods, S4Vectors, IRanges, GenomicRanges, matrixStats,
reldist, doParallel, foreach, parallel, qvalue, DESeq2,
ggplot2, BiocFileCache, BiocGenerics, txdbmaker
methods, BiocGenerics, Seqinfo, 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, S4Vectors, baySeq, Seqinfo, seqLogo
AnnotationDbi, BiocGenerics, Biostrings, BSgenome, EDASeq,
GenomicAlignments, GenomicFeatures, Seqinfo, GenomeInfoDb,
IRanges, methods, motifStack, rtracklayer, Rsamtools, RUVSeq,
Rsubread, S4Vectors, XVector, ggplot2, ggfittext, scales,
ggrepel, utils, cluster, stats, graphics, grid, txdbmaker,
ggExtra
car, cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2,
graphics, grDevices, grid, methods, nls2, nnet, rlang,
S4Vectors, scales, stats, stringr, SummarizedExperiment,
tibble, rtracklayer, reshape2, utils
cowplot, doMC, parallel, dplyr, egg, foreach, ggplot2,
ggrepel, graphics, grDevices, grid, methods, nnet, rlang,
S4Vectors, scales, stats, stringr, tibble, rtracklayer, utils,
writexl, DTA, LSD, reshape2, devtools, SummarizedExperiment
methods, httr2, rjsoncons, dplyr, tidyr, rlang, memoise,
cachem, whisker, jsonlite, GenomicRanges, IRanges, Seqinfo
plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools,
utils, RSQLite
graphics, methods, stats, utils, grid, gridExtra, reshape2,
gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL,
linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph,
BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb,
AnnotationFilter, EnsDb.Hsapiens.v86
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, Seqinfo,
S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods,
grDevices
Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
assertthat, Biobase, ChemmineR, data.table, digest, dplyr,
enviPat, glue, httr, httr2, logger, methods, MSnbase, mzR,
purrr, R.utils, rcdk, readJDX, readr, rjson, S4Vectors, tibble,
tidyselect, webchem, XML, yaml
Rcpp (>= 0.12.8), methods, S4Vectors, GenomicRanges,
SummarizedExperiment, devtools, TBX20BamSubset,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, DESeq2,
apeglm, BiocStyle
processx, BiocManager, rtracklayer, stats, tools, methods,
GenomicRanges, stringr
ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats,
SummarizedExperiment, methods
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr,
scales
GenomicRanges, IRanges, BiocGenerics, Seqinfo, bumphunter,
S4Vectors, stats, survival, logistf, plyr, corrplot
methods, stats, grDevices, matrixStats, BiocGenerics,
Biostrings (>= 2.57.2), BiocParallel, txdbmaker,
GenomicFeatures, GenomicAlignments, Seqinfo, 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
Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr,
magrittr, rlang, edgeR, foreach, mice
affy, boot, impute, splines, graphics, qvalue, reshape2
methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges,
SummarizedExperiment, GenomicAlignments (>= 0.99.4),
rtracklayer, GenomeInfoDb
parallel, grDevices, graphics, utils, stats, methods, grid,
RColorBrewer, gplots, ggplot2, limma, Biobase
stats, methods, ROTS, matrixStats, foreach, parallel,
doParallel, doRNG, rngtools, SummarizedExperiment, nlme,
qvalue, grDevices, graphics, utils
httr2, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1)
Biobase, ggplot2, graphics, grDevices, methods, plotly, stats,
MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils
Rcpp, stats, Biobase, methods, BiocParallel, lme4
Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods,
patchwork, reshape2, S4Vectors, shiny, shinycssloaders,
shinyFeedback
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,
umap
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops,
BiocParallel, stats
methods, stats, igraph, stringr, grDevices, Biobase,
S4Vectors, SummarizedExperiment, BiocGenerics
XML, RCurl, assertthat, stringi, rvest, data.table, xml2,
dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis,
knitr, scales, rmarkdown, htmltools
BiocGenerics, data.table, DelayedArray, GenomicRanges,
Seqinfo, httr, methods, RaggedExperiment, RCurl, RJSONIO,
rvest, S4Vectors, stats, stringr, SummarizedExperiment,
TCGAutils, utils
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
XML (>= 1.98-0), BiocGenerics (>= 0.35.3), S4Vectors (>=
0.23.18), IRanges (>= 2.13.13), XVector (>= 0.19.7), Seqinfo,
Biostrings (>= 2.77.2), curl, httr, Rsamtools (>= 1.31.2),
GenomicAlignments (>= 1.15.6), BiocIO, tools, restfulr (>=
0.0.13)
shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db
dplyr, fastDummies, ggplot2, stringr, tibble, Matrix,
ComplexHeatmap, grid, circlize, SingleCellExperiment,
SummarizedExperiment, tidyverse, tidyr, magrittr, S4Vectors
corrplot, MASS, stats, lattice, grDevices, gridExtra,
snowfall, psych, BiocParallel, grid, bladderbatch, reshape2,
graphics
GENLIB, gRain, snpStats, kinship2, methods, stats, utils,
R.utils
httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr,
readr, stringr, purrr, lubridate
methods, stats, utils, Matrix, RcppParallel, CompQuadForm,
survey
Rcpp, BiocGenerics, BiocParallel, MatrixGenerics, methods,
S4Vectors, scuttle, SingleCellExperiment, SummarizedExperiment
tidyverse, utils, reshape2, DescTools, metap, multtest,
plyranges, data.table, scales, RColorBrewer, grid, gtable,
gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges
rJava, Biostrings, IRanges, utils, stats, cluster, binom
ASpli, BiocGenerics, BiocParallel, data.table, DESeq2, dplyr,
edgeR, GenomicAlignments, GenomicFeatures, GenomicRanges,
igraph, IRanges, limma, methods, MASS, MatrixGenerics,
S4Vectors, stats, SummarizedExperiment, parallel, PRROC
locfdr, SummarizedExperiment, BiocParallel, limma, pbapply,
ggplot2, boot, Matrix, stats, methods, graphics
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
magrittr, shiny, shinycssloaders, DT, dplyr, waiter, ggplot2,
tibble, stringr, reshape2, shinyjs, shinyBS, shinycustomloader,
factoextra, markdown, plotly, ggbio, GenomicRanges, rhdf5,
ComplexHeatmap, biomaRt, org.Hs.eg.db, SummarizedExperiment,
SingleCellExperiment, S4Vectors, parallel, httr, jsonlite,
scales, tidyr, txdbmaker, circlize, R.utils, dbscan, igraph,
RANN
Biostrings, pwalign, GenomicRanges, IRanges, data.table,
BiocParallel, methods, Seqinfo, S4Vectors, ggplot2, stats,
stringi, utils, graphics, grid, seqLogo, cowplot
AnnotationDbi, AnnotationFilter, AnnotationHub, BiocParallel,
Biostrings, data.table, digest, DT, ensembldb, fst,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2,
htmlwidgets, IRanges, Matrix, methods, plotly, rintrojs,
rtracklayer, S4Vectors, scanMiRData, shiny, shinycssloaders,
shinydashboard, shinyjqui, stats, utils, txdbmaker, waiter
dplyr, ggplot2, caret, ROCR, pROC, data.tree, methods, stats,
e1071, ape, kernlab, AnnotationHub, utils
S4Vectors, utils, Matrix, SparseArray (>= 1.5.13),
BiocParallel, DelayedMatrixStats, SummarizedExperiment,
SingleCellExperiment, BiocSingular
S4Vectors, utils, stats, BiocGenerics, BiocParallel, gdsfmt,
DelayedArray, BiocSingular, SummarizedExperiment, Matrix
grid, ggplot2, plyr, spatstat.geom, stats, grDevices
SingleCellExperiment, SummarizedExperiment, Seurat, MASS,
zinbwave, stats, copula, ggplot2, DESeq2, utils, grid, methods,
Matrix
reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree,
patchwork, proxy, methods, stats, base, utils, dplyr
SingleCellExperiment, SummarizedExperiment, Matrix, methods,
utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel,
iterators, foreach, Seurat
S4Vectors, limma, ggraph, igraph, methods, cluster,
minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix,
ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo
stats, boot, utils, scales, lifecycle, rlang, tidyselect,
magrittr, crayon, cli, fansi, dplyr, tidyr, purrr, tibble,
ggplot2, ggrepel, patchwork, forcats, readr, stringr, glue,
SingleCellExperiment
ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales,
RColorBrewer, corrplot, stats, grDevices, graphics, utils,
MASS, matrixStats, methods
igraph, Matrix, BiocGenerics, BiocParallel, BiocNeighbors,
BiocSingular, S4Vectors, SummarizedExperiment, scran, scater,
scuttle, bluster, methods, DelayedArray, xgboost, stats, utils,
MASS, IRanges, GenomicRanges, GenomeInfoDb, Rsamtools,
rtracklayer
fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm,
SingleCellExperiment, SummarizedExperiment, grDevices,
graphics, stats, S4Vectors, scran
Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq,
BiocParallel, mclust, SingleCellExperiment, cluster, Oscope,
SummarizedExperiment, stats, methods
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
dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist,
SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm,
parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba,
viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop
SingleCellExperiment, methods, isotree, ggplot2, ggridges,
SummarizedExperiment, ranger, transport, speedglm, cramer,
rlang, bluster, patchwork
aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree,
grDevices, magrittr, purrr, rlang, scales, scater, Seurat,
SingleCellExperiment, stats, stringr, tibble, tidyr
Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment,
xgboost, methods, stats, dplyr, pROC
matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph,
Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils,
methods, survival
DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79,
EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools,
msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom,
tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli,
SingleCellSignalR, MatrixGenerics, Seurat, DT
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,
grid, rlang, concaveman
grDevices, graphics, stats, utils, dplyr, ggplot2, gtools,
HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix,
tidyr, rlang, data.table, BiocParallel
S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix,
SummarizedExperiment, IRanges, methods, stats, BiocParallel,
reshape, ggplot2, igraph, grDevices, ggforce, graphics
SpatialExperiment, SummarizedExperiment, spatstat.geom,
spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly,
shiny, igraph, janitor, knitr, methods, utils, rlang, isoband,
S4Vectors, grDevices
dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr,
ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra,
tibble, scales, rlang, flowCore, methods, basilisk,
basilisk.utils, reticulate, here, pwalign, utils
Biobase, SingleCellExperiment, SummarizedExperiment,
BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy,
utils, googleVis, ggplot2, methods, stats, e1071, randomForest,
Rcpp (>= 0.12.12)
BiocParallel, BiocSingular, BiocNeighbors, cluster,
DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>=
1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran,
methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>=
1.7.3), SummarizedExperiment
methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>=
2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS,
logitnorm, ggplot2, matrixStats, assertthat, viridis, coda,
BiocStyle, cowplot, stats, SummarizedExperiment,
SingleCellExperiment, Matrix, dplyr, S4Vectors
BiocGenerics, bsseq, AnnotationHub, Seqinfo, GenomicRanges,
reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15),
annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb,
Biostrings, DT, HDF5Array (>= 1.7.5)
data.table, Rcpp, magrittr, plyr, stringr, utils, stats,
methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr,
parallel, grDevices
foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats,
phytools, KernelKnn, gplots, zeallot, crayon, assertthat,
igraph, methods, grDevices, graphics, stats, utils, markdown,
SummarizedExperiment, BiocParallel
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,
DelayedMatrixStats, sparseMatrixStats, SparseArray (>= 1.7.6)
tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils,
stats, readr
stats, grDevices, graphics, utils, DescTools, RColorBrewer,
gplots, foreach, parallel, doParallel, DNAcopy, BSgenome,
Biostrings, BiocGenerics, S4Vectors
Biostrings, methods, snpStats, VariantAnnotation,
GenomicRanges, BiocParallel, graphics, SummarizedExperiment
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
cluster, kernlab, origami, RSpectra, coop, Matrix,
DelayedArray, ScaledMatrix, MatrixGenerics
AnnotationDbi, basilisk, BiocGenerics, biomaRt, Biostrings,
data.table, dplyr, DropletUtils, flexmix, GenomicRanges,
GenomicAlignments, GGally, ggplot2, glue (>= 1.3.0), grDevices,
graphics, hash, IRanges, magrittr, MASS, Matrix (>= 1.5.0),
mclust, methods, MultiAssayExperiment, org.Hs.eg.db,
org.Mm.eg.db, purrr, Rcpp (>= 0.11.3), reshape, reticulate,
Rhtslib, rlang, robustbase, Rsamtools, Rsubread, rtracklayer,
SummarizedExperiment, S4Vectors, scales, stats, stringr,
tibble, tidyr, tools, utils, vctrs (>= 0.5.2)
SummarizedExperiment, S4Vectors, BiocGenerics, BiocParallel,
Rcpp, stats, methods, utils, Matrix, edgeR, limma, igraph,
statmod, MatrixGenerics, S4Arrays, DelayedArray, BiocSingular,
bluster, metapod, dqrng, beachmat
methods, Rcpp, beachmat (>= 2.25.1), DelayedArray,
BiocNeighbors (>= 1.99.0), Rigraphlib, parallel
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), BiocParallel (>=
1.12.0)
dplyr, evmix, ggalluvial, ggdendro, ggraph, grDevices, igraph,
immApex, iNEXT, Matrix, quantreg, Rcpp, rjson, rlang,
S4Vectors, SeuratObject, SingleCellExperiment,
SummarizedExperiment, tidygraph, purrr, lifecycle, methods
bibtex, bslib, circlize, ComplexHeatmap, colourpicker,
data.table, DBI, DT, fs, GenomicRanges, GenomeInfoDb, ggdendro,
ggforce, ggplot2, ggrepel, ggridges, grDevices, grid,
gridExtra, htmltools, IRanges, jsonlite, Matrix, magrittr,
methods, patchwork, plotly, RColorBrewer, RefManageR, reshape2,
rhdf5, Rsamtools, RSQLite, rtracklayer, S4Vectors, scales,
scrypt, Seurat, SeuratObject, shiny, shinyhelper, shinymanager,
slingshot, SingleCellExperiment, sortable, stats, tools, xfun,
xml2, utils
data.table, GenomicAlignments, GenomicFeatures, txdbmaker,
GenomicRanges, Rsamtools, ShortRead, parallel, plyr,
BiocGenerics, BiocParallel, S4Vectors, AnnotationDbi,
Biostrings, methods, ggplot2, ggthemes, scales, GenomeInfoDb,
stringdist, ggbio, rtracklayer, SingleCellExperiment,
SummarizedExperiment, Rsubread, parallelly
DelayedArray, glmpca (>= 0.2.0), 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, S4Arrays,
MatrixGenerics, SparseArray, DelayedArray, beachmat
reticulate, BiocFileCache, utils, pheatmap,
SummarizedExperiment, S4Vectors, limma, scater, stats,
MatrixGenerics
S4Vectors, seriation, circlize, methods, randomcoloR, stats,
grid, grDevices, matrixStats
ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges,
S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils,
methods, chromhmmData
Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind
nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods,
stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2
(>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings,
grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1)
BiocParallel, Biostrings, BSgenome, ChIPseeker, cli,
clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2,
ggimage, graphics, grDevices, gridExtra, heatmaps, magick,
methods, RColorBrewer, scales, seqArchR, seqPattern, stats,
utils
methods, parallel, digest, S4Vectors, IRanges, GenomicRanges,
Seqinfo, Biostrings
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
ggplot2, grid, igraph, utils, yulab.utils
Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
cowplot, data.table, eulerr, Seqinfo, GenomicAlignments,
GenomicRanges, ggplotify, grDevices, grid, IRanges, limma,
methods, pbapply, pbmcapply, png, RColorBrewer, Rsamtools,
rtracklayer, S4Vectors, scales, stats, UpSetR
e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges,
methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors,
stats, utils
grDevices, graphics, stats, methods, Biobase, BiocGenerics,
gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW,
logistf, Matrix, data.table,
BiocParallel, ggplot2, Matrix, methods, rearrr, sf,
SpatialExperiment, SummarizedExperiment
graphics, BiocParallel, utils, methods, stringr, readr,
tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges (>= 1.61.1),
IRanges, grid, preprocessCore, S4Vectors, ggplot2,
BiocFileCache, Seqinfo, stats, SummarizedExperiment (>=
1.39.1), dplyr, reshape2
BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR,
openxlsx, pheatmap, stats, circlize, methods, sva
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, data.table
ggplot2, expm, caret, plyr, dplyr, GO.db, annotate,
SummarizedExperiment, genefilter, GOstats, RColorBrewer,
xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools,
org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph
AnnotationDbi, BiocGenerics (>= 0.31.5), Biostrings (>=
2.47.6), GenomicAlignments (>= 1.15.7), GenomicFeatures (>=
1.31.5), GenomeInfoDb, RUnit, S4Vectors (>= 0.23.19), Seqinfo,
grDevices, graphics, igraph, parallel, rtracklayer (>= 1.39.7),
stats
htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest,
rjson
AnnotationHub, BiocGenerics, bsicons, bslib, circlize,
ComplexHeatmap, cowplot, dplyr, DT, edgeR, ExperimentHub,
ggplot2, ggpubr, ggrepel, grDevices, grid, htmltools, limma,
magrittr, pals, readr, S4Vectors, scales, scater, shiny,
shinycssloaders, shinyjs, shinyvalidate, shinyWidgets,
SingleCellExperiment, standR, stats, stringr,
SummarizedExperiment, tibble, tidyr, utils, withr
Biobase, BiocGenerics, graphics, grDevices, htmltools,
MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats,
utils
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
Seqinfo, GenomicRanges (>= 1.31.8), pwalign, hwriter, methods,
lattice, latticeExtra,
beanplot, glmnet, graphics, grDevices, grid, gridBase,
gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC,
RColorBrewer, scales, stats, stringr, utils, infotheo,
progress, corrplot, lmerTest, mlr3learners, mlr3tuning,
paradox, lgr
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, tibble
BiocGenerics, Biostrings, class, grDevices, GenomeInfoDb,
GenomicRanges, IRanges, nloptr, methods, stats, utils,
PMCMRplus, parallel, pvclust, ppclust, clue, survival, maxstat,
future, VGAM, MASS, kknn, glmnet, e1071, randomForest, ada,
future.apply, ggplot2, pROC, pheatmap, RColorBrewer, listenv,
reshape2, scales, survminer, dplyr, ggpubr, cowplot, tibble,
readr, shiny, shinydashboard, shinycssloaders, shinyWidgets,
bsplus, DT, magrittr, tidyr, BiocFileCache, proxy, rtracklayer,
BSgenome, broom
AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV,
cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges,
GSVA, IRanges, magrittr, matrixStats, maxstat, methods,
openair, org.Hs.eg.db, patchwork, RColorBrewer,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats,
scales, SummarizedExperiment, survival, survminer, viridis
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
basilisk, BiocParallel, data.table, dplyr, ggplot2, tools,
Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer,
RCurl, reticulate, sparseMatrixStats, SummarizedExperiment,
tidyr
dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges,
Rsamtools, parallel, graphics, stats, utils, methods
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions,
igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize,
ComplexHeatmap, grDevices, stats, utils, shiny, fastmatch
BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats,
actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors,
methods, scales, scuttle, edgeR, withr
BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors,
grDevices, SummarizedExperiment, methods, cytomapper
simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong,
digest, tm, GO.db, AnnotationDbi, slam, methods, clue,
grDevices, stats, utils, cluster (>= 1.14.2), colorspace,
GlobalOptions (>= 0.1.0)
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
SummarizedExperiment, BiocParallel, DelayedArray, methods,
utils, Matrix, S4Vectors, stats
methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges,
DelayedArray
BiocManager, circlize, limma, igraph, gplots, grDevices,
edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr,
foreach, multtest, scran, utils,
BiocGenerics, Biostrings, BSgenome, cluster, dplyr, Seqinfo,
GenomicRanges, ggpointdensity, ggplot2, ggrepel, grDevices,
IRanges, magrittr, Matrix, methods, miscTools, parallel,
parallelDist, patchwork, plyranges, qs, QuasR, RColorBrewer,
rlang, S4Vectors, stats, stringr, tibble, tidyr, utils, viridis
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>=
2.25.1)
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
Biobase, BiocGenerics, biomaRt, Biostrings, Seqinfo,
GenomicFeatures, GenomicRanges, IRanges, methods, parallel,
Rsamtools, RSQLite, rtracklayer, S4Vectors, tools, txdbmaker,
utils
S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS,
IRanges, GenomicRanges
RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree,
graphics, grDevices, gridExtra, methods, parallel, seqinr,
stats, tidytree, utils
basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods,
reticulate, rlang, scales, stats
minfi, S4Vectors (>= 0.19.1), RColorBrewer
graphics, grDevices, igraph, matrixStats, methods, S4Vectors,
SingleCellExperiment, SummarizedExperiment
magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0)
dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools,
sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils
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
SpatialExperiment, SummarizedExperiment, BiocNeighbors,
Matrix, methods, 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 (>= 1.34.8),
BiocParallel, VariantAnnotation, BiocGenerics, IRanges,
methods, SummarizedExperiment, RColorBrewer, Biostrings,
grDevices, gridExtra, stats, grid, utils, reshape2, scales,
S4Vectors
methods, reshape2, ggplot2, S4Vectors, IRanges, Seqinfo,
GenomicRanges, Biostrings, Rsamtools, GenomicAlignments,
rtracklayer, preprocessCore, chipseq, BiocParallel
Matrix, mgcv, stats, VGAM, IRanges, GenomeInfoDb,
GenomicRanges, rtracklayer, S4Vectors, BiocManager, annotatr,
yaml, utils, bsseq, reshape2, data.table, ggplot2, tidyr,
terra, sf, smoothr, spatstat.explore, spatstat.geom,
SpatialExperiment, SingleCellExperiment, dplyr, ggplot2,
patchwork, SummarizedExperiment, stats, rlang, parallel,
EBImage, spatstat.random, S4Vectors
matrixStats, matrixTests, rstatix, spatstat.explore,
spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix,
qvalue, stats, utils, methods, ggplot2, reshape2
DropletUtils, S4Vectors, SummarizedExperiment, arrow,
data.table, dplyr, e1071, ggplot2, ggpubr, robustbase, scater,
scuttle, sf, sfheaders, tmap, cowplot, glmnet, rhdf5, methods,
rlang, SpatialExperimentIO
ggplot2, Matrix, parallel, quadprog, httr, methods, memoise,
BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie,
SpatialExperiment
Seurat, SingleCellExperiment, SummarizedExperiment, dplyr,
methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg,
magrittr, utils, S4Vectors, DropletUtils, jsonlite, png
edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran,
SeuratObject, SingleCellExperiment, SpatialExperiment, stats,
SummarizedExperiment, S4Vectors, utils
Rcpp, stats, Matrix, SpatialExperiment, SummarizedExperiment,
BiocParallel (>= 1.0)
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
utils, stats, matrixStats, IRanges, XVector
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
methods, glmnet, huge, stats, graphics, utils
nnlasso, nnls, parallel, data.table, Biostrings,
GenomicRanges, IRanges, BSgenome, Seqinfo, ggplot2, gridExtra,
reshape2, RhpcBLASctl
ggplot2, methods, stats, dplyr, spatstat.geom,
spatstat.random, SpatialExperiment, SummarizedExperiment, RANN
reticulate, basilisk (>= 1.9.10), checkmate, stats,
SpatialExperiment, methods, SummarizedExperiment, Matrix,
ggplot2, ggrepel, scales, gridExtra
grDevices, stats, utils, graphics, SeuratObject, Biobase,
GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
rjson, grDevices, magick, utils, S4Vectors,
SummarizedExperiment, BiocGenerics, BiocFileCache
DropletUtils, SpatialExperiment, SingleCellExperiment,
methods, data.table, arrow, purrr, S4Vectors
dplyr, ggplot2, parallel, patchwork, purrr, refund,
SpatialExperiment, spatstat.explore, spatstat.geom,
SummarizedExperiment, tidyr, methods, stats, fda, graphics,
magrittr, ExperimentHub, scales, progress
data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid,
gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices,
graphics, ggplotify, parallel, reshape2, stats,
SummarizedExperiment, SingleCellExperiment, shinydashboard,
S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2
S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML,
scattermore, dplyr, pbapply, data.table, readxl, magick,
grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats,
utils, methods, ggtext, tools, RBioFormats
BiocGenerics, BSgenome, Seqinfo, GenomicFeatures,
GenomicInteractions, GenomicRanges, ggplot2, IRanges,
MatrixGenerics, matrixStats, motifmatchr, S4Vectors, stats,
SummarizedExperiment, TFBSTools, utils
limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods,
stats, grDevices, graphics
ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>=
1.7.5), graphics, grDevices, stats, tools, utils, fs,
BiocGenerics, MetaboCoreUtils
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges, utils
Spectra (>= 1.5.6), MsCoreUtils, methods
apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3),
gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN
(>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>=
1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom,
dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp,
SummarizedExperiment, rlang
GenomicRanges, GenomicFeatures, AnnotationDbi, S4Vectors,
ggplot2, dplyr, tidyr, tibble, GenomeInfoDb, scales, cowplot
BiocParallel, ClassifyR, S4Vectors, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, cli, concaveman,
coxme, data.table, dplyr, ggforce, ggh4x, ggnewscale, ggplot2,
ggthemes, grDevices, lifecycle, lmerTest, magrittr, methods,
pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore,
spatstat.geom, stats, survival, tibble, tidyr
stats, scales, bamlss, methods, tools, IRanges, Biostrings,
GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome,
S4Vectors, graphics, ggplot2, utils
dplyr, tibble, tidyselect, stats, ggplot2, tidyr,
spatstat.univar, S4Vectors, parallel
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon,
edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods,
rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils,
withr
ompBAM, methods, stats, utils, tools, parallel, scales,
magrittr, Rcpp (>= 1.0.5), data.table, fst, ggplot2,
AnnotationHub, RSQLite, BiocFileCache, BiocGenerics,
BiocParallel, Biostrings, BSgenome, DelayedArray,
DelayedMatrixStats, genefilter, GenomeInfoDb, GenomicRanges,
HDF5Array, h5mread, htmltools, IRanges, patchwork, pheatmap,
progress, plotly, R.utils, rhdf5, rtracklayer,
SummarizedExperiment, S4Vectors, shiny, shinyFiles,
shinyWidgets, shinydashboard, stringi, rhandsontable, DT,
grDevices, heatmaply, matrixStats, RColorBrewer, rvest, httr
methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>=
0.17.5), BiocParallel, IRanges (>= 2.21.2), Seqinfo,
GenomicRanges (>= 1.23.21), Rsamtools, graph
plotly, dplyr, scuttle, methods, Biobase, BiocGenerics,
S4Vectors, sparseMatrixStats, SingleCellExperiment,
SummarizedExperiment, Matrix (>= 1.6.4), utils
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse,
caret, dplyr, biomaRt, randomForest, ggridges, cvms,
ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr,
stringr, tidyr
SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix,
methods, SummarizedExperiment, stats, utils, scuttle
stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment,
SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap,
rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang
ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment,
sparseMatrixStats, stats
SpatialExperiment, SummarizedExperiment, BiocNeighbors,
SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco,
grDevices, BiocParallel
stats, methods, SingleCellExperiment, fitdistrplus, graphics,
edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
stats, utils, methods, BiocGenerics, RSQLite, duckdb, DBI
xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble,
ggplot2, shiny, plotly, data.table, caret, stats, graphics,
utils, keys
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils, graphics, doFuture, doRNG, future, foreach
Rcpp (>= 0.12.8), stats, methods, S4Vectors, Seqinfo,
rtracklayer, SummarizedExperiment, IRanges, GenomicRanges,
DESeq2, edgeR, Rsamtools, GenomicFeatures, GenomicAlignments,
grDevices, Gviz, BiocParallel, BiocManager, BiocStyle
dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble,
ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment,
edgeR, methods, ggforce, pheatmap, utils, stringr, gtools,
tidyr
igraph, slam, BiocNeighbors, Matrix, MASS, abind,
SummarizedExperiment, methods, MatrixGenerics, BiocGenerics,
BiocSingular, BiocParallel
dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment,
SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2,
tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics,
grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
BiocParallel, spatstat.geom, concaveman, data.table,
spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble,
stringr, tidyselect, ggplot2, methods, stats,
SummarizedExperiment, S4Vectors, plotly, purrr, ranger,
magrittr, limma, SpatialExperiment, cluster, treekoR, edgeR
graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2,
pheatmap, grDevices, Seurat, SpatialExperiment,
SummarizedExperiment
BiocGenerics, dplyr, Seqinfo, GenomicAlignments,
GenomicRanges, gridExtra, IRanges, grid, methods, reshape2,
rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene,
tidyselect
methods, graph, RBGL, parallel, BiocGenerics
png, sqldf, plyr, igraph, httr, 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
assertthat, Biostrings, pwalign, 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 (>= 0.51.3),
S4Vectors (>= 0.33.7), IRanges (>= 2.23.9), Seqinfo, S4Arrays
(>= 1.1.1), DelayedArray (>= 0.31.12)
dplyr, nloptr, magrittr, methods, tibble, tidyselect,
BEDASSLE, scales, visNetwork, randomcoloR
assertthat, caret, dplyr, tidyr, rsample, methods, rlang,
utils, Biostrings, stats, SummarizedExperiment
httr, BiocFileCache, SPsimSeq, DESeq2, edgeR, openxlsx,
stringr, rhdf5, ggplot2, ggrepel, stats, magrittr, assertr,
tidyr, dplyr, TCGAbiolinks, biomaRt, metaRNASeq, scales, venn,
gridExtra, SummarizedExperiment, knitr, rjson, grDevices,
graphics, curl, utils
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma, edgeR
assertthat, stringr, dplyr, methods, rlang, S4Vectors,
Seqinfo, GenomeInfoDb, GenomicFeatures, pwalign
VariantAnnotation, assertthat, Biostrings, stringr, dplyr,
methods, rlang, S4Vectors, Seqinfo, GenomeInfoDb,
GenomicFeatures, utils
Rcpp, RcppParallel, methods, cli, dplyr, rlang, S4Vectors,
SummarizedExperiment, SingleCellExperiment, SpatialExperiment,
BiocGenerics, BiocParallel, fastmatch, pracma, stats, withr,
Matrix, DelayedMatrixStats, deldir, utils, BiocNeighbors,
ggplot2, ggstar, ggtree, ggfun
SummarizedExperiment, dplyr, ggplot2, methods, stats
methods, Biostrings, S4Vectors, IRanges, utils, stats,
parallel, graphics, grDevices, RSQLite, DBI
data.table, ggplot2, grDevices, magrittr, methods, patchwork,
RankProd, RColorBrewer, stats, utils
seqinr, methods, Biostrings, stringr, BiocGenerics
Rcpp (>= 1.0.8), BiocParallel, GenomicRanges, rlang,
Biostrings, utils, methods, igraph, stats, grDevices,
RColorBrewer, pheatmap, ggplot2, ggnetwork, intergraph
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
BiocGenerics, Seqinfo, Gviz, IRanges, lifecycle,
MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats,
VariantAnnotation
dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2,
tidyr, ggpubr, RColorBrewer, reshape2, cowplot
ape (>= 5.0), phangorn (>= 2.12), 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, miniUI, mzID, mzR, shiny, stats
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
ASSIGN (>= 1.23.1), BiocParallel, ComplexHeatmap, DESeq2, DT,
edgeR, gdata, ggplot2, glmnet, GSVA (>= 1.51.3), HGNChelper,
magrittr, methods, pROC, RColorBrewer, reshape2, ROCit,
S4Vectors, singscore, stats, SummarizedExperiment, tibble
AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb,
GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges,
methods, MultiAssayExperiment, RaggedExperiment, rvest,
S4Vectors, Seqinfo, stats, stringr, SummarizedExperiment,
utils, xml2
edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges,
SummarizedExperiment, GenomicAlignments, Rsamtools, e1071,
cluster, ggplot2, grid, grDevices, stats, utils, methods,
locfit
GenomicRanges, rTensor, readr, methods, MOFAdata, tximport,
tximportData, graphics, stats, utils, shiny
TDbasedUFE, Biobase, GenomicRanges, utils, rTensor, methods,
graphics, RTCGA, stats, enrichplot, DOSE, STRINGdb, enrichR,
hash, shiny
apeglm, biomaRt, dplyr, doParallel, DESeq2, foreach, Seqinfo,
magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats, utils
graphics, grDevices, stats, utils, tools, S4Vectors,
GenomicRanges, IRanges, parallel, pastecs, ggplot2, RCircos,
survival, BSgenome.Hsapiens.UCSC.hg38, seqLogo, Biostrings,
matlab, TCGAbiolinks, methods, R.utils, MultiAssayExperiment,
SummarizedExperiment, sesame, sesameData, AnnotationHub,
ExperimentHub, TENET.ExperimentHub, rtracklayer, MotifDb,
BAMMtools, survminer
methods, ontoProc (>= 0.99.7), SummarizedExperiment,
AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils,
BiocFileCache
S4Vectors, Seqinfo, GenomicRanges, Biobase (>= 2.15.1)
DESeq2, KEGGREST, stats, utils, dplyr, plotly, htmlwidgets,
biomaRt, methods
utils, igraph, methods, graphics, stats, BiocParallel
AnVIL, BiocFileCache, dplyr, GenomicRanges, methods,
RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils,
utils
arules, fields, GenomicRanges, graphics, stringr, methods,
stats, gplots
GenomicRanges, IRanges, biomaRt, GenomicFeatures,
GenomicRanges, grDevices, dplyr, stats, utils, R.utils,
methods, org.Hs.eg.db, org.Mm.eg.db, rlang, ExperimentHub
GenomicRanges, S4Vectors, grDevices, graphics, stats, utils,
IRanges, methods, ORFik
methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase,
rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi,
org.Hs.eg.db, utils, GenomicFiles, SummarizedExperiment
tibble, dplyr (>= 1.1.0), magrittr, tidyr, stringr, rlang,
purrr, tidyselect, stats, parallel, utils, lifecycle, scales,
ggplot2, SummarizedExperiment, GenomicRanges, methods,
S4Vectors, crayon, Matrix
S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, BiocParallel,
BiocIO, rtracklayer, methods, tidyr, ggplot2, dplyr, fansi,
pillar, rlang, scales, cli, purrr, vctrs, stats
Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang,
stats, stringr, tibble, tidyr
tidySummarizedExperiment, tidySingleCellExperiment,
tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang,
stringr, cli, utils
dplyr, tidyr, ttservice (>= 0.4.0), SummarizedExperiment,
tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle,
methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar,
stringr, cli, fansi, Matrix, stats
ttservice, SummarizedExperiment, SingleCellExperiment,
BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig,
tibble, dplyr, tidyr, ggplot2, plotly, rlang, purrr, stringr,
vctrs, tidyselect, pillar, cli, fansi, lifecycle, magick,
tidygate (>= 1.0.13), shiny
dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang,
purrr, lifecycle, methods, utils, S4Vectors, tidyselect,
ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig
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, lmtest, plyr, checkmate
scales, stats, utils, ggplot2, data.table, purrr, dplyr,
VariantAnnotation, GenomicRanges, MatrixGenerics,
bestNormalize, depmixS4, naniar, stringr
gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel,
flexclust, grDevices, graphics, Biobase, SPEM
circlize, ComplexHeatmap, data.table, grDevices, grid,
GSEABase, Matrix, methods, stats, utils
methods, stats, utils, grDevices, htmlwidgets, jsonlite,
data.table, Biobase, GenomeInfoDb, IRanges, S4Vectors, knitr
stats, methods, SummarizedExperiment, corpcor, doParallel,
parallel, ggplot2, tidyr, GGally
methods, stats, grDevices, reshape2, Rtsne, umap,
RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
grDevices, graphics, animation, tibble, dplyr, stringr, purrr,
methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2
assertthat, caret, ClassifyR, directPA, doParallel, dplyr,
ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc,
igraph, latex2exp, limma, magrittr, methods, plotly, pROC,
purrr, reshape2, stats, stringr, survival, tibble, tidygraph,
tidyr, statmod
methods, utils, stats, assertthat, ggplot2, scales, grid,
grDevices
grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2),
MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 2.2.1),
mzR (>= 2.27.5)
SummarizedExperiment, BiocGenerics, 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
stats, BiocParallel, MatrixGenerics, methods,
SingleCellExperiment, SummarizedExperiment, SpatialExperiment
IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base,
stringr, RColorBrewer, methods
Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures,
Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales,
tools, IRanges, AnnotationDbi, grImport, htmlwidgets,
InteractionSet, utils, rhdf5, strawr, txdbmaker
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, Rcpp
BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>=
0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0),
grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>=
1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8),
stringr (>= 1.5.1), utils
BSgenome, data.table, Seqinfo, GenomicFeatures, ggplot2 (>=
3.5.0), IRanges, jsonlite, matrixStats, methods, parallel,
rlang, scales, stats, S4Vectors, SummarizedExperiment,
VariantAnnotation
RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
BiocGenerics, S4Vectors (>= 0.9.25), IRanges, gplots
ggplot2, viridis, mgcv, SingleCellExperiment, slingshot,
princurve, Biobase, methods, RColorBrewer,
SummarizedExperiment, grDevices, graphics, rgl
TreeSummarizedExperiment (>= 1.99.0), edgeR, methods,
SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr,
ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree,
stats, utils, rlang
ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble,
tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)
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
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, ggnewscale, AnnotationDbi, scater,
GenomicRanges, IRanges, S4Vectors, scattermore, dplyr,
RColorBrewer, grDevices, stats, SummarizedExperiment, utils
graphics, utils, stats, dplyr, ggplot2, patchwork, stringr,
tidyr, roll
grDevices, graphics, methods, stats, survival, utils,
siggenes, LogicReg (>= 1.6.1), data.table
shinyjs, shinyFiles, plyr, data.table, DT, stringr,
stringdist, plot3D, gridExtra, RColorBrewer, plotly, dplyr,
config (>= 0.3.1), golem (>= 0.3.1), methods, grDevices,
graphics, stats, utils, vegan
stringr, S4Vectors, methods, BiocGenerics, IRanges, XVector,
Biostrings, Modstrings, ggplot2, scales
Biostrings, stringr, httr2, xml2, S4Vectors, methods, IRanges,
utils
methods, stringr, BiocGenerics, Biostrings, Structstrings,
S4Vectors, IRanges, XVector, Seqinfo, rtracklayer, BSgenome,
Rsamtools
bnlearn, Rgraphviz, gtools, parallel, foreach, doParallel,
iterators, RColorBrewer, circlize, 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,
SparseArray (>= 1.5.23), DelayedArray (>= 0.31.9), S4Vectors
tm, text2vec, tokenizers, textstem, stopwords, data.table,
purrr, DiagrammeR, stats
AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel,
Biostrings, ensembldb, Seqinfo, GenomicRanges, GGally, ggplot2,
Gviz, limma, IRanges (>= 2.21.6), reshape2, Rsamtools,
S4Vectors (>= 0.25.14), SummarizedExperiment, VariantAnnotation
(>= 1.19.9)
Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn,
grDevices, graphics, stats, utils
Biobase, graphics, grDevices, splines, stats
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
AnnotationDbi, GenomicFeatures, txdbmaker, IRanges,
GenomicRanges, BiocGenerics, Biostrings, S4Vectors,
rtracklayer, BiocParallel, stats, methods, utils
methods, utils, stats, tools, httr, rjson, DBI, RSQLite (>=
2.0), IRanges, UCSC.utils, GenomeInfoDb, AnnotationDbi,
Biobase, BiocIO, rtracklayer, biomaRt (>= 2.59.1)
SummarizedExperiment (>= 1.39.1), tximport, jsonlite,
S4Vectors, IRanges, GenomicRanges (>= 1.61.1), AnnotationDbi,
GenomicFeatures, txdbmaker, ensembldb, BiocFileCache,
AnnotationHub, Biostrings, tibble, Seqinfo, tools, utils,
methods, Matrix
methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel,
BiocNeighbors, SingleCellExperiment, SummarizedExperiment
methods, stats, httr, jsonlite, S4Vectors
AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings,
BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures,
GenomeInfoDb, GenomeInfoDbData, GenomicAlignments,
GenomicRanges, ggplot2, ggrepel, gsubfn, moments,
Organism.dplyr, plotgardener,R.utils, S4Vectors, shiny,
shinydashboard, shinyFiles, shinyjs, yaml
magick, cowplot, scales, GenomicRanges, ShortRead, zoo,
ggplot2, reshape2, regioneR, IRanges, S4Vectors, dplyr,
BSgenome, Biostrings, DESeq2, R.utils, Rsamtools, stringr,
Rbowtie2, methods, GenomeInfoDb, GenomicAlignments,
RColorBrewer, utils, grDevices, stats, org.Hs.eg.db, annotate,
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,S4Vectors,
EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v86, OrganismDbi, processx,
Rsamtools, GenomicRanges
AnnotationDbi, BiocFileCache, BiocBaseUtils, BiocGenerics,
httr2, jsonlite, methods, progress, rjsoncons, rlang, utils
stringr, R.utils, WriteXLS, stats, doParallel, foreach,
GenomicRanges, IRanges, VariantAnnotation, data.table,
GenomeInfoDb
methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp,
Biostrings, BiocGenerics, S4Vectors, rlang, grid,
MatrixGenerics
HMM, utils, VariantAnnotation, GenomicRanges, S4Vectors,
IRanges, stats
igraph, Matrix, RANN, RSpectra, VGAM, gplots, parallel, plyr,
methods, cluster, Biobase, fpc, BiocGenerics, monocle,
grDevices, graphics, stats, utils
SingleCellExperiment, SummarizedExperiment, tensorflow,
scater, 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 (>= 1.4.0),
iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2,
gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack,
rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods,
utils, stats
utils, DBI, Biobase, S4Vectors (>= 0.27.12), IRanges (>=
2.23.9), XVector (>= 0.29.2), Biostrings (>= 2.77.2),
AnnotationDbi (>= 1.27.9), rtracklayer (>= 1.69.1), BSgenome
(>= 1.77.1), GenomicFeatures (>= 1.61.4)
utils, stats, Biobase, S4Vectors (>= 0.9.25), IRanges (>=
2.3.23), RBGL, graph, AnnotationDbi, BiocParallel, Seqinfo (>=
0.99.2), GenomeInfoDb (>= 1.45.7), Biostrings (>= 2.77.2),
GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1),
GenomicFeatures (>= 1.61.4), Rsamtools (>= 2.25.1), BSgenome
(>= 1.77.1), GenomicScores (>= 2.21.4), Gviz (>= 1.53.1),
shiny, shinythemes, shinyjs, DT, shinyTree
IRanges, GenomicRanges, S4Vectors, parallel, matrixStats,
GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats,
graphics, methods
tools, GenomicRanges, VariantAnnotation (>= 1.29.3),
GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools
BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix,
methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
stats, SummarizedExperiment, utils
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
dplyr, DT, methods, ggplot2, grDevices, magrittr, patchwork,
plotly, purrr, rlang, shiny, stats, tibble, tidyr, htmlwidgets,
utils
utils, data.tree, ape, parallel, Rfast, stats
Biobase, DESeq2, edgeR, GGally, ggplot2, ggrepel, knitr,
RColorBrewer, rmarkdown, scales, stats, SummarizedExperiment,
tidyr, utils
mixtools, stats, parallel, e1071, KernSmooth
data.table, AnnotationDbi, dendextend, dynamicTreeCut,
GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT,
DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea,
ggplot2, htmlwidgets, igraph, methods, plotly, scales,
ComplexHeatmap, circlize
BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite,
methods, S4Vectors, SingleCellExperiment, SpatialExperiment,
SummarizedExperiment
BiocBaseUtils, BiocGenerics, dplyr, DropletUtils, grDevices,
imager, Matrix, methods, pkgcond, readr, rjson, S4Vectors,
SingleCellExperiment, spatialLIBD (>= 1.17.8), stringr,
SummarizedExperiment, tibble, tidyr, xml2
igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm,
ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb,
ggrepel, textstem, tidygraph, stats, scales, ggraph
bumphunter, dplyr, BiocParallel, DelayedArray, GenomicRanges,
ggplot2, methods, tidyr, locfit, gamlss.dist, recommenderlab,
HDF5Array, data.table, SummarizedExperiment, IRanges,
S4Vectors, devtools
BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>=
3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics,
memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales,
scico, sf, SingleCellExperiment, SpatialExperiment, spdep,
stats, SummarizedExperiment, terra, utils, zeallot
cowplot, magrittr, Seqinfo, GenomeInfoDb, GenomicAlignments,
RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2,
methods, graphics, stats
matrixStats, limma, parallel, shiny, qvalue, grDevices, stats,
MultiAssayExperiment, clusterProfiler, DOSE, httr, graphics
wordcloud, csaw, gplots, stats, utils, caTools, graphics,
DESeq2, Biobase
methods, BiocGenerics, S4Vectors (>= 0.17.25), IRanges (>=
2.13.12), Biostrings (>= 2.47.6), foreach, GenomicFeatures (>=
1.31.3), ggplot2, Hmisc, mclust, rtracklayer (>= 1.39.7),
seqinr, stringr
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
limma, randomForest, kernelshap, caret, lime, DT, methods,
SummarizedExperiment, ggplot2
SummarizedExperiment, SingleCellExperiment, Rfast, singscore,
AnnotationHub, ontologyIndex, tibble, dplyr, BiocParallel,
Matrix, minpack.lm, pracma, methods, readr, magrittr, progress,
quadprog
MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase,
BiocGenerics, ProtGenerics (>= 1.37.1), lattice,
MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges,
SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures,
MsExperiment (>= 1.5.4), Spectra (>= 1.16.1), progress,
RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table
BiocGenerics, genefilter, graphics, grDevices, gtools,
methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta,
siggenes
BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods,
S4Vectors, SingleCellExperiment, SpatialExperiment,
SummarizedExperiment, VisiumIO
SpatialExperiment, BiocFileCache, Matrix, S4Vectors,
SummarizedExperiment, methods, utils, EBImage, shiny,
HDF5Array, arrow, ggplot2, SingleCellExperiment, TENxIO, dplyr,
graphics, stats
methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
methods, utils, tools, BiocGenerics, S4Vectors, IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
limSolve, SomaticSignatures, VariantAnnotation, Seqinfo,
reshape2, gridExtra, corrplot, dendextend, GetoptLong,
circlize, gtrellis, doParallel, parallel, 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
basilisk, cli, DelayedArray, Matrix, methods, reticulate,
S4Vectors, SingleCellExperiment (>= 1.11.6), SparseArray,
SummarizedExperiment, utils
variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0),
GSEABase (>= 1.54.0), msigdbr, Rfast, ggplot2, tidyr, dplyr,
reshape2, progress, utils, Rdpack, stats
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
phyloseq, pscl, ggplot2, MatrixGenerics, SummarizedExperiment,
stats, VGAM, matrixStats, tidyr, tibble, dplyr, DESeq2,
reshape2, RColorBrewer, magrittr, BiocGenerics, graphics, utils
GenomicAlignments, GenomicRanges, Rsamtools, IRanges,
VariantAnnotation, DelayedArray, dplyr, stringr, purrr, tibble,
methods, knitr, igraph, readr, stats, magrittr, rlang
cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
flowWorkspace
Rcpp, beachmat, assorthead, Rhdf5lib, BH, dqrng, scuttle
cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings
Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Rcpp, assorthead (>= 1.3.10), beachmat, BiocNeighbors
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
Rcpp, beachmat, assorthead (>= 1.3.5), BiocNeighbors
Rcpp, RcppArmadillo (>= 14.0), RcppParallel, RcppEigen,
dqrng
S4Vectors, IRanges, XVector, Biostrings, Rhtslib (>= 2.99.0)
MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db
knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr,
LoomExperiment
R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf
affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl,
rmarkdown
BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics,
DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext,
RColorBrewer, pheatmap, viridis
BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown,
methods, CompoundDb (>= 1.1.4)
knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0),
gplots, tidyr
BiocStyle, rmarkdown, knitr, testthat, digest, Matrix,
alabaster.matrix
BiocStyle, rmarkdown, knitr, testthat, jsonlite
BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation,
rtracklayer, Biostrings
testthat, knitr, SummarizedExperiment, BiocParallel,
BiocStyle, rmarkdown
testthat, knitr, BiocStyle, chihaya, BiocSingular,
ResidualMatrix
testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick,
png, digest
testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern,
ggplot2, cowplot, tidyverse, magick
knitr, BiocStyle, testthat (>= 3.0.0), BiocManager
testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown
BiocManager, BiocGenerics, S4Vectors, Seqinfo, GenomeInfoDb,
GenomicRanges, AnnotationHub, ExperimentHub, ensembldb, httr,
tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, gghalves,
colorspace, knitr, rmarkdown, testthat (>= 3.0.0)
ASICS, BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5),
GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr,
NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment,
S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>=
2.0.4)
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment,
SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr,
magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr,
tidyverse
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
BiocStyle, biomformat, devtools, glmnet, 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, BiocStyle, knitr
utils, 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,
rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit
IRanges, Seqinfo, GenomeInfoDb, GenomicRanges,
VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr,
AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR,
Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment,
ExperimentHub, gdsfmt, rmarkdown, HubPub
RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData,
rmarkdown, HubPub
GenomeInfoDb, BiocStyle, devtools, knitr, org.Dm.eg.db,
org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
rmarkdown, roxygen2, testthat,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Ggallus.UCSC.galGal5.refGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Rnorvegicus.UCSC.rn5.refGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene
knitr, rmarkdown, testthat, withr, readr, BiocStyle,
devtools, AnVILAz, AnVILGCP, lifecycle
BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest
AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown,
testthat (>= 3.0.0), tinytest
AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr
knitr, BiocStyle, GCPtools, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, org.Mm.eg.db, AnnotationDbi,
TBX20BamSubset, testthat, pasillaBamSubset
DESeq2, airway, knitr, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran,
sparseMatrixStats, 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
AssessORFData, BiocStyle, knitr, rmarkdown, RSQLite (>= 1.1)
testthat, BiocStyle, lintr, knitr, rmarkdown
ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi,
BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat
(>= 3.0.0)
BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19,
MotifDb, trackViewer, testthat, rmarkdown
BSgenome.Drerio.UCSC.danRer10, knitr, testthat, ATACseqQC,
rmarkdown, BiocStyle
covr, BiocStyle, knitr, rmarkdown, RUnit,
TxDb.Dmelanogaster.UCSC.dm6.ensGene, RColorBrewer
Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne,
testthat, zoo
affy, AnnotationDbi, AnnotationHub, apcluster, Biobase,
BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071,
ensembldb, GenomicDataCommons, GenomicRanges, GEOquery,
ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite,
knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme,
OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork,
pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite,
remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer,
statmod, testthat, UniProt.ws, writexl, XML
AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown,
testthat (>= 3.0.0)
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, purrr, apeglm, utils, DEXSeq
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
testthat, interp, fields, pheatmap, viridis, rmarkdown,
spelling
knitr, rmarkdown, pals, scuttle, scater, scran, cowplot,
ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub,
spatialLIBD, BiocStyle
knitr, rmarkdown, methods, testthat, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
BiocStyle, knitr, magick, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick
knitr, rmarkdown, BiocStyle, testthat, callr
testthat, BiocStyle, knitr, rmarkdown, scran, scater,
bluster, scRNAseq
BiocManager, BiocStyle, bladderbatch, devtools, knitr, lintr,
plotly, rmarkdown, spelling, testthat (>= 3.0.0)
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD
testthat, knitr, rmarkdown, igraph, spatialLIBD, viridis,
patchwork, RColorBrewer, Seurat
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel, HDF5Array, beachmat.hdf5
testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
testthat, BiocStyle, knitr, rmarkdown, Matrix
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
testthat, BiocStyle, knitr, rmarkdown, pander, seewave
BiocStyle, knitr, liftOver, testthat (>= 3.0.0)
testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr,
rmarkdown, dplyr, ggplot2, spelling
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>=
3.0.0)
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, GenomicAlignments,
scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify,
SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr,
txdbmaker, ggrepel, stringr
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
limma, DESeq2, airway, ggplot2, plyr, GenomicRanges,
testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase,
rmarkdown, SummarizedExperiment
BiocFileCache, BiocStyle, GenomicFeatures, knitr, httr2,
rmarkdown, rvest, tinytest, txdbmaker,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0)
BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown
BiocStyle, devtools, gert, jsonlite, rmarkdown, tinytest,
usethis
knitr, testthat, rjsoncons, igraph, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, S4Arrays, SparseArray,
DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools,
AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase,
annotate, MultiAssayExperiment, RUnit
BiocManager, BiocStyle, curl, glue, knitr, rmarkdown,
sessioninfo, shinytest2
BiocParallel, testthat, BiocStyle, knitr, rmarkdown
airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1),
GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db,
rmarkdown, spelling, testthat (>= 3.0.0), WGCNA
BiocGenerics, tools, foreach, BBmisc, doParallel,
GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,
knitr, batchtools, data.table
BiocStyle, knitr, rmarkdown, testthat, tm, networkD3,
visNetwork, clipr, blastula, kableExtra, DiagrammeR,
SummarizedExperiment
BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0)
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
testthat, HDF5Array, BiocStyle, rmarkdown, knitr
BiocStyle, covr, devtools, knitr, pkgdown, RefManageR,
rmarkdown, sessioninfo, testthat, utils
BiocGenerics, BiocPkgTools, knitr, commonmark, BiocStyle
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, xml2
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, lgr
roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr,
rmarkdown, covr, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr, covr
BiocStyle, httptest2, knitr, mockery, rmarkdown, testthat (>=
3.0.0)
cluster, parallel, GenomicFeatures, dynamicTreeCut,
Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, BiocStyle, magick, rmarkdown, igraphdata, testthat (>=
3.0.0), vdiffr, devtools, pander, plotly, randomcoloR
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle, DESeq2,
networkD3, covr
rgl, impute, DLBCL, genefilter, xtable, ALL, limma,
hgu95av2.db, XML
testthat, knitr, rmarkdown, lattice, latticeExtra,
rbenchmark, gplots, gridExtra, org.Hs.eg.db, hgu133plus2.db,
ggplot2, reshape2, plyr, ineq, covr, limma, RColorBrewer
graphics, pwalign, 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, BiocStyle, knitr,
testthat (>= 3.0.0), covr
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,
BiocStyle
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, DirichletMultinomial, vegan, fastcluster
BiocStyle, knitr, rmarkdown, RUnit,
BSgenome.Hsapiens.UCSC.hg19
knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0),
utils, testthat
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr,
tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
shiny (>= 1.9.1), bslib (>= 0.8.0), BiocStyle, knitr,
rmarkdown, testthat
testthat, BiocStyle, knitr, rmarkdown, devtools
testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle,
rtracklayer
knitr, limma (>= 3.54.0), rmarkdown, stats (>= 4.2.2), samr
BiocManager, GenomeInfoDb, 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,
BSgenomeForge
GenomicFeatures, Rsamtools, testthat, knitr, rmarkdown,
BiocStyle, devtools, BSgenome.Celegans.UCSC.ce2
testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix,
doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38,
batchtools
BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>=
3.0.0)
knitr, markdown, rmarkdown, STexampleData, testthat (>=
3.0.0), codetools, Matrix, lattice, cluster, survival, MASS,
nlme
testthat, RUnit, doParallel, GenomeInfoDb, txdbmaker,
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat
(>= 3.1.6)
knitr, rmarkdown, BiocStyle, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm9.knownGene
testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle,
rmarkdown, covr, sessioninfo
BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,
DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown
testthat (>= 3.1), knitr, rmarkdown, BiocStyle
BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat,
VGAM
RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0),
sessioninfo
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
fossil, interp, knitr, BiocStyle, tictoc
BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown,
testthat
knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown,
withr, BiocStyle, testthat (>= 3.0.0)
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
testthat (>= 3.0.0), rmarkdown, markdown, knitr, tidyverse,
DescTools, cowplot, BiocStyle, GenomicRanges,
SummarizedExperiment, S4Vectors, IRanges
knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater,
mclust, testthat (>= 3.0.0), splatter
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
knitr, BiocStyle, BiocGenerics, testthat, RUnit
knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle
testthat, knitr, roxygen2, rmarkdown, biomaRt, covr,
BiocManager, BiocStyle, TENxPBMCData, singleCellTK,
M3DExampleData
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, knitr, RUnit, BiocGenerics,
AnnotationDbi, destiny, RUnit, scater, scran, knitr,
org.Mm.eg.db, rmarkdown
zellkonverter, SingleCellExperiment, HDF5Array, tidyr,
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery
BiocStyle, knitr, rmarkdown, testthat, ggplot2
knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater,
scMerge, fgsea, escape, pheatmap
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
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL,
BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineDrugs,
png,rmarkdown, BiocManager,bibtex,codetools
knitr, rmarkdown, Matrix, testthat, vdiffr
BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0)
BiocStyle, knitr, RefManageR, rmarkdown, testthat (>= 3.0.0),
EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86
argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat,
GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges,
IRanges, AnnotationHub
BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix,
BiocStyle, testthat, rmarkdown, knitr
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, EnsDb.Hsapiens.v86,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR,
knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack,
OrganismDbi, BiocFileCache
clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram,
knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat
BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene,
BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
testthat, knitr, markdown, rmarkdown, BiocStyle, Signac,
future, igraph, bluster, httr
JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat,
knitr, rmarkdown, pheatmap, motifmatchr
AnnotationDbi (>= 1.38.2), knitr, markdown, 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, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot,
BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales,
e1071, rmarkdown, IRanges, robustbase, glmnet, class,
randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale,
TOP, BiocNeighbors
BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0)
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86,
ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>=
3.0.0)
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown,
BRAIN, UniProt.ws (>= 2.36.5)
RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS,
BiocStyle
knitr, rmarkdown, bookdown, testthat, BiocStyle,
BSgenome.Mmusculus.UCSC.mm10
BiocParallel, knitr, rmarkdown, testthat, CAMERA
RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2
BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph,
rmarkdown
knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, knitr, jsonlite, readr, rmarkdown,
org.Hs.eg.db, prettydoc, BiocManager, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel,
BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr,
data.table, R.utils
BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork
knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2,
patchwork, dplyr, scattermore
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
minet, Rgraphviz, RUnit, BiocGenerics, igraph
knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked, rmarkdown
AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked,
BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment,
TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData,
ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown,
statmod
knitr, parallel, testthat, BiocStyle, rmarkdown,
AnnotationHub, LOLA
testthat, knitr, rmarkdown, BiocStyle, SeuratObject,
BiocFileCache, xml2
testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle,
rmarkdown, covr
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, randomForest, e1071
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod
BiocStyle, corrplot, knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2, progress
BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq,
TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree,
tidytree, statmod, covr, sva, tcltk
BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr,
rtracklayer
testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,
fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,
grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),
gridGraphics, gplots, rmarkdown, Cairo, magick
knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19),
MsBackendMgf
BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans,
patchwork, rmarkdown, scater, SFEData,
SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0)
knitr, testthat, rmarkdown, covr, viridis, ggplot2,
RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats
BiocStyle, ggplot2, knitr, rmarkdown, magick
BiocStyle, ggplot2, knitr, rmarkdown, RUnit
knitr, BiocStyle, rmarkdown, testthat, Seurat
BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra,
magick, Cairo, limma
BiocStyle, knitr, rmarkdown, minfiData, RCurl
BiocStyle, knitr, rmarkdown, panelcn.mops,
BSgenome.Hsapiens.UCSC.hg19.masked, DNAcopy, testthat
knitr, rmarkdown, bluster, ComplexHeatmap, circlize, scater,
viridis, scRNAseq, SingleR, MouseGastrulationData, testthat (>=
3.0.0), BiocStyle, scrapper
pander, markdown, BiocStyle, rmarkdown, knitr, formatR,
testthat
ade4, BiocStyle, CellBench, DuoClustering2018, knitr,
rmarkdown, scater, testthat
Biobase, knitr, rmarkdown, testthat, BiocStyle
testthat, knitr, rmarkdown, piano, ggplot2
testthat (>= 3.2.0), proto, spelling, knitr, data.table,
gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS,
Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch,
SummarizedExperiment, S4Vectors
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat
(>= 3.0.0), knitr, rmarkdown
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
testthat
biomaRt, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, BiocStyle, crisprBwa (>= 0.99.7),
knitr, rmarkdown, Rbowtie, Rbwa, RCurl, testthat
RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Mmusculus.UCSC.mm10.knownGene, org.Mm.eg.db, lattice,
MASS, tensorflow, BSgenome.Hsapiens.UCSC.hg38, BiocFileCache,
TxDb.Hsapiens.UCSC.hg38.knownGene, testthat, knitr
BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>=
3.0.0), BSgenome.Hsapiens.UCSC.hg38
BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl,
rtracklayer, sangerseqR, testthat, VariantAnnotation
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr,
rmarkdown, rtracklayer, testthat, utils
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat,
ExperimentHub, scater, HMP, reshape2, glue, tidyverse,
BiocGenerics, compositions
GenomeInfoDb, testthat, BiocStyle, knitr, rmarkdown
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, knitr, patchwork, rmarkdown, scRNAseq, scuttle,
stringr, testthat (>= 3.0.0)
testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown,
SummarizedExperiment, SingleCellExperiment
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0),
InteractiveComplexHeatmap
testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges,
rjson
zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow,
reticulate, spelling, forcats, ggplot2,
tidySingleCellExperiment, rprojroot
magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet,
BiocStyle, flowStats
knitr, rmarkdown, MatrixGenerics, htmltools, RUnit,
BiocGenerics, BiocManager, BiocStyle, Biobase
gridExtra, knitr, RColorBrewer, testthat, uwot
BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat,
shinytest
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, HDCytoData
testthat, flowWorkspaceData , knitr, rmarkdown, parallel
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, reshape2, dplyr, CytoPipelineGUI
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, patchwork
BiocStyle, knitr, rmarkdown, markdown, testthat
XML, grImport, grImport2, BiocStyle, knitr, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
BSgenome.Hsapiens.UCSC.hg19
BiocStyle, biomaRt, biovizBase,
BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db,
rmarkdown, testthat (>= 3.0.0),
TxDb.Dmelanogaster.UCSC.dm6.ensGene
BiocStyle, fields, knitr, rmarkdown, RColorBrewer, scater,
scRepertoire, DelayedMatrixStats, slingshot, testthat
testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph,
diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR,
factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster,
forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr,
norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr,
limma, preprocessCore, stringr, tidyr, impute, gplots,
grDevices, reshape2, graphics, stats, methods, ggplot2,
RColorBrewer, Matrix, org.Sc.sgd.db
ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr,
DESeq2, devtools, furrr, future, knitr, lefser, limma,
Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2,
roxyglobals, roxytest, rstatix, SummarizedExperiment,
TreeSummarizedExperiment, testthat (>= 3.0.0)
EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa,
SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle,
edgeR
testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse,
rmarkdown, BiocStyle
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
BiocStyle, dplyr, knitr, rmarkdown, scran,
SingleCellMultiModal, TENxPBMCData, testthat (>= 3.0.0)
Biobase, BiocStyle, covr, HDF5Array, knitr, RColorBrewer,
RefManageR, rmarkdown, sessioninfo, testthat (>= 3.0.0), tidyr,
tidyverse
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
macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db,
topGO, clusterProfiler, DEFormats, testthat (>= 3.0.0)
BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat
BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick,
knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat
(>= 3.0.0)
BiocStyle, AnnotationDbi, limma, pheatmap, rmarkdown,
statmod, testthat
BiocParallel, HDF5Array (>= 1.17.12), genefilter,
SummarizedExperiment, airway, lobstr, DelayedMatrixStats,
knitr, rmarkdown, BiocStyle, RUnit
testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray
testthat, knitr, rmarkdown, BiocStyle, microbenchmark,
profmem, HDF5Array, matrixStats (>= 1.0.0)
testthat, knitr, BiocStyle, rmarkdown, Matrix
markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr,
dplyr, reticulate
biomaRt, knitr, rmarkdown, stringr, BiocStyle
BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown,
testthat (>= 3.0.0)
knitr, rmarkdown, ComplexHeatmap, viridisLite, ggpubr,
dittoSeq, EnsDb.Hsapiens.v86, BiocStyle, RefManageR, testthat
(>= 3.0.0), Seurat
knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat
uwot, testthat, knitr, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble,
ggplot2, missForest, pheatmap, RColorBrewer, ggrepel,
BiocStyle, ggbeeswarm
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, glmGamPoi, BiocManager
knitr, rmarkdown, testthat, BiocStyle, muSpaData,
ExperimentHub, spatialLIBD, purrr, reshape2, tidyverse,
concaveman
knitr, rmarkdown, igraph, testthat, FNN, tidyverse,
gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq,
org.Mm.eg.db, scran, repr
knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW
GenomeInfoDb, GenomicFeatures, txdbmaker, pasilla (>=
0.2.22), BiocStyle, knitr, rmarkdown, testthat,
pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi
BiocStyle, GenomeInfoDb, GenomicRanges, IRanges, knitr,
rmarkdown, sessioninfo, testthat (>= 3.0.0), tibble
BiocStyle, testthat, xtable, rgl, XLConnect, edgeR, csaw,
BSgenome, GenomeInfoDb, profileplyr, rtracklayer, grid
BiocStyle, knitr, rmarkdown, testthat, HDCytoData, CATALYST
testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata,
BiocStyle, reshape2, utils
testthat (>= 2.1.0), knitr, rmarkdown, BiocStyle, devtools,
ggplot2, gridExtra, ggpubr, grid, magick, hexbin
lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown,
BiocStyle
knitr, rmarkdown, testthat, UpSetR, BiocStyle
plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR,
ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq,
ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran
knitr, RUnit, BiocGenerics, GenomeInfoDb,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICv2anno.20a1.hg38,
FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest
knitr, rmarkdown, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
knitr, rmarkdown, BiocGenerics, RUnit, tinytest, BiocStyle,
Biostrings
knitr, rmarkdown, testthat, sessioninfo, BiocStyle
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap,
rmarkdown, testthat (>= 3.0.0), withr, airway
knitr, patchwork, rmarkdown, Seurat, testthat, formatR,
BiocFileCache, SingleCellExperiment
BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat
prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise,
org.Hs.eg.db, rmarkdown, testthat
txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork,
BiocStyle, rmarkdown, covr, sessioninfo
covr, testthat, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub,
RUnit, muscData, scater, scuttle
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
testthat, knitr, BiocStyle, rmarkdown, jsonlite,
DropletTestFiles
RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT,
EnsDb.Hsapiens.v86
BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0)
knitr, UpSetR, BiocStyle, rmarkdown, testthat (>= 3.0.0)
limma, convert, GEOquery, dyebiasexamples, methods
knitr, rmarkdown, BiocStyle, testthat, SummarizedExperiment,
viper
knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager,
devtools, BiocStyle
testthat (>= 3.0.0), IRanges, knitr, BiocStyle, rmarkdown
distill, BiocStyle, knitr, readxl, edgeR, limma, EDASeq,
statmod
BiocStyle (>= 2.32.1), BSgenome (>= 1.72.0),
BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr,
rmarkdown, RUnit (>= 0.4.33)
BiocStyle, digest, knitr, rmarkdown, shiny
ecoliLeucine, ecolicdf, graph, multtest, affy
BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR,
KernSmooth, testthat, DESeq2, rmarkdown
arrow, jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject,
splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db,
SummarizedExperiment
knitr, tximportData, testthat (>= 3.0.0)
knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie,
Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38,
ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker,
rtracklayer, withr
BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat,
data.table, DT, GenomicInteractions, webshot, R.utils, covr,
sesameData
Rsamtools, BiocManager, knitr, testthat (>= 3.0.0)
ggalt, ggrastr, 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, limma, rmarkdown
minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, org.Hs.eg.db, testthat (>= 3.0.0),
BiocStyle
testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter,
RColorBrewer
ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools,
airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr,
rmarkdown, statmod
clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue,
knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr,
ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges,
grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr
BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick
BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat,
BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>=
1.20.0), rmarkdown, AnnotationHub
GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit,
knitr, rmarkdown, ggplot2
rworkflows, BiocFileCache, BiocParallel, BiocStyle,
clusterProfiler, GenomicAlignments, grDevices, knitr,
org.Hs.eg.db, testthat (>= 3.0.0), tidyr,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm9, BSgenome.Mmusculus.UCSC.mm10,
ComplexUpset, plyranges, scales, Matrix, consensusSeekeR,
heatmaply, viridis
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
GenomeInfoDb, testthat, knitr, rmarkdown, BiocStyle,
BSgenome.Rnorvegicus.UCSC.rn4, gcapc, chromstaRData
BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr,
org.Hs.eg.db, regioneR, Seurat, survival, survminer,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
multiMiR, miRBaseConverter
testthat, knitr, rmarkdown, BiocStyle, a4Base, kableExtra,
methods, grDevices
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo
knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0),
coin, scater, beachmat.hdf5
epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat
(>= 3.0.0), msigdb, GSEABase, dorothea, scMultiome, S4Vectors,
scuttle, vdiffr, ggrastr, ggrepel
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown,
EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat
(>= 3.0.0)
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
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, testthat,
webshot, prettydoc
AUCell, BiocParallel, BiocStyle, DelayedMatrixStats, dplyr,
fgsea, GSEABase, ggraph, ggridges, ggpointdensity, GSVA,
hexbin, igraph, irlba, knitr, msigdb, patchwork, rmarkdown,
rlang, scran, SeuratObject, Seurat, SingleCellExperiment,
spelling, stringr, testthat (>= 3.0.0), UCell
STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle,
ggpubr, scran, scater, scuttle, Seurat, hexbin
ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
kableExtra
rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat
(>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2,
MAST, DelayedMatrixStats, ggdendro, scales, patchwork
knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments
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
apeglm, BiocStyle, ComplexUpset, covr, DESeq2,
EnrichedHeatmap, GenomicAlignments, GenomicInteractions, Gviz,
ggforce, harmonicmeanp, here, knitr, limma, magrittr,
plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse,
VennDiagram
AnnotationHub (>= 2.22), BSgenome (>= 1.58),
BSgenome.Mmusculus.UCSC.mm10, testthat, knitr, rmarkdown,
markdown, zeallot, rmdformats, bio3d (>= 2.4), signalHsmm (>=
1.5), tidyverse (>= 1.3), covr, patchwork
BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, BiocManager
BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown,
spelling, testthat (>= 3.0.0)
rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0),
BiocStyle
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
BiocStyle, testthat, knitr, rmarkdown, topGO
knitr, rmarkdown, GOstats, GO.db, BiocGenerics, pROC, RUnit,
BiocStyle
RCurl, gage, topGO, GO.db, reactome.db, RUnit, BiocGenerics,
org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, BiocManager
testthat, knitr, rmarkdown, reactome.db, AnnotationDbi,
parallel, org.Mm.eg.db, limma, GEOquery, msigdbr, aggregation,
Seurat
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,
ensembldb, EnsDb.Hsapiens.v86, GenomicFeatures, AnnotationDbi,
pheatmap, Gviz, GenomeInfoDb, data.table
BiocStyle, GEOquery, ggrastr, knitr, rmarkdown, uwot,
testthat (>= 3.0.0), xml2
testthat, flowWorkspace, flowWorkspaceData, knitr, rmarkdown,
openCyto, flowStats(>= 4.7.1)
Rgraphviz, flowViz, flowStats (>= 3.43.4), testthat,
flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto,
gridExtra
RUnit, BiocGenerics, knitr, markdown, rmarkdown
knitr, rmarkdown, stringr, tidyverse, testthat
BiocStyle, dplyr, knitr, rmarkdown, testthat (>= 2.1.0)
BiocStyle, testthat, CytoML, flowWorkspace, ggrepel,
scattermore, pheatmap, ggpointdensity
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
BiocStyle, knitr, knitcitations, knitrBootstrap,rmarkdown,
codetools
BiocStyle, covr, ggrepel, kableExtra, knitr,
metabolomicsWorkbenchR, POMA, rmarkdown, rvest,
SummarizedExperiment, testthat (>= 2.3.2), tidyverse
magick, BiocStyle, knitr, rmarkdown, testthat, covr,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, rtracklayer,
SGSeq, ggbio, biovizBase, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.NCBI.GRCh38,
BSgenome.Hsapiens.1000genomes.hs37d5,
BSgenome.Hsapiens.UCSC.hg19
oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM,
hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf,
hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData
knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment,
SummarizedExperiment, airway
knitr, BiocStyle, rmarkdown, BiocManager,
BSgenome.Hsapiens.UCSC.hg19, DT, rtracklayer, testthat (>=
3.0.0), RBGL
GenomeInfoDb, 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
testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi,
org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
knitr, ggplot2, testthat, BEDMatrix, genio
edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db,
BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
BiocStyle, knitr, rmarkdown, RUnit,
TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData
BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.7.1),
gDRtestData (>= 1.7.1), kableExtra, knitr, markdown, purrr,
rmarkdown, SummarizedExperiment, testthat, yaml
BiocStyle, gDRstyle (>= 1.7.1), gDRimport (>= 1.7.1),
gDRtestData (>= 1.7.1), IRanges, knitr, pkgbuild, qs, testthat,
yaml
BiocStyle, gDRtestData (>= 1.7.1), gDRstyle (>= 1.7.1),
knitr, purrr, qs, testthat
BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.7.1),
gDRtestData (>= 1.7.1), IRanges, knitr, lintr, mockery, purrr,
rcmdcheck, rmarkdown, scales, testthat, tools, withr, yaml
testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools,
pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt,
ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db
knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown
testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2,
ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap,
viridis, poolr, listviewer, shiny
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, shiny, STRINGdb, BiocStyle,
magick, rmarkdown, org.Hs.eg.db
RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown,
Fletcher2013b, geneplast.data, geneplast.data.string.v91,
ggplot2, ggpubr, plyr
Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db,
BiocStyle, knitr
CompQuadForm, COMPoissonReg, poibin, SPAtest, survey,
testthat, BiocStyle, knitr, rmarkdown, GWASdata, dplyr,
ggplot2, GGally, RColorBrewer,
TxDb.Hsapiens.UCSC.hg19.knownGene, GenomeInfoDb
knitr, BiocStyle, htmltools, clusterProfiler, macrophage,
org.Hs.eg.db, magrittr, testthat (>= 2.1.0)
knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db,
org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db,
org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods, BiocStyle
BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown,
RUnit
spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr
GenomeInfoDbData, R.utils, data.table, GenomicRanges,
Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
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, knitr, BiocStyle
BiocStyle, knitr, rmarkdown, DT, testthat, listviewer,
ggplot2, GenomicAlignments, Rsamtools, BiocParallel,
TxDb.Hsapiens.UCSC.hg38.knownGene, VariantAnnotation, maftools,
R.utils, data.table
AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle,
rmarkdown, GenomicDistributionsData
GenomeInfoDb, txdbmaker, 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), 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,
AnnotationFilter, RUnit, BiocStyle, knitr, markdown
BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens,
knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats
RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
knitr, rmarkdown, R.utils, Biobase, BiocStyle, testthat,
AnnotationDbi, GenomeInfoDb
GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings
(>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools,
GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures,
txdbmaker, Gviz, VariantAnnotation, AnnotationHub, DESeq2,
DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14,
pasillaBamSubset, KEGGREST, hgu95av2.db, hgu95av2probe,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
rmarkdown, BiocStyle
RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation,
gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader,
data.table, DT, magrittr, shinydashboard,
BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38,
MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38,
SNPlocs.Hsapiens.dbSNP144.GRCh37,
TxDb.Hsapiens.UCSC.hg38.knownGene
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,
GenomicAlignments, Biostrings, GenomeInfoDb
VAExprs, stringdist, knitr, testthat, rmarkdown
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
BiocCheck, roxygen2, knitr, rmarkdown, testthat
knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud
RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, manipulateWidget, shiny,
BiocStyle, knitr, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph,
Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork
knitr, rmarkdown, BiocGenerics, testthat, covr, markdown,
quarto, DropletUtils, SingleCellExperiment
knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr,
clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq,
testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery,
BiocGenerics
devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat
(>= 3.0.0)
airway, knitr, DESeq2, recount3, rmarkdown, stringr, testthat
(>= 3.0.0)
airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat,
vdiffr
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
knitr, clusterProfiler, bnlearn, rmarkdown, BiocStyle,
AnnotationDbi, testthat (>= 3.0.0)
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0),
GenomicRanges
ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl,
ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat
(>= 3.0.0), yulab.utils
aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph,
knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater,
scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject,
SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS
Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix,
scater, scran, uwot, testthat, patchwork
emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,
prettydoc, rmarkdown, testthat, tibble, glue, Biostrings
aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust,
rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils
treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc,
markdown, testthat (>= 3.0.0), pillar
knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0)
roxygen2, knitr, rmarkdown, testthat, BiocStyle
testthat, knitr, rmarkdown, BiocStyle, IRanges,
GenomicRanges, pryr, AnnotationHub, scRNAseq, scater, scran,
scRNAseq,
testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS,
statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData, muscData, scran, dplyr
BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC,
rmarkdown, survival, testthat, VennDiagram, withr
GO.db, golubEsets, hu6800.db, vsn, Rgraphviz
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown,
zellkonverter
testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle,
BiocManager, GenomeInfoDb
org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Mmu.eg.db,
org.Rn.eg.db, org.Ce.eg.db, org.Pt.eg.db, org.Dr.eg.db, knitr,
rmarkdown, BiocStyle
Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat,
tidyr, tidyselect, ROCR
BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db,
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.EcSakai.eg.db, org.EcK12.eg.db,
org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db,
ggplot2, ggrepel, DT, magick
hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter,
RColorBrewer, xtable, SparseM, GSEABase, geneplotter,
org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr
knitr, rmarkdown, RUnit, BiocManager, BiocGenerics,
BiocStyle, devtools
knitr, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7,
BSgenome.Dmelanogaster.UCSC.dm6,
BSgenome.Mmulatta.UCSC.rheMac10,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm39.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene,
TxDb.Rnorvegicus.UCSC.rn7.refGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW,
clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker,
testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA,
variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024,
RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR
SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle,
knitr
checkmate, a4Preproc, ALL, BiocStyle, 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, RUnit
BiocStyle, GSE62944, knitr, rappdirs, rmarkdown
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm
SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi,
knitr, plotly, 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, sva,
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,
BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene,
org.Hs.eg.db, testthat (>= 3.0.0)
testthat (>= 3.0.0), ggplot2, withr, knitr, rmarkdown
BSgenome.Hsapiens.UCSC.hg19, xml2, BiocStyle, knitr,
rmarkdown, testthat
BiocStyle, knitr, rmarkdown, formatR, rrBLUP
DO.db, DT, knitr, RBGL, testthat, rmarkdown, dplyr, Gviz,
Rsamtools, 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, BiocStyle, knitr
knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate,
DBI, RSQLite, S4Vectors, methods
BiocParallel, ExperimentHub, TENxBrainData, HDF5Array,
testthat, knitr, rmarkdown, BiocStyle
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
LoomExperiment, SummarizedExperiment, SingleCellExperiment,
S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown,
BiocStyle
BiocParallel, GenomicRanges, SummarizedExperiment (>=
1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter,
GenomicFeatures, SingleCellExperiment, DelayedMatrixStats,
genefilter, RSpectra, RUnit, knitr, rmarkdown, BiocStyle
RColorBrewer, pheatmap, MASS, patchwork, testthat
GenomeInfoDb, HelloRangesData, BiocStyle, RUnit,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, DelayedArray, DT, grid, httr, knitr, rmarkdown,
statmod, testthat (>= 3.2.2), vdiffr (>= 1.0.8)
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
knitr, doParallel, testthat, BiocGenerics, markdown
parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray,
knitr, markdown, rmarkdown, Rsamtools
GenomeInfoDb, covr, tools, kableExtra (>= 1.3.4), knitr (>=
1.45), rmarkdown, testthat (>= 3.0.0), BiocFileCache (>= 2.6.1)
BSgenome.Hsapiens.NCBI.GRCh38, knitr, rmarkdown, DT,
testthat, BiocStyle, kableExtra
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, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5
HiContacts, HiContactsData, BiocFileCache, rtracklayer,
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
HiContactsData, rtracklayer, GenomicFeatures, Biostrings,
BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra,
patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
HiContacts, HiContactsData, AnnotationHub, BiocFileCache,
BiocStyle, testthat, knitr, rmarkdown
rhdf5, BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)
BiocStyle, knitr (>= 1.30), rmarkdown (>= 2.10), ggplot2 (>=
3.5.0), reshape2 (>= 1.4.4), testthat (>= 3.0.0), BiocManager
BiocStyle, knitr, rmarkdown, testthat, ChIPpeakAnno, grid,
TxDb.Hsapiens.UCSC.hg38.knownGene
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown
knitr, annotate, gwascat, testthat, rmarkdown
BiocStyle, DT, ggh4x, ggsignif, knitr, MGnifyR, mia, miaViz,
MOFA2, patchwork, reticulate, rmarkdown, scater, shadowtext,
testthat, UpSetR
org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle,
testthat, rmarkdown, dplyr, DT
rmarkdown, colorspace, e1071, kernlab, ranger,
SummarizedExperiment, Biostrings, randomForest, gprofiler2,
gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools,
knitr
EDASeq, testthat, knitr, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle,
pryr
AnnotationHubData, ExperimentHubData, GenomeInfoDbData,
testthat, knitr, rmarkdown, BiocStyle,
SingleCellExperiment, SummarizedExperiment, Seurat,
SeuratObject, ggplot2, progress, testthat, splatter, scater,
devtools, knitr, rmarkdown, BiocStyle, ExperimentHub
BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)
knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot,
DescTools, RColorBrewer
GenomeInfoDb, knitr, rmarkdown, Rsubread (>= 1.29.0),
testthat
testthat, BiocStyle, markdown, airway, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, htmltools, edgeR
knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
GenomicAlignments, parallel, testthat, knitr, rmarkdown,
BiocStyle, ggplot2, dplyr, scales, ggseqlogo
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, ggrepel, patchwork
RUnit, BiocStyle, knitr, rmarkdown, MotifDb, seqLogo
BiocStyle, GenomicAlignments, knitr, Rsamtools, rtracklayer,
RUnit, shinytest2, VariantAnnotation
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
BiocManager, BiocStyle, knitr, curl, glue, rmarkdown,
sessioninfo, testthat, tibble, GenomicDataCommons
BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown,
Peptides, randomForest, rmarkdown, scRepertoire, spelling,
testthat, tidygraph, viridis
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT
BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
knitr, org.Hs.eg.db, org.Mm.eg.db,
IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi,
sesameData, TCGAbiolinks (>= 2.29.4)
knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0),
SummarizedExperiment
BiocGenerics,BiocManager, BiocStyle,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19,
EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown,
rmarkdown, rtracklayer, RUnit, grDevices,
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
gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gridExtra, testthat,
minionSummaryData
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown,
roxygen2, withr, extraDistr, ggalluvial, scales, gridExtra,
R.utils, RefManageR, flexdashboard, circlize, plotly, gtools,
eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr,
future, doFuture, foreach, psych, Rcapture
testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq,
TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer,
viridis, htmltools, GenomicRanges
airway, BiocStyle, covr, knitr, limma, org.Hs.eg.db,
RefManageR, rmarkdown, scuttle, sessioninfo, statmod, testthat
(>= 3.0.0)
knitr, rmarkdown, scater, scRNAseq, org.Mm.eg.db, scuttle,
BiocStyle, testthat (>= 3.0.0)
BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 3.0.0), scRNAseq, scater
BiocStyle, covr, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 3.0.0), nullrangesData
BiocStyle, covr, knitr, RefManageR, rmarkdown, markdown,
scRNAseq, sessioninfo, testthat (>= 3.0.0), yaml
airway, BiocStyle, covr, edgeR, fgsea, GO.db, iSEEde, knitr,
org.Hs.eg.db, RefManageR, rmarkdown, scater, scuttle,
sessioninfo, testthat (>= 3.0.0)
biomformat, BiocStyle, knitr, RefManageR, remotes, rmarkdown,
scater, testthat (>= 3.0.0), vegan
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
BiocStyle, knitr, rmarkdown, htmltools, RUnit, dplyr
MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots,
RColorBrewer, gridExtra, limma, boot, DBI, MASS
IsoCorrectoRGUI, knitr, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, org.Mm.eg.db, pheatmap, BiocStyle, testthat
knitr, png, limma, grid, DT, randomForest, digest, testthat,
rmarkdown, BiocStyle, magick, statmod, codetools
BiocStyle, knitr, rmarkdown, spatstat, Seurat, statmod,
corrplot, ggplot2, ggraph, ggrepel, gridExtra, reshape2,
igraph, jsonlite, vdiffr, patchwork, ggpubr, tidyr,
SpatialFeatureExperiment, ExperimentHub, TENxXeniumData,
SingleCellExperiment, SFEData, Matrix, data.table, scran,
scater, grid, testthat (>= 3.0.0)
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, BiocGenerics, BiocStyle, knitr, markdown
testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr,
sesame, gprofiler2, ggrastr
BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice,
msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat,
mzR
BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats,
VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75,
Rsamtools, GenomicFiles (>= 1.13.6)
knitr, rmarkdown, curatedMetagenomicData, BiocStyle,
phyloseq, pkgdown, covr, withr
testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr,
rmarkdown, BiocStyle
BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines,
affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio,
org.Hs.eg.db, vsn
BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat
(>= 3.0.0)
BiocStyle, ggplot2, magick, testthat (>= 3.0.0), knitr,
rmarkdown, caret, ROTS
BiocStyle, RefManageR, rmarkdown, knitr, testthat (>= 3.0.0)
MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer,
moments, testthat, matrixStats
knitr, rmarkdown, igraph, reshape2, limma,
knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling,
testthat
BiocStyle, devtools, knitr, roxygen2, rmarkdown, testthat (>=
3.0.0), S4Vectors,
SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>=
3.0.0)
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
nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges,
limma, ExperimentHub, AnnotationHub, DelayedMatrixStats,
BisqueRNA, DelayedArray
ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat,
Biobase
knitr, testthat (>= 2.1.0), rmarkdown, markdown
knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra
knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown,
markdown
testthat, knitr, rmarkdown, BiocStyle, MACSdata
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors
gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil,
rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools,
BiocGenerics, BiocManager
knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset,
BiocGenerics, BiocStyle
BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo,
testthat (>= 3.0.0)
knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub,
marinerData, GenomeInfoDb
knitr, rmarkdown, BiocStyle, testthat, covr
biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>=
2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>=
0.12.2), knitr, testthat, readr, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, AnnotationHub
signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench
BiocManager, BiocStyle, clusterProfiler, ComplexHeatmap,
depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite,
knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore,
splatter, testthat (>= 3.0.0), UpSetR
Matrix, sparseMatrixStats, SparseArray, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0)
knitr, markdown, BiocStyle, testthat (>= 3.0.0)
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, cvms, data.table, dplyr, ggplot2, gridExtra,
knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0)
testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny,
shinyjs, DT, microbenchmark, mzR
BiocStyle, testthat, knitr, rmarkdown, robustbase
BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown,
structToolbox, testthat, pmp, grid, png
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
knitr, rmarkdown, DT, ggraph, tidyverse, testthat (>= 3.0.0)
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
BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit
BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr
(>= 1.48), testthat (>= 3.2.1.1)
BiocStyle, knitr, rmarkdown, RUnit, methylInheritance
rmarkdown, BiocStyle, testthat (>= 2.1.0), parallel, R.utils,
doParallel, reshape2, motifmatchr, matrixStats, biomaRt,
dorothea, viper, stageR, BiocFileCache, png, htmltools, knitr,
jpeg, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
data.table, downloader
knitr, rmarkdown, DSS, bsseq, plotly,
BSgenome.Mmusculus.UCSC.mm9, MafDb.1Kgenomes.phase3.GRCh38,
MafDb.1Kgenomes.phase3.hs37d5, BSgenome.Hsapiens.UCSC.hg19,
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, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit,
methInheritSim, testthat (>= 3.0.0)
testthat (>= 2.1.0), knitr, rmarkdown, genomation,
BiocManager
BiocStyle, doParallel, testthat, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, devtools, R.utils
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
biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2,
BiocStyle, miaViz, vegan, scater, phyloseq, magick
ade4, BiocStyle, biomformat, dada2, knitr, mediation, miaViz,
microbiomeDataSets, NMF, patchwork, philr, phyloseq, reldist,
rhdf5, rmarkdown, testthat, topicdoc, topicmodels, yaml
BiocStyle, knitr, philr, remotes, rmarkdown, testthat (>=
3.0.0)
ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2,
igraph, network, reshape2, sna, vegan, rmarkdown, knitr,
BiocStyle, testthat, mia, miaViz, colourvalues, philentropy
BiocStyle, devtools, ggplot2, knitr, lubridate, miaViz,
rmarkdown, scater, testthat, vegan
beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap,
ggh4x, knitr, patchwork, rmarkdown, shadowtext, testthat,
vegan, vipor
BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), prettydoc
rmarkdown, prettydoc, testthat, knitr, nlme, phangorn,
DECIPHER, randomForest, jsonlite, biomformat, scales, yaml,
withr, S4Vectors, purrr, seqmagick, glue, ggupset,
ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats,
phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel,
shadowtext, DirichletMultinomial, ggpp, BiocManager
BiocStyle, gghighlight, knitr, rmarkdown, methods,
RefManageR, sessioninfo, SingleCellExperiment,
SummarizedExperiment, testthat (>= 3.0.0)
testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle
testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown,
uwot, scuttle, BiocStyle, MouseGastrulationData,
MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq,
graphics, sparseMatrixStats
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, 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, biomaRt, BSgenome.Hsapiens.UCSC.hg38,
GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr,
MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, R.cache, SPONGE
BiocStyle, edgeR, knitr, minfiData, rmarkdown,
tweeDEseqCountData, DMRcate, ExperimentHub
knitr, rmarkdown, RUnit, ggplot2, BiocStyle
stringi, testthat (>= 2.1.0), HGNChelper,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Biobase, BiocStyle, clusterProfiler, GSVA, methods,
rmarkdown, knitr, SummarizedExperiment, testthat
BiocStyle, knitr, rmarkdown, mime, testthat, microbenchmark,
magick, vdiffr, kableExtra, devtools
class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL,
hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07),
golubEsets, ada, keggorthology, kernlab, mboost, party, klaR,
BiocStyle, knitr, testthat
MMDiffBamSubset, MotifDb, knitr, BiocStyle,
BSgenome.Mmusculus.UCSC.mm9
testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan,
phyloseq, curatedMetagenomicData, genefilter
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM,
BiocStyle
testthat (>= 1.0.0), timecoursedata, knitr, rmarkdown,
markdown, covr, BiocStyle
testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny,
shinyFiles, shinydashboard, shinyjs
BiocStyle, knitr, rmarkdown, testthat, usethis
BiocStyle, knitr, rmarkdown, testthat, viper
BiocManager, BiocStyle, BSgenome.Mmusculus.UCSC.mm10,
ggrepel, gridExtra, JASPAR2020, JASPAR2024, knitr, rmarkdown,
testthat, TxDb.Mmusculus.UCSC.mm10.knownGene
destiny, Hmisc, knitr, Seurat, scater, testthat
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), devtools,
roxygen2, png
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
png, edgeR
knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat
(>= 3.0.0)
RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq,
rmarkdown, kableExtra, testthat (>= 3.0.0)
knitr, rmarkdown, macrophage, org.Hs.eg.db, GeneTonic,
testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg38.knownGene,
BiocStyle
testthat, knitr, rmarkdown, codetools, BiocStyle, stats,
utils, purrr, scales, tibble, tidyr, Biobase, scater,
SingleCellExperiment, decor, markdown, Rsamtools, igraph,
leiden, bluster
BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805
BSgenome.Hsapiens.UCSC.hg19,
SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown,
BSgenome.Drerio.UCSC.danRer7, BiocStyle,
BSgenome.Hsapiens.1000genomes.hs37d5,
BSgenome.Hsapiens.UCSC.hg19.masked,
BSgenome.Hsapiens.NCBI.GRCh38,
BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR,
markdown
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
downloadthis, knitr, markdown, methods, remotes, rworkflows,
testthat (>= 3.0.0), withr, emoji, curl, jsonlite
Cairo, grImport, grImport2, BiocGenerics, MotifDb,
RColorBrewer, BiocStyle, knitr, RUnit, rmarkdown, JASPAR2020
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
extraChIPs, ggdendro, knitr, MASS, MotifDb, rmarkdown,
rtracklayer, testthat (>= 3.0.0), VGAM
rmarkdown, knitr, svglite, bookdown(>= 0.34), testthat (>=
3.0.0)
Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, rmarkdown
testthat, rmarkdown, mzR, knitr, BiocStyle
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown
BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr,
lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5),
testthat
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, msdata, rmarkdown, microbenchmark, mzR
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest
ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat
(>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3)
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite
testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick,
msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub,
BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots,
XML, shiny, magrittr, SummarizedExperiment, Spectra
knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown,
BiocStyle, imputeLCMD
MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
msPurityData, CAMERA, RPostgres, RMySQL
multcomp, gridExtra, knitr, BiocStyle, RefManageR,
sessioninfo, rmarkdown, testthat, tidyverse, plotly, MsDataHub,
MSnbase, matrixStats, MsCoreUtils, covr
BiocStyle, knitr, rmarkdown, tinytest, covr, markdown,
mockery, kableExtra
data.table, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0),
mockery, MSstatsConvert
BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
knitr, rmarkdown, tinytest, covr, mockery, testthat (>=
3.0.0)
rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0),
shinytest2,
HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr,
SingleCellMultiModal, CiteFuse, scater
BiocStyle, HDF5Array, h5mread, knitr, maftools,
RaggedExperiment, reshape2, rmarkdown, survival, survminer,
testthat, UpSetR
knitr, rmarkdown, gplots, RUnit, BiocGenerics,
preprocessCore, Biobase, GEOquery
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Scerevisiae.UCSC.sacCer1, ensembldb, IRanges,
GenomeInfoDb, 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, knitr, rmarkdown,
BiocStyle, testthat (>= 2.1.0)
BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2)
BiocGenerics (>= 0.40.0), BiocStyle, e1071 (>= 1.7.12),
knitr, rmarkdown, testthat (>= 3.0.0)
testthat, BiocStyle, knitr, covr, rmarkdown
BiocStyle, doParallel, ExperimentHub, knitr, markdown,
rmarkdown, testthat (>= 3.0.0), vegan
testthat, knitr, BiocStyle, rmarkdown, scater, bluster,
DropletUtils, scRNAseq
SNPlocs.Hsapiens.dbSNP144.GRCh37,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
SNPlocs.Hsapiens.dbSNP155.GRCh37,
SNPlocs.Hsapiens.dbSNP155.GRCh38,
BSgenome.Hsapiens.1000genomes.hs37d5,
BSgenome.Hsapiens.NCBI.GRCh38, BiocGenerics, S4Vectors,
rmarkdown, markdown, knitr, testthat (>= 3.0.0), UpSetR,
BiocStyle, covr, Rsamtools, MatrixGenerics, badger,
BiocParallel, GenomicFiles
BiocStyle, cowplot, countsimQC, AnnotationHub, ExperimentHub,
iCOBRA, knitr, patchwork, phylogram, RColorBrewer, reshape2,
rmarkdown, statmod, stageR, testthat, tidyr, UpSetR
TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard,
shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr,
rmarkdown, survival, XVector, qpdf, covr, shinyWidgets,
cowplot, withr
testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign,
plotly, scattermore, BiocManager
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, rmarkdown
RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
testthat, BiocManager, rmarkdown
BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>=
1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown,
rtracklayer, testthat (>= 3.0.0), covr
biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf
grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly,
rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics
testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran,
DropletUtils, igraph, BiocFileCache, Seurat
knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle
AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db,
rmarkdown, testthat (>= 3.0.0), tidyverse
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db,
org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr,
markdown
knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI,
pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp,
BiocStyle, knitr
BiocStyle, Cairo, DT, knitr, pander, readr, testthat,
truncnorm
BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth,
knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>=
4.0.0), spatstat.explore, stringr, survival, tidyverse,
testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, STexampleData,
WeberDivechaLCdata, scran, ggplot2, testthat
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, 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, testthat
testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM,
AnnotationHub, ExperimentHub, GenomeInfoDb, nullrangesData,
excluderanges, ensembldb, EnsDb.Hsapiens.v86,
BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr,
magrittr, tidyr, cobalt, DiagrammeR, MatchIt, mariner
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
arrow, knitr, BiocStyle, curatedMetagenomicData, testthat (>=
3.0.0), cBioPortalData
BiocStyle, knitr, rmarkdown, testthat, GEOquery,
VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges,
FDb.InfiniumMethylation.hg19, snpStats
knitr, rmarkdown, BiocStyle, magick, testthat
BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr,
mlrMBO, parallelMap, ParamHelpers, R.matlab, sigmajs, smoof,
testthat
RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis,
desc, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, testthat, Matrix, graph
testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle
knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle,
SingleCellExperiment, celldex, rmarkdown, AnnotationDbi,
magick,
flowWorkspaceData, knitr, rmarkdown, markdown, testthat,
utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2),
MASS
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, GenomeInfoDbData
GenomeInfoDb, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown,
magick, BiocStyle, ggplot2
txdbmaker, GenomeInfoDbData, Homo.sapiens, Rattus.norvegicus,
BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs,
rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr
rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown,
testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape,
phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat
(>= 3.0.0)
BiocStyle, DropletUtils, knitr, VisiumIO, SpatialExperimentIO
testthat, knitr, rmarkdown, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMariaDB,
AnnotationDbi, beeswarm, covr, GenomeInfoDb, ggbio, biovizBase
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, reshape2
bcellViper, BSgenome.Hsapiens.UCSC.hg19, JASPAR2018,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, TFBSTools,
GenomicFeatures, annotate
writexl, readxl, readr, rhdf5, plotly, testthat (>= 3.0.0),
knitr, rmarkdown, BiocStyle, covr
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle, rmarkdown
rmarkdown, knitr, IRanges, testthat (>= 3.0.0)
AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite,
knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0),
vdiffr
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
testthat, BiocStyle, markdown, 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
diffviewer, gridExtra, testthat (>= 3.0.0), vdiffr,
rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools,
R.devices, usethis, rlang, magick, cowplot
statmod, BiocStyle, knitr, rmarkdown, tidyr
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, org.Hs.eg.db,
org.Mm.eg.db
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5,
GEOquery
pander, rmarkdown, knitr, knitcitations, crayon, testthat,
markdown, BiocStyle, R.utils
BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4,
rmarkdown, testthat
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
yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown,
BiocStyle
GenomeInfoDb, knitr, rtracklayer, testthat, BiocStyle,
prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6,
BiocManager, rmarkdown, ggplot2
org.Hs.eg.db (>= 3.7.0), org.Mm.eg.db (>= 3.7.0), biomaRt (>=
2.30.0), knitr, AnnotationDbi, energy
BiocManager, knitr, rtracklayer, testthat,
BSgenome.Hsapiens.UCSC.hg19
ExperimentHub, mixOmics, ggplot2, testthat, tidyr, scales,
minfi, EpiDISH, knitr, rmarkdown
BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>=
3.0.0)
knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf,
BiocStyle, biocViews, testthat (>= 3.0.0)
AnnotationDbi, AnnotationHub, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures,
ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer,
plotgardenerData, pdftools, png, rmarkdown, scales, showtext,
testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene
knitr, htmltools, BiocStyle, rmarkdown, testthat
tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings,
BiocParallel, GenomeInfoDb, scales, HiContactsData,
rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo,
testthat (>= 3.0.0), RefManageR
devtools, knitr, rmarkdown, testthat, airway, IRanges, here
BSgenome.Hsapiens.UCSC.hg38.masked,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
VariantAnnotation, SummarizedExperiment, knitr
testthat (>= 3.0.0), BiocStyle, knitr, DT, dplyr, kableExtra,
scico, cowplot, ggnetwork, ggplot2, tidyr, STexampleData
knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, rmarkdown, ddPCRclust
BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly,
tidyverse, testthat (>= 2.3.2)
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
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
GenomeInfoDbData, testthat, rmarkdown, knitr, Rtsne,
gridExtra
testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr,
tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown,
BiocStyle
GenomeInfoDb, 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, CoGAPS, gridExtra, grid, testthat, devtools,
knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject
testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2,
xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr,
akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13),
nipals, reshape, magick, umap
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat
(>= 3.0.0)
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
msdata, rpx, mzID, mzR, SummarizedExperiment, BiocStyle,
rmarkdown, knitr, factoextra, vdiffr (>= 1.0.0), testthat
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData,
ropls
pumadata, affydata, snow, limma, ROCR,annotate
BiocParallel, BiocStyle, PSCBS, R.utils,
TxDb.Hsapiens.UCSC.hg19.knownGene, 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,
markdown
SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix,
HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny,
shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn,
preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute,
norm, ComplexHeatmap
Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute,
imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr,
rmarkdown
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
patchwork, knitr, qPLEXdata, rmarkdown, statmod, testthat,
UniProt.ws, vdiffr
devtools, DESeq2, knitr, rmarkdown, testthat, BiocStyle
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR,
rmarkdown, sessioninfo, testthat (>= 3.0.0)
testthat, BiocStyle, knitr, rmarkdown, covr
AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery,
knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat,
tibble
rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle
Gviz, BiocStyle, GenomeInfoDbData, GenomicAlignments,
Rhisat2, knitr, rmarkdown, covr, testthat
QUBICdata, qgraph, fields, knitr, rmarkdown
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
testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown,
BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh38,
BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle,
AnnotationHub, covr, raerdata, txdbmaker
BiocStyle, knitr, rmarkdown, testthat, GenomeInfoDb,
MultiAssayExperiment
testthat, knitr, rmarkdown, BiocStyle, withr, Seqinfo,
BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86
RUnit, knitr, rmarkdown, ggplot2, gridExtra, annotatr, LOLA,
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, parallel,
doParallel, foreach, doRNG, matrixStats, EnvStats, ExtDist,
gamlss, gamlss.dist
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Ecoli.NCBI.20080805
markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>=
3.0.0)
BiocStyle, covr, knitr, tinytest, mockery, withr
BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat
BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7),
rmarkdown, tartare (>= 1.5), testthat
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph
testthat, parallel, BiocStyle, knitr, rmarkdown
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
testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse,
tinytex
BiocStyle, testthat, knitr, rmarkdown, base64enc, graph
BiocStyle, knitr, rmarkdown, igraph, grDevices
devtools, knitr, ReactomeGSA.data, rmarkdown, scater, scran,
scRNAseq, scuttle, Seurat (>= 3.0), SingleCellExperiment,
testthat
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, txdbmaker,
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, recount
minfiData, minfiDataEPIC, knitr, testthat, ggplot2,
gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma,
ExperimentHub, AnnotationHub
GenomeInfoDb, grid, BiocStyle, knitr, rmarkdown, zoo, RUnit,
BiocManager, BSgenome, RMySQL
knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf
knitr, rmarkdown, testthat, biocViews, BiocCheck, BiocStyle,
airway
GEOquery, rmarkdown, knitr, BiocManager, testthat
knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle,
tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges
knitr, rmarkdown, gplots, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown,
BSgenome.Hsapiens.UCSC.hg19.masked, testthat
rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>=
3.0.0)
BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot
(>= 1.29.1), sessioninfo, DT, edgeR, ggbio (>= 1.35.2),
ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap,
RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker
BiocStyle, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 2.1.0), covr
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
BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2,
corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl
mclust, flexmix, testthat, BiocStyle, knitr, formatR,
rmarkdown
R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics,
RUnit
testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra,
BiocManager, stringr, stringi, ggplot2, tibble, lipidr
RUnit, BiocStyle, BiocGenerics, xtable, sna
testthat (>= 0.3), knitr, rmarkdown, BiocManager,
org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
boot, tools, BiocGenerics, knitr, xtable
bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr,
ggplot2, mockery, BiocParallel
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7)
BiocStyle, knitr, rmarkdown, tinytest, mockery
knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0)
testthat, rmarkdown, 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,
GenomeInfoDbData, edgeR, DESeq2, limma, ashr, testthat,
rmarkdown, vsn, Biobase
DescTools, devtools, knitr, rmarkdown, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), plyranges,
plotgardener, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown,
RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1)
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
BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr,
testthat (>= 3.0.0)
Category, GOstats, Gviz,
IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19,
RnBeads.mm9, RnBeads.hg38, 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, IlluminaHumanMethylation450kanno.ilmn12.hg19,
scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin,
RUnit, MethylSeekR, sesame
BiocStyle, knitr, rmarkdown, GSEABenchmarkeR,
EnrichmentBrowser, preprocessCore, DESeq2
GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat,
lubridate, DT, rmarkdown,
BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis,
rmarkdown, testthat
knitr, rmarkdown, testthat, RUnit, BiocGenerics
BiocStyle, covr, kableExtra, knitr, rmarkdown, styler,
testthat (>= 3.0.0)
Biostrings, BiocStyle, testthat, knitr, tibble, 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.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,
VariantAnnotation, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr
testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
e1071, parallel, doParallel
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign
Rtsne, ape, Seurat, knitr, rmarkdown, tictoc, BiocStyle,
testthat (>= 3.0.0)
devtools, testthat, pander, Biobase, GenomicRanges, IRanges,
S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations,
RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation,
RTCGA.CNV, magrittr, tidyr
BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
knitr, BiocStyle, TPP, testthat, rmarkdown
GenomeInfoDb, 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, BiocManager, BiocStyle, remotes, ggpubr,
ggcorrplot, ggh4x, testthat (>= 3.0.0)
BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
knitr, rmarkdown, DESeq2, limma, SummarizedExperiment,
airway, BiocStyle, matrixTests, BiocManager
knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
BiocParallel, SparseArray (>= 0.0.4), DelayedArray,
HDF5Array, testthat, knitr, rmarkdown, BiocStyle
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle,
knitr
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit,
knitr, ggmanh, BiocGenerics
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), scater,
Rtsne
BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db,
markdown, rmarkdown, RUnit
knitr, kableExtra, testthat,
TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens,
TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus,
GenomicAlignments
knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub,
ensembldb, edgeR, DEXSeq, stageR, DelayedArray
knitr, rmarkdown, mclust, scater, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, BiocSingular,
DelayedMatrixStats
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), shinytest,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Mmusculus.UCSC.mm39, BSgenome.Rnorvegicus.UCSC.rn6
BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown,
rmarkdown, rhdf5, HDF5Array
future, RUnit, knitr, markdown, rmarkdown, BiocStyle
BiocStyle, knitr, testthat, cluster, SingleCellExperiment
testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle,
rmarkdown
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown,
loo, prettydoc, SeuratObject, tidyseurat,
tidySingleCellExperiment, bayesplot, posterior
PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra,
rmarkdown
BiocStyle, knitr, rmarkdown, testthat, scRNAseq, circlize,
ComplexHeatmap, ggplot2, dplyr, viridisLite, mbkmeans
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0),
RefManageR, sessioninfo, BiocStyle
AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq,
SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0)
AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
scuttle, SeuratObject, testthat, vdiffr
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR,
org.Hs.eg.db, clusterProfiler
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, Seurat, shinydashboard, iSEE, igraph,
scran, tibble, scuttle
knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra
knitr, markdown, rmarkdown, scater, scattermore, scales,
matrixStats, deldir
BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0)
BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales,
proxy, testthat, badger
knitr, rmarkdown, BSgenome.Mmusculus.UCSC.mm10,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase,
ggplot2, ggthemes
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM,
R.utils
knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0)
BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2,
rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray,
visNetwork, doParallel, batchtools, splatter, scater,
kableExtra, mclust, TENxPBMCData
knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0)
BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat
(>= 3.0.0), yaml
DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0),
covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter,
SingleCellExperiment, microbenchmark
BiocStyle, DT, GenomicFeatures, grid, igraph, kableExtra,
knitr, locStra, plotly, rmarkdown, RColorBrewer, readr,
reshape2, RANN, shiny, scater (>= 1.11.0), testthat, xml2, umap
BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db,
org.Ce.eg.db, org.At.tair.db, testthat (>= 3.2.1.1)
testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats,
HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix,
ScaledMatrix, DESeq2, pheatmap, scater
testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics,
sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment,
SingleCellExperiment, scRNAseq, igraph
testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown,
testthat
BiocManager, BiocStyle, circlize, knitr, Peptides, rmarkdown,
scales, scater, Seurat, spelling, testthat (>= 3.0.0)
rmarkdown, knitr, testthat, BiocStyle, shinytest2
BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array,
knitr, markdown, rmarkdown, TENxPBMCData, testthat
testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens
knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s,
metagenomeSeq, epivizrStandalone, GenomeInfoDb
BiocStyle, knitr, scRNAseq, rmarkdown, testthat,
sparseMatrixStats, DelayedMatrixStats, scran
knitr, testthat, reshape2, ggplot2, rhdf5, BiocStyle
testthat, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22),
rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>=
0.3.0)
BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2),
covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>=
1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
crayon, knitr, markdown, rmarkdown, Rsamtools,
VariantAnnotation
knitr, BiocStyle, rmarkdown, testthat, BiocManager
emojifont, knitr, rmarkdown, prettydoc, tibble
testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit,
knitr, rmarkdown, BiocStyle
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno,
GenomeInfoDb, covr, knitr, rmarkdown, testthat
CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr,
rmarkdown, BiocManager, remotes
scales, BiocManager, GenomeInfoDb, knitr, DNAcopy, e1071,
randomForest, RPMM, rmarkdown, testthat, tidyr, BiocStyle,
ggrepel, grDevices, KernSmooth, pals
testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions,
covr
knitr, rmarkdown, BiocManager, devtools, BiocStyle
BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
testthat, parallel, knitr, rmarkdown, BiocStyle
config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck,
rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0),
GenomicRanges, VariantAnnotation, StructuralVariantAnnotation,
biovizBase, ggbio
BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite,
testthat (>= 3.0.0)
knitr (>= 1.30.0), mCSEA (>= 1.10.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICmanifest, testthat, minfiData,
BiocStyle
shinyMethylData, minfiData, BiocStyle, knitr, testthat
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi,
knitr
BiocStyle, 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, signatureSearchData,
DT
BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat
(>= 3.0.0)
IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr,
rmarkdown
curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0),
SeuratObject (>= 5.0.0), testthat (>= 3.0.0)
RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments,
rtracklayer, rmarkdown, BiocStyle
BiocGenerics, BiocStyle, testthat, knitr, igraph
knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC,
AnnotationDbi, Matrix, DiagrammeR, ragg, png,
InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment,
AnnotationHub, jsonlite
ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>=
3.0.0), scater, scran, magick
BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan,
igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics,
flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11),
shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter,
gridtext, fpc
BiocStyle, knitr, biomaRt, stringr, monocle
scaeData, knitr, rmarkdown, BiocStyle, scran, scater,
scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi,
DropletUtils, testthat (>= 3.0.0)
testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>=
2.9.1), Rtsne
BSgenome.Mmusculus.UCSC.mm10, devtools, ExperimentHub, knitr,
qs, rmarkdown, readr, rrapply, SingleMoleculeFootprintingData,
testthat (>= 3.0.0), tidyverse
testthat, knitr, rmarkdown, BiocStyle, BiocGenerics,
SingleCellExperiment, scuttle, scrapper, scRNAseq, ggplot2,
pheatmap, grDevices, gridExtra, viridis, celldex
pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
GenomeInfoDb, BiocStyle, BSgenome, knitr, rmarkdown, RMySQL,
RUnit
BiocStyle, devtools, knitr, magick, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle,
scran, scater, SingleR, celldex, cowplot, SummarizedExperiment,
beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment,
snifter, uwot, bluster, class
BiocGenerics, BiocStyle, clusterExperiment,
DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl,
rmarkdown, testthat, uwot, covr
BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater,
splatter, testthat (>= 3.0.0), tidytext, UpSetR
BiocStyle, knitr, STexampleData, scuttle, scran, scater,
ggspavis, testthat
BiocManager, bit64, covr, knitcitations, knitr (>= 1.6),
devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat
(>= 2.1.0)
knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0)
BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
BiocStyle, covr, devtools, dplyr, knitr, magick, rmarkdown,
testthat, TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest,
ggfortify, tidyr, testthat (>= 3.0.0)
data.table, devtools, dplyr, hrbrthemes, knitr, RColorBrewer,
cowplot, readbitmap, rjson, rmarkdown, BiocStyle, testthat (>=
3.0.0), viridis, CoGAPS
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), withr,
viridis
testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown,
covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale
FNN, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle,
DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin,
KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0),
orthogene, PANTHER.db (>= 1.0.3), R.utils, reactome.db,
rmarkdown, SummarizedExperiment, statmod, stringr, testthat,
webshot
HDF5Array, ExperimentHub, testthat, knitr, rmarkdown,
BiocStyle
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,
RefManageR, BiocStyle, knitr, testthat (>= 3.0.0),
sessioninfo, rmarkdown, markdown
testthat, knitr, rmarkdown, qpdf, Seurat
knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix,
DropletUtils, VisiumIO
stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0),
mgcv
AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics,
BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend,
DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array,
htmltools, htmlwidgets, kableExtra, knitr, limma, magick,
memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db,
org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly,
rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater,
scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable,
Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA,
xlsx, yaml
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), stringi,
qpdf, pheatmap, viridis, cowplot, vdiffr, sf
testthat (>= 3.0.0), STexampleData, ggplot2, knitr
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
BiocStyle, knitr, rmarkdown, statmod, CellBench, scater,
patchwork, jsonlite, vdiffr, testthat (>= 3.0.0)
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2,
BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0),
rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat, covr
testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr,
S4Vectors, BiocStyle, mzR
BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown,
testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap,
elsa
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, testthat (>=
3.0.0)
SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown,
imcRtools, testthat (>= 3.0.0)
covr, testthat, rmarkdown, markdown, knitr, devtools,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle,
hexbin
BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle,
Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2
(>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick,
mfa, phenopath, preprocessCore, progress, pscl, rmarkdown,
scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling,
testthat, VariantAnnotation, zinbwave
knitr, rmarkdown, crayon, splines, testthat (>= 3.0.0),
DESeq2, limma, DoubleExpSeq, edgeR, DBI, GO.db, AnnotationDbi,
fgsea, Rsubread
testthat, knitr, rmarkdown, ggplot2, tidyr
igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
knitr, DelayedMatrixStats, rmarkdown, BiocStyle, ggplot2,
ggpubr, MASS, scales, scRNAseq, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr,
ggplot2
testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra,
digest, doParallel, bigmemory, GSVA
testthat, STexampleData, knitr, rmarkdown, BiocStyle
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, R.utils,
spelling
BiocStyle, colorBlindness, DelayedArray, DropletUtils,
ExperimentHub, ggcorrplot, grDevices, grid, igraph, jpeg,
knitr, methods, png, rmarkdown, scater, scatterpie, scran,
SpatialExperiment, SummarizedExperiment, S4Vectors,
TabulaMurisSenisData, TENxVisiumData, testthat
knitr, BiocStyle, rmarkdown, scuttle, STexampleData, ggpubr,
testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, tools, spqnData (>= 0.99.3),
RUnit
knitr, rmarkdown, LSD, testthat, BiocStyle
knitr, rmarkdown, testthat, BiocManager, BiocStyle
BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools,
knitr, pander, patchwork, rmarkdown, spelling, testthat (>=
3.0.0), tidyverse
scran, scater, knitr, UpSetR, gridExtra,
SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0),
purrr, sparseMatrixStats
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq, testthat
knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr,
ggrepel, cluster, testthat (>= 3.0.0)
RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>=
1.3), roxygen2, doSNOW
BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR,
ggsurvfit, lisaClust, survival
BiocStyle, knitr, magrittr, rmarkdown, testthat
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
GenomeInfoDb (>= 1.45.5), rhdf5, HDF5Array (>= 1.7.5),
annotate, AnnotationDbi, GenomicFeatures, SparseArray,
SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene,
hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown,
RUnit, testthat, digest
rmarkdown, markdown, knitr, testthat (>= 3.0.0)
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel
Hmisc, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
TxDb.Hsapiens.UCSC.hg19.knownGene,
BSgenome.Hsapiens.UCSC.hg19, ggplot2, devtools, testthat (>=
2.1.0), roxygen2, knitr, readr, plyranges, circlize, IRanges,
SummarizedExperiment, rmarkdown
TxDb.Hsapiens.UCSC.hg19.knownGene, ggplot2, devtools,
testthat (>= 2.1.0), roxygen2, knitr, BiocStyle, plyranges,
circlize, tictoc, IRanges, stats, SummarizedExperiment,
rmarkdown
BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6)
rmarkdown, prettydoc, broman, RSpectra, BiasedUrn, knitr, ks,
igraph, testthat (>= 3.0.0), scuttle, magrittr, DropletUtils,
tibble, tidyr, harmony, aplot, scales, ggsc, scatterpie, scran,
scater, STexampleData, ape
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse,
BiocStyle
BiocStyle, knitr, igraph, markdown, rmarkdown
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
rtracklayer, BiocStyle, ggtree, labdsv, covr, knitr,
rmarkdown, testthat (>= 3.0.0), xml2, networkD3
BiocStyle, knitr, rmarkdown, systemPipeRdata,
GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
GenomicFeatures, txdbmaker, GenomeInfoDbData, VariantAnnotation
(>= 1.25.11)
testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>=
2.12.0), systemPipeRdata (>= 2.10.0), rhandsontable, zip,
callr, pushbar, fs, readr, R.utils, DESeq2,
SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne,
UpSetR, tidyr, esquisse (>= 1.1.0), cicerone
systemPipeR, knitr, BiocStyle, rmarkdown, testthat (>=
3.0.0), BiocGenerics, Biostrings, methods
BiocStyle, covr, knitr, limma, rmarkdown, testthat (>=
3.0.0), tidyverse
BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr,
pheatmap, SpectralTAD, magick, qpdf
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
BiocStyle, bugsigdbr, fgsea, knitr, rmarkdown, testthat
BiocStyle, caret, circlize, class, covr, dplyr, e1071,
impute, knitr, lintr, MASS, plyr, randomForest, rmarkdown,
shiny, spelling, sva, testthat
AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap,
devtools, dplyr, httr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr,
magrittr, org.Hs.eg.db, RColorBrewer, readr, rmarkdown,
RTCGAToolbox, rtracklayer, R.utils, testthat,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, testthat (>= 3.0.0), RTCGA.rnaseq,
RTCGA.clinical, BiocStyle, MOFAdata
BiocStyle, GenomeInfoDb, bslib, ggplot2, ggpubr, plotly,
rmarkdown, shiny, knitr, testthat (>= 3.0.0)
org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle
apeglm, BiocStyle, knitr, rmarkdown, testthat
AnVILBase, knitr, rmarkdown, BiocStyle, withr, testthat (>=
3.0.0)
knitr, rmarkdown, BiocStyle, S4Vectors, Seqinfo, meta,
plotly, scales, tidyr, purrr, tibble, ggplot2, DESeq2, edgeR,
limma, babelgene, BiocGenerics, ggrepel, rcompanion,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, RColorBrewer,
RUnit, testthat (>= 3.0.0)
knitr, data.table, testthat, AnnotationFilter, Biobase,
GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors,
EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, Seqinfo,
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, widyr,
clusterProfiler, msigdbr, DESeq2, broom, survival, boot,
betareg, tidyHeatmap, pasilla, ggrepel, devtools, functional,
survminer, tidySummarizedExperiment, markdown, uwot,
matrixStats, preprocessCore, igraph, EGSEA, IRanges, here,
glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS, pkgconfig,
enrichplot, patchwork, airway
tidySummarizedExperiment, plyranges,
TxDb.Hsapiens.UCSC.hg19.knownGene, AnnotationHub,
GenomicFeatures, BiocStyle, hues, knitr, rmarkdown,
sessioninfo, testthat (>= 3.0.0)
BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown,
sessioninfo, testthat (>= 3.0.0)
tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>=
1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6)
rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>=
3.0.0)
BiocStyle, testthat, knitr, markdown, rmarkdown,
SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph,
GGally, uwot, celldex, dittoSeq, plotly
BiocStyle, testthat, knitr, markdown, scater, igraph,
cowplot, DropletUtils, tidySummarizedExperiment
BiocStyle, testthat, knitr, markdown, rmarkdown, plotly
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat
BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse,
igraph, gplots
knitr, aroma.light, affxparser, RUnit, BiocGenerics
GenomicFeatures, shiny, BiocManager, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData,
ggbeeswarm, ggsci, survminer, tidyverse
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
BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle,
STexampleData, escheR, ggpubr, colorspace, BumpyMatrix,
sessioninfo, testthat (>= 3.0.0)
biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit,
org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr,
htmltools, rmarkdown, motifStack
knitr, rmarkdown, testthat, covr, clusterExperiment,
DelayedMatrixStats
BiocNeighbors, DelayedArray, DelayedMatrixStats,
BiocParallel, testthat, knitr, BiocStyle, rmarkdown
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, ComplexUpset, edgeR,
extraChIPs, InteractionSet, knitr, readr, rmarkdown,
rtracklayer, testthat (>= 3.0.0)
testthat, roxygen2, knitr, BiocStyle, rmarkdown
scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors,
rmarkdown, knitr
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer
knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle,
GenomeInfoDb
Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0)
ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap,
sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0),
tibble, tidyr, SingleCellExperiment
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats,
cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db
BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0)
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, pryr
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
BiocGenerics, knitr, rmarkdown, testthat, httptest,
BiocStyle, rtracklayer
BiocStyle, knitr, rmarkdown, testthat, ggplot2,
BSgenome.Scerevisiae.UCSC.sacCer3
BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways,
magick
knitr, testthat, scuttle, scran, metapod, BiocParallel,
BiocNeighbors, batchelor
fgsea, knitr, testthat, reticulate, rmarkdown
EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT
(>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>=
1.12), rmarkdown, testthat, covr, pander
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
RefManageR, BiocStyle, knitr, sessioninfo, rmarkdown,
testthat (>= 3.0.0), TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
BSgenome.Scerevisiae.UCSC.sacCer3, GenomeInfoDbData
RMariaDB, ensembldb, GenomeInfoDbData, RUnit, BiocStyle,
knitr
knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db,
DESeq2, fishpond, edgeR, limma, devtools
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow,
limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats,
Matrix, eds
scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle,
Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown
DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown,
BiocStyle
BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr,
org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
knitr, rmarkdown, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
tidyr, testthat
BiocStyle, knitr, testthat, rmarkdown, dplyr
spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
testthat, BiocParallel, seqLogo, motifStack, dplyr, ape,
ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
GenomicRanges, SummarizedExperiment, InteractionSet,
SingleCellExperiment, MultiAssayExperiment, BiSeq, testthat,
knitr, rmarkdown, BiocStyle
knitr, testthat (>= 2.1.0), BiocStyle, rmarkdown, markdown,
karyoploteR, regioneR, dplyr
SC3, knitr, testthat, reticulate, rmarkdown
BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
tximport, tximportData, ballgown, DESeq2, RUnit, cowplot,
Rfast, zenith, statmod, BiocGenerics, r2glmm, readr
GenomeInfoDb, RUnit, AnnotationHub,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, SIFT.Hsapiens.dbSNP132,
SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats,
ggplot2, BiocStyle, knitr, magick, jsonlite, httr, rjsoncons
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
SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown
breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
knitr, markdown, RColorBrewer, rmarkdown, rstudioapi,
testthat (>= 3.0.0)
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager, stats, utils,
grDevices, processx
arrow, BiocStyle, data.table, knitr, readr, rmarkdown,
tinytest
BiocFileCache, BiocStyle, ggplot2, knitr, RefManageR,
rmarkdown, sessioninfo, Seurat, testthat (>= 3.0.0)
testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore,
knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr
arrow, automap, BiocSingular, BiocStyle, cowplot, data.table,
DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat,
hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5,
rmarkdown, scater, scattermore, scran, sfarrow, SFEData,
testthat (>= 3.0.0), vdiffr, xml2
GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
testthat, covr, knitr, rmarkdown, pkgdown
knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
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
knitr, ggforce, shapr (>= 1.0.1), airway, xgboost,
BiocGenerics, RUnit, S4Vectors
testthat, knitr, rmarkdown, ggplot2, randomForest, tidyr,
EnhancedVolcano, BiocStyle
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown,
MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal,
mgcv, rhdf5
arrow, BiocFileCache, BiocStyle, knitr, rmarkdown, tinytest
knitr, testthat, BiocStyle, yesno, terra,
SpatialFeatureExperiment, SFEData, tiff
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr,
pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq,
SpatialExperiment, spelling, testthat, withr
BiocStyle, BiocGenerics, knitr, pander, rmarkdown,
tweeDEseqCountData, edgeR, kableExtra, RUnit
knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq,
ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), tidyverse,
microbiome
BioPlex, biscuiteerData, bodymapRat, CLLmethylation,
CopyNeutralIMA, curatedAdipoArray, curatedAdipoChIP,
curatedMetagenomicData, curatedTCGAData, DMRcatedata,
DuoClustering2018, easierData, emtdata, epimutacionsData,
FieldEffectCrc, GenomicDistributionsData, GSE103322, GSE13015,
GSE62944, HDCytoData, HMP16SData, HumanAffyData, imcdatasets,
mcsurvdata, MetaGxBreast, MetaGxOvarian, MetaGxPancreas,
MethylSeqData, muscData, NxtIRFdata, ObMiTi, quantiseqr,
restfulSEData, RLHub, sesameData, SimBenchData,
SingleCellMultiModal, SingleMoleculeFootprintingData,
spatialDmelxsim, STexampleData, TabulaMurisData,
TabulaMurisSenisData, TENxVisiumData, tissueTreg,
VectraPolarisData, xcoredata
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
celldex, future, SingleR, SummarizedExperiment, tricycle
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