a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata
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 (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>=
0.22.1), BSgenome, IRanges
R (>= 3.5.0), 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 (>= 4.0.0), methods, utils, graphics, stats, generics
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 (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 3.5), GenomicRanges, cowplot, breakpointRdata
R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=
0.47.6), 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 (>= 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 (>= 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
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 (>= 4.0.0), 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 (>= 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), 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)
BiocParallel, ProtGenerics (>= 1.39.2), R (>= 4.5.0)
stats, utils, graphics, grDevices, datasets, base, biomaRt,
GenomicRanges, R (>= 3.1.0)
methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges,
Biostrings
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), 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 (>= 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 (>= 2.13.0), 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 (>= 0.47.6),
IRanges (>= 2.17.3), S4Arrays (>= 1.9.3), 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 (>= 4.0.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment
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, S4Vectors (>= 0.23.18)
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
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
R (>= 4.1.0), GenomicRanges, BiocFileCache
R (>= 4.0.0), 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)
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 (>= 4.0.0),
ggside (>= 0.4.0), Seqinfo, SummarizedExperiment (>= 1.39.1),
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 (>=
0.47.6), 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 (>= 3.6), Biobase, NanoStringNCTools, S4Vectors
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
R (>= 2.15.0), methods, Seqinfo, GenomicRanges (>= 1.61.1),
Rsamtools (>= 1.31.2)
circlize, GenomicRanges, graphics, R (>= 4.0)
R(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0)
Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr
R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2)
R (>= 3.5.0), methods, GenomicRanges, Biostrings, BSgenome,
data.table
R (>= 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 (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures,
AnnotationDbi
R (>= 4.0.0), grid, IRanges, GenomicRanges
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
InteractionSet, GenomicRanges, SummarizedExperiment, R (>=
4.1.0)
R (>= 4.1), igraph (>= 1.0.1), zen4R(>= 0.10.4),
MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
R (>= 2.15.0), methods, IRanges, GenomicRanges
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
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 (>= 3.6), methods, Biobase, BiocParallel
R (>= 3.5), methods, S4Vectors, IRanges, GenomicRanges,
MultiAssayExperiment, SummarizedExperiment,stats
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 (>= 0.47.6)
R(>= 4.2.0), Matrix, parallel, BiocParallel,
SummarizedExperiment, BiocGenerics, lme4, nnls
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (> 3.0.0),GenomicFeatures, ggplot2, Biobase
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 2.13.2), methods, graphics, fdrtool
R (>= 4.1), ExperimentHub, AnnotationHub
S4Vectors, adabag, GenomicRanges, R (>= 4.1)
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
SingleCellExperiment (>= 1.2.0), R(>= 3.5)
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 (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign
R (>= 3.5.0), GenomicRanges (>= 1.18.1), methods
R (>= 3.5.0), methods, grDevices, graphics, stats, utils,
GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools
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 (>= 4.1), MultiAssayExperiment (>= 1.8.3)
R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
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 (>= 3.6), 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 (>= 4.5.0), ggplot2, SummarizedExperiment
R (>= 4.5.0), sgdGMF, SingleCellExperiment, scuttle, scater
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 (>= 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 (>= 4.1.0), SummarizedExperiment (>= 1.3.81)
R (>= 4.1.0), methods, Rcpp, DelayedArray,
SummarizedExperiment
R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges
(>= 1.28.4), dplyr
R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges
R (>= 4.1), Biobase, SingleCellExperiment, MAST
biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb,
yeastExpData
R (>= 2.14.0), GenomicAlignments, affy, RPA
R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
methods, annotate
R (>= 3.2.0), 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
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 (>= 3.2), Biobase, rcellminerData (>= 2.0.0)
R (>= 4.4.0), SummarizedExperiment, methods
R (>= 2.6.0), methods, utils, graph, grid
R (>= 4.0.0), GenomicRanges, IRanges, methods
R (>= 3.0.2), methods, GenomicRanges, abind
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)
R (>= 2.6.0), BiocGenerics (>= 0.3.2), methods, utils
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 (>= 0.47.6), IRanges
R (>= 4.1.0), methods, utils, stats, stats4, BiocGenerics (>=
0.53.2)
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 (>= 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 (>= 4.0), SummarizedExperiment, ComplexHeatmap
R (>= 3.5.0), methods, baySeq (>= 2.9.0), S4Vectors, parallel,
GenomicRanges, ShortRead, stats
R (>= 3.1), AnnotationDbi, GO.db, annotate
R (>= 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 (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
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
R (>= 3.5.0), GenomicFeatures (>= 1.17.13), GenomicAlignments
(>= 1.1.22), Rgraphviz (>= 2.3.7)
R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines,
GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
R (>= 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 (>= 4.0.0), 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)
R (>= 4.1.0), Rsamtools (>= 1.31.2), Biostrings, ShortRead (>=
1.37.1), methods
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 4.4.0), SingleCellExperiment, ttservice (>= 0.4.0)
R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment,
ttservice
R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.5.0)
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 (>= 3.6.0), stats, utils, dplyr, methods
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
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 (>= 4.0.0), methods, BiocGenerics (>= 0.37.0),
MatrixGenerics, Seqinfo, GenomicRanges (>= 1.61.1),
SummarizedExperiment (>= 1.39.1), Rsamtools (>= 2.25.1)
R (>= 3.6.0), S4Vectors (>= 0.21.24), SummarizedExperiment (>=
1.13.0), GenomicRanges,
R (>= 3.6), methods, BiocGenerics, DelayedArray (>= 0.7.28)
R (>= 4.0), GenomicRanges, IRanges, ggplot2
R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel,
foreach
R (>= 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 (>= 3.4), methods, SparseArray, DelayedArray
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
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.schemas, methods, utils, S4Vectors, rhdf5 (>=
2.47.6), jsonlite, jsonvalidate, Rcpp
methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges
methods, S4Vectors, BiocGenerics, IRanges, Seqinfo, rhdf5
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
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
S7, stats, methods, igraph, Matrix, forcats, S4Vectors,
SummarizedExperiment, MultiAssayExperiment,
SingleCellExperiment, TreeSummarizedExperiment, rlang, ggplot2,
ggforce, patchwork, ggraph, tidygraph
ggplot2, ROCR, knitr, qvalue, locfit, methods, stats, utils,
plyr, DESeq2
igraph, Biobase, survival, MASS, stats, RColorBrewer
bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix,
pbapply, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tidyr, withr
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
cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0),
reticulate (>= 1.41.1), rlang, stats
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, BiocBaseUtils
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 (>=
3.5.0), IRanges, methods, readr, regioneR, reshape2, rlang,
rtracklayer (>= 1.69.1), S4Vectors (>= 0.23.10), stats, utils
multtest,qvalue,limma,DESeq2,edgeR,RColorBrewer, grDevices,
graphics, stats, utils, SummarizedExperiment
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 (>= 0.99.4), httr,
jsonlite, methods, rlang, stats, tibble, tidyr, utils
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
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,
jsonlite, lattice, latticeExtra, limma, methods, RColorBrewer,
setRNG, stats, utils, vsn (>= 3.23.3), XML, svglite
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
SummarizedExperiment, spsUtil, lubridate, survival, glmnet,
siggenes, survcomp, scales, ROCR, ggplot2, grDevices, graphics,
utils, Rdpack
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
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
BiocGenerics, BiocParallel, data.table, dplyr, tidyr,
GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
aricode, BiocParallel, data.table, dbscan, SpatialExperiment,
SingleCellExperiment, SummarizedExperiment, S4Vectors, stats,
Matrix, MatrixGenerics, mclust, igraph, irlba, leidenAlg (>=
1.1.0), utils, uwot, RcppHungarian, GenomeInfoDb
magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap,
ggplot2, logistf, limma, stats, igraph, utils, data.table,
S4Vectors, SummarizedExperiment
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
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats,
BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat
scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2,
RColorBrewer, scales, SummarizedExperiment
stats, RANN, dplyr, SummarizedExperiment, methods
Rcpp (>= 1.0.4.6), stats, methods, purrr, scater, scran,
SummarizedExperiment, coda, rhdf5, S4Vectors, Matrix, magrittr,
assertthat, arrow, mclust, RCurl, DirichletReg, xgboost (>=
3.0.0), 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, tiledb, TileDBArray, DelayedArray, Rcpp
limma, AnnotationDbi, stats4, reshape2, GenomicRanges,
IRanges, methods, ggplot2, BeadDataPackR
logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp, abind,
stats, graphics, utils, methods, dixonTest, ids
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
BiocParallel, Biostrings, GenomicRanges, IRanges, Matrix,
matrixStats, methods, S4Vectors, stats
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, jsonlite, utils
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
BiocGenerics, pak, 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, commonmark, graph, httr2, knitr, methods,
rvest, stringdist, tools, utils, xml2
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
shiny, jsonlite, DT, shinyjs, shinythemes
stats, utils, futile.logger, parallel, snow, codetools
BiocBaseUtils, BiocPkgTools (>= 1.27.6), BiocManager, bsicons,
bslib, dplyr, DT, ggplot2, gh, htmlwidgets, plotly, rmarkdown,
shinybiocloader, shinyjs, tibble, tidyr, utils, whisker, yaml
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
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>=
2.25.1)
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), jsonlite,
lgr, lifecycle, methods, openssl, plyr, progress, rappdirs,
sched (>= 1.0.1), sqlq, 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
methods, BiocGenerics, Biobase, S4Vectors, IRanges, Seqinfo,
GenomicRanges, SummarizedExperiment, rtracklayer, parallel,
betareg, lokern, Formula, globaltest
grid, stats, grDevices, utils, circlize, viridis,
RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla
SummarizedExperiment, SingleCellExperiment, ggplot2, viridis,
patchwork, Matrix, scater, methods, rlang, BiocParallel, boot,
dplyr, mgcv, stats, MatrixGenerics, Seurat (>= 4.0.0), lsa
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
CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
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, utils
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
GenomicRanges, methods, rlang, S4Vectors, utils
utils, stats, matrixStats, XVector, Rsamtools (>= 2.25.1)
utils, stats, Biobase, S4Vectors (>= 0.47.6), GenomicRanges
(>= 1.61.1), BiocIO, rtracklayer (>= 1.69.1)
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
AnnotationDbi, AnnotationFilter, AnnotationHub, biomaRt,
BiocGenerics, Biostrings, BSgenome, dplyr, ensembldb,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2, IRanges,
lifecycle, magrittr, Matrix, methods, plyranges, Rcpp,
S4Vectors, stats, stringr, tibble, tidyr, utils, zeallot
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
BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR,
data.table, formula.tools, Seqinfo, GenomicAlignments (>=
1.45.1), GenomicFeatures (>= 1.61.4), GenomicRanges (>=
1.61.1), ggplot2 (>= 4.0.0), gtools, IRanges (>= 2.18.0),
KernSmooth, Matrix, 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
checkmate, dplyr, ggplot2, magrittr, openxlsx, scales,
SummarizedExperiment, tidyr
ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr,
DT, MesKit, maftools, data.table, utils, stats, methods, tidyr
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, NMF,
spatstat.random, gtools, SingleCellExperiment,
SpatialExperiment
readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson,
rmarkdown
circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel, ggridges,
graphics, grDevices, grid, gridExtra, Matrix, matrixStats,
methods, nnls, RColorBrewer, reshape2, Rtsne,
SummarizedExperiment, S4Vectors, scales, scater, stats
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
R6, ggraph, tidygraph, ggplot2, patchwork, cowplot, magrittr,
igraph, rlang, grDevices, coda, graphics, stats, TCGAbiolinks,
BiocParallel
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
stats, S4Vectors, utils, methods, Matrix,
SummarizedExperiment, SingleCellExperiment, Rtsne, graphics,
grDevices, gtools, RColorBrewer, ape, Rmpi, irlba, Rcpp, Rdpack
(>= 0.7)
Rcpp, sparseMatrixStats, stats, BiocParallel, irlba,
SingleCellExperiment, Matrix, SummarizedExperiment
plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph,
scatterpie, circlize, ComplexHeatmap, tibble, grid, stringr,
ggtext, ggh4x, patchwork, RColorBrewer, scales, viridis,
grDevices, graphics, stats, methods
matrixStats, SeuratObject, Seurat, stats, BiocParallel,
ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment,
SummarizedExperiment, methods
MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang,
BiocGenerics, S4Vectors, readr, tibble, DelayedArray
plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable,
grDevices, graphics, matrixStats, doParallel, digest, methods,
reshape2, S4Vectors, data.table, Rcpp, RcppEigen, uwot,
enrichR, SummarizedExperiment, MCMCprecision, ggrepel, Rtsne,
withr, scater (>= 1.14.4), scran, 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
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
methods, Matrix, BiocParallel, SingleR, Seurat (>= 4.0.0),
utils, stats, parallel, progress, ggplot2, data.table,
magrittr, graphics, RMTstat, sparsesvd, cluster, skmeans,
MLmetrics, tibble, lsa, nnls, SingleCellExperiment, entropy,
irlba, aricode
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
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
Biobase, CGHbase, CGHcall, methods, stats, utils
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, 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 (>= 0.2.0)
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
graphics, stats, utils, methods, survival
data.table, methods, S4Vectors, MsCoreUtils (>= 1.7.5),
Spectra
Biobase (>= 2.17.8), graphics, grDevices, methods, stats,
IRanges, rtracklayer, GenomicRanges
shiny, colourpicker, shinyjs, rtracklayer, shinyFiles,
shinyhelper, shinyWidgets, shinydashboardPlus, flexdashboard,
shinycssloaders, Matrix, plotly, shinydashboard, colorRamps,
kableExtra, viridis, batchelor, BiocParallel, parallel,
Rsamtools, ggplot2, ggrepel, gggenes, gridExtra, qualV,
stringdist, stringr, fs, qs2, 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
XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx,
igraph, circlize, graph, stats, utils, grDevices, graphics,
methods, biomaRt, rJava
dplyr, ggplot2, glue, tidyr, igraph, networkD3, visNetwork,
ggcorrplot, purrr, ggraph, stats, utils, maftools, assertthat,
tidygraph, expm, Matrix
dplyr, magrittr, readr, rtracklayer, stringr, stringi, DESeq2,
edgeR, GenomicRanges, IRanges, seqinr, R.utils, reshape2,
ggplot2, utils, rlang, S4Vectors, stats, GenomeInfoDb,
universalmotif, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
Biostrings, gwascat, BSgenome,
SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>=
1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid,
dbscan, 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
FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach,
dplyr, fpc, mice, modeest, flock, networkD3, methods,
ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices,
ggplot2, grid, stats, utils, pbapply
methods, igraph, ggplot2, scales, BiocParallel, graphics,
stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat,
SeuratObject, SingleCellExperiment, ggdendro
colorRamps, dplyr, e1071, factoextra, ggplot2, grDevices,
grid, Matrix, methods, purrr, reshape2, scales, stats, tibble,
SingleCellExperiment, SummarizedExperiment, igraph, VGAM,
scuttle
aisdk, AnnotationDbi, dplyr, enrichit (>= 0.1.1), enrichplot
(>= 1.9.3), ggplot2, GO.db, GOSemSim (>= 2.27.2), gson (>=
0.0.7), httr, igraph, jsonlite, magrittr, methods, plyr,
qvalue, rlang, stats, tidyr, utils, yulab.utils (>= 0.2.3)
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
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, msa, Biostrings, RADanalysis,
ggseqlogo, rBLAST
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
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
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
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
checkmate, dplyr, flowCore, flowDensity, ggcyto, ggplot2 (>=
3.5.2), methods, ParallelLogger, reshape2, rlang, stats,
tibble, tidyr, utils
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
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
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
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
stats, methods, grDevices, Matrix, ggplot2, ggrepel, ggdist,
ggthemes, graphics, parallel, parallelly, tibble, tidyr, dplyr,
BiocSingular, parallelDist, ComplexHeatmap, circlize, grid,
scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat,
dendextend, zeallot, assertthat, withr, SummarizedExperiment,
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, rlang
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
rlang, methods, dplyr, doFuture, doParallel, foreach, future,
future.apply, pROC, progress, progressr, stats, tibble, tidyr,
TreeSummarizedExperiment, ggplot2, GUniFrac, magrittr,
parallel, withr, SummarizedExperiment, caret, ranger, utils,
graphics, grDevices
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
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
AnnotationDbi, BiocParallel, Biostrings, methods,
GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices,
grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>=
0.9.38), utils
methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils,
lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats,
VGAM, parallel, graphics, limma, beanplot
Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods,
S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod,
utils
WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
dplyr, ggplot2, henna, kerntools, methods, paletteer, qs2,
reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment,
spatstat.utils, stats, textshape
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
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
stats, pscl, qvalue, BiocParallel, methods, knitr,
SpatialExperiment, SummarizedExperiment
AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats,
rappdirs, BiocFileCache
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
CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, matrixStats,
randomForest, rmarkdown, SingleCellExperiment, stats,
SummarizedExperiment, ssc, S4Vectors, graphics, methods,
mixtools
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
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
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
ggplot2, ggrepel, dplyr, tibble, stringr, tools, fs, rlang,
BiocParallel, AnnotationHub, DBI, ensembldb, GenomeInfoDb,
IRanges, GenomicRanges, S4Vectors, rtracklayer, limma, NOISeq,
BioVenn, clusterProfiler, enrichplot, forcats, scales,
colorspace, ggnewscale, methods, stats, igvShiny, shiny, DT,
dbscan, circlize, ComplexHeatmap, patchwork, splines
BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods,
miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam,
stats, SummarizedExperiment, uwot, RANN
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
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
bayesplot, cowplot, dplyr, GenomicRanges, ggplot2, IRanges,
magrittr, Matrix, matrixStats, MEDIPS, methods, purrr, R.utils,
Rcpp, RcppParallel, rlang, rstan, rstantools, S4Vectors,
SummarizedExperiment
methods, DBI, S4Vectors, IRanges, XVector
methods, Matrix, quadprog(>= 1.5-5), GenomicRanges, stats,
GenomicFeatures, Biostrings, BiocGenerics, S4Vectors, plyr,
utils, graphics, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
SummarizedExperiment, ggseqlogo, gridExtra, data.table,
Seqinfo, readxl
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, BiocParallel,
DelayedMatrixStats, dplyr, ExperimentHub, ggplot2, ggrepel,
graphics, grDevices, MatrixGenerics, methods, purrr, rafalib,
reshape2, S4Vectors, scran, SingleCellExperiment, spatialLIBD,
stats, stringr, SummarizedExperiment, tibble, utils
SummarizedExperiment, methods, S4Vectors, utils, DESeq2,
edgeR, limma, writexl, 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
graph, KEGGgraph, lattice, mvtnorm, R.methodsS3, RBGL,
Rgraphviz, rrcov, NCIgraph
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)
DESeq2, dplyr, reshape2, limma, SummarizedExperiment, ggplot2,
matrixStats, stats
IRanges, GenomicRanges, SummarizedExperiment, ggplot2, DESeq2,
tictoc
matrixStats, stats, truncdist, base64enc, ggplot2, KernSmooth,
matrixcalc, sva, dendextend, fitdistrplus, pbapply, psych,
magrittr, graphics, grDevices, S4Vectors
stats, MASS, Matrix, ggplot2, gridExtra, methods
MatrixGenerics, BiocGenerics, class, Seqinfo, IRanges, Matrix,
SummarizedExperiment, demuxmix, methods, KernelKnn, dplyr
flexmix, hexbin, pbapply, sparseMatrixStats,
SpatialExperiment, stats, SummarizedExperiment, parallel,
Matrix, dbscan, methods
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)
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,
scales, scatterplot3d
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
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, Rsamtools, GenomicRanges,
GenomicAlignments, Biostrings, BSgenome, BiocManager,
S4Vectors, IRanges, InteractionSet, stringr, inflection,
BiocParallel, Seqinfo, GenomeInfoDb
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, Seqinfo,
methods, mvtnorm, stats, parallel
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
scales, ggnewscale, SummarizedExperiment, dplyr, rlang,
ggforce, geomtextpath, ggplot2
biomaRt, data.table, utils, stats, Biostrings, pwalign,
SummarizedExperiment, VariantAnnotation, AnnotationDbi,
Seqinfo, 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, enrichit (>= 0.0.4), ggplot2, GOSemSim (>=
2.37.1), methods, reshape2, utils, yulab.utils (> 0.2.2)
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
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
tibble, rlang, dplyr, purrr, readr, stringr, stats, lifecycle,
S4Vectors, httr2, curl, DFplyr
utils, RSQLite, UniProt.ws, biomaRt,ensembldb,
BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
ape, Biostrings, data.table, DECIPHER, DESeq2, dplyr, edgeR,
flextable, ggalluvial, ggnewscale, ggplot2, ggpubr, ggraph,
ggrepel, ggridges, ggtree, ggtreeExtra, graphics, grDevices,
igraph, limma, matrixStats, methods, microbiome, officer, grid,
reshape2, patchwork, phangorn, phyloseq, randomForest,
RColorBrewer, rlang, S4Vectors, scales, stats, tibble, tidyr,
SummarizedExperiment, TreeSummarizedExperiment, utils, msa,
xml2, ggstar
zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors,
rlang, grDevices, stats, utils
BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr,
tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode
Gviz, Biostrings, rtracklayer, GenomicAlignments,
GenomicRanges, ggsci, igraph, rlang, scales, stringr, dplyr,
tibble, tidyr, purrr, methods, grDevices, stats, utils, vctrs
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
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
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
BiocGenerics, Biostrings, BSgenome, BiocParallel,
BiocFileCache, Seqinfo, 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, hash, S4Vectors, dplyr, ggplot2,
graph, magrittr, methods, pheatmap, graphics, utils, purrr,
tidyr, stats
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
aplot (>= 0.2.1), DOSE, dplyr, enrichit, ggfun (>= 0.1.7),
ggnewscale, ggplot2 (>= 3.5.0), ggrepel (>= 0.9.0), ggtangle
(>= 0.0.9), ggtree, GOSemSim (>= 2.37.2), graphics, grid,
igraph, methods, purrr, RColorBrewer, reshape2, rlang,
scatterpie, stats, tidydr, utils, yulab.utils (>= 0.2.2)
gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot,
igraph, reshape2, 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, genefilter
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
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, checkmate, entropy, lifecycle,
methods, scran, scuttle, stats, utils, AnnotationHub,
GenomeInfoDb, GenomicRanges, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
motifmatchr, IRanges, scrapper
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
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)
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, rlang
stats, ggplot2, igraph, SummarizedExperiment, S4Vectors, utils
csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb,
glue, ggrepel, InteractionSet, IRanges, matrixStats, methods,
patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer,
S4Vectors, 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, ReactomePA, enrichplot
methods, shiny, stats, IRanges, Biostrings, ShortRead, DT,
S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
methods, S4Vectors, IRanges, GenomicRanges, GenomeInfoDb, Rcpp
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
methods, igraph, Matrix, KEGGREST, plyr, stats, graphics,
utils
tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect,
tibble, purrr, readr, stringr, httr2, rvest, progress,
BiocFileCache, shiny, ggplot2
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
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
flowCore, car, caTools, knitr, rmarkdown, minpack.lm, shiny,
methods, graphics, 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
Biostrings, data.table, dplyr, future, future.apply,
GenomeInfoDb, GenomicRanges, ggh4x, ggplot2, ggseqlogo,
IRanges, purrr, RColorBrewer, readr, rlang, Rsamtools (>=
2.4.0), S4Vectors, VariantAnnotation, scales, stringr, tibble,
tidyr
Rcpp, ShortRead, Biostrings, RcppParallel, edlibR, stringfish
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
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
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
data.table, igraph, BioNet, plyr, methods, XML, sna,
intergraph, network, ggnetwork, scales, grid, ggplot2, mwcsr,
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, ggplot2, SummarizedExperiment, grid,
rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats,
utils, parallel, MatrixGenerics, methods
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
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, qs2
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, qs2, utils
tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray
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
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, cigarillo
(>= 0.99.2)
S4Vectors, Seqinfo, InteractionSet, methods, plyranges,
plyinteractions
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
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
xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
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
grDevices, graphics, methods, stats, utils, dbscan,
fastcluster, matrixStats
bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, cowplot, dplyr,
DT, ggbeeswarm, ggplot2, ggrepel, ggh4x, htmltools, magrittr,
pals, RColorBrewer, rlang, R.utils, shiny, shinyjs, S4Vectors,
SummarizedExperiment, tibble, tidyselect, tidyr, yaml
DESeq2, dplyr, edgeR, ggrepel, glue, janitor, limma, magrittr,
methods, purrr, rlang, scales, stats, stringr, tibble, tidyr
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, cli, dplyr, ggfun (>= 0.1.7), ggiraph (>= 0.9.1),
ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang,
scales, stats, tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0),
utils, yulab.utils (>= 0.2.3)
ggplot2 (>= 4.0.0), utils, rlang, ggnewscale, stats, ggtree,
tidytree (>= 0.3.9), cli, magrittr, yulab.utils
interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools,
rlang, tibble, tidyr, tidyselect, stats
KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise,
cachem, jsonlite, rvest
DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel,
stats, methods, graphics, grDevices, xtable, tools, brew,
stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML
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, RColorBrewer, pheatmap,
vegan, cluster, boot, permute
igraph, SummarizedExperiment, pbapply, car, ggplot2, rlang
S4Vectors (>= 0.17.25), IRanges (>= 2.13.12), BiocGenerics (>=
0.25.1), rtracklayer (>= 1.39.7), GenomicFeatures (>= 1.31.3),
Biostrings, VariantAnnotation (>= 1.25.11), tools, Biobase,
BSgenome, GenomicAlignments (>= 1.15.6), BiocParallel, BiocIO
grid, gridBase, Rsamtools, ComplexHeatmap, BiocGenerics,
Biostrings, Seqinfo, methods, GenomicAlignments,
GenomicFeatures, IRanges, rtracklayer, pracma, colorspace,
S4Vectors
AnnotationDbi, grid, grDevices, GO.db, igraph, methods,
plotly, rlang, stats, scales, vctrs
AnnotationDbi, dendextend, doParallel, foreach, parallel,
org.Hs.eg.db, GO.db, Rcpp, stats, graphics,
MultiAssayExperiment, IRanges, S4Vectors
AnnotationDbi, DBI, digest, GO.db, methods, rlang, stats,
utils, yulab.utils (>= 0.2.3)
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
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
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats,
utils, graphics, rlang, lifecycle, purrr, dir.expiry
graphics, grDevices, reshape2, stats, utils
GenomicAlignments, BSgenome, Rsamtools, rtracklayer, MASS,
parallel, Seqinfo, SummarizedExperiment, stats, utils
SummarizedExperiment, nloptr, fGarch, methods, BiocParallel,
graphics
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)
circlize (>= 0.4.8), GetoptLong, grDevices, utils
ComplexHeatmap, eulerr, GenomicRanges, IRanges, lubridate,
methods, rtracklayer, 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
cluster, dplyr, ggplot2, ggrepel, grDevices, henna, liver,
rlang, scLang, stats, text2vec,
Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel,
methods, matrixStats
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
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
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
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
Rcpp (>= 1.0.0), utils, stats, Matrix, HiCExperiment
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, utils, stringr,
whisker, purrr, rlang
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
ggplot2, ggforce, R6, magrittr, dplyr, purrr, stats, stringr,
scales, rlang, httr, openxlsx, htmltools, reshape2, reactable,
msigdbr, kableExtra, rmarkdown, igraph, visNetwork, shiny,
BiocStyle
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
fields, ggplot2, truncnorm, tidyr, data.table, dplyr,
grDevices, graphics, stats, utils, rlang
shiny (>= 0.9.1.9008), shinydashboard, reshape2, ggplot2 (>=
3.4.0), scales, ROCR, dplyr, DT, limma, methods, UpSetR, utils,
rlang, prompter
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
BiocBaseUtils, data.table, dplyr, grDevices, methods, rlang,
S4Vectors, SpatialExperiment, SummarizedExperiment
STRINGdb, pwalign, igraph, graphics, utils, seqinr
immReferent, Matrix, matrixStats, methods, Rcpp,
SingleCellExperiment, stats, stringr, utils
Biostrings, httr, jsonlite, methods, rvest, tibble, yaml
methods, stats, graphics, grid, lattice, grDevices
ggplot2, httr, jsonlite, patchwork, UniProt.ws
stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
xml2, maps, rlang
config (>= 0.3.2), golem (>= 0.4.1), shiny (>= 1.7.5),
ComplexHeatmap, DT, RColorBrewer, WGCNA, corrplot, cowplot,
dynamicTreeCut, ggplot2, glassoFast, impute, purrr, stringr,
tidyr, visNetwork, shinyBS, httr, dplyr, stats, iModMixData,
SummarizedExperiment, ExperimentHub (>= 2.99.0)
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 (>= 3.0.0)
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
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
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
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
Rcpp, Matrix, data.table, methods, pbapply, parallelly,
stringfish,
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2 (>=
3.4.0), 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
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
BiocNeighbors, BiocParallel, Matrix, bluster, data.table,
methods, processx
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
survival, tools, methods, pracma, doParallel, foreach,
parallel, SummarizedExperiment, S4Vectors
sesameData, ExperimentHub, AnnotationHub, dplyr, methods,
rlang, GenomicRanges, IRanges, reshape2, S4Vectors, stats,
stringr, utils, ggplot2, ggrepel, tibble, wheatmap, magrittr,
readr
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
data.table, vcfR, tidyr, stats, utils, graphics, grDevices,
ggplot2, gridExtra, survival, survminer, RColorBrewer,
Biostrings
BiocGenerics (>= 0.25.1), Seqinfo, httr, Matrix
stats, gplots, readr, tibble, gplots, methods, ggplot2, dplyr,
stringr, tidyr, SummarizedExperiment, BiocStyle
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
methods, corpcor, RSpectra, BEDMatrix, genio
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
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
dplyr, ggnewscale, ggplot2, magrittr, methods, rlang,
SummarizedExperiment, MKmisc, matrixTests
Biobase, graphics, grDevices, methods, stats
pheatmap, wordcloud, RColorBrewer, data.table, methods,
grDevices, stats, graphics, GenomicRanges, BiocParallel,
S4Vectors
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
reshape2, utils, stats, methods
stats, utils, SummarizedExperiment, SingleCellExperiment,
BiocBaseUtils, jsonlite
methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase
BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
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,
reformulas
BiocParallel, DelayedArray, WGCNA, ff, data.table,
dynamicTreeCut, Maaslin2, plyr, stats, psych, logging, methods,
utils
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy, pheatmap
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 (>= 3.0.0), parallel, pbapply, reshape2, gtools,
utils, stats, cowplot, methods, grDevices, graphics
circlize, edgeR, ComplexHeatmap, ggh4x, ggplot2, ggpubr, grid,
gridExtra, pROC, RColorBrewer, reshape2, rstatix, scales,
stats, utils, fgsea, limma, ggrepel, effectsize, msigdbr,
tibble
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
Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr,
stringr, abind, methods, parallel, reshape2, stats, stats4,
graphics, utils, SummarizedExperiment(>= 1.5.3), progress,
Matrix
AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr,
graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb,
org.Hs.eg.db, patchwork, SeuratObject (> 5.0.0),
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
CytoMDS (>= 1.3.5), rlang, ggplot2, plotly, shiny, shinyjs,
methods
GenomicAlignments, GenomicRanges, IRanges, Biostrings,
DNAcopy, Rsamtools, parallel, stringr
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
Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2,
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
enrichit, gson, AnnotationDbi, GOSemSim (> 2.37.0), methods,
utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5)
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 (>= 1.21.5), 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
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
utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats,
clusterProfiler, RecordLinkage, RCy3
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
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
dplyr, methods, httr, scales, ggthemes, utils, rlang, stats,
ggplot2
mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors,
urltools, utils
ape, BiocGenerics, BiocParallel, Biostrings, bluster,
DECIPHER, decontam, DelayedArray, DelayedMatrixStats,
DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics,
methods, ecodive, rlang, S4Vectors, scater, 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, patchwork, 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)
enrichit, 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)
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
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
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
DBI, RSQLite, stringr, sqldf, plyr, methods
WGCNA, flashClust, dynamicTreeCut, GFA, igraph, RColorBrewer,
grid, MCL, fabia, NMF, BicARE, isa2, methods, rJava, Biobase,
PMA, stats, dbscan, mclust, SOMbrero, ppclust, Rcpp, utils,
SummarizedExperiment, GSEABase, org.Hs.eg.db, clusterProfiler,
ReactomePA, DOSE, MatrixCorrelation, energy
purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap,
reshape2, corrplot, grDevices, graphics, stats, utils,
data.table, R.utils, viridis
BiocParallel, MCMCpack, Matrix, S4Vectors, methods,
rtracklayer, car, mvtnorm, SummarizedExperiment,
SingleCellExperiment, BiocGenerics, stats, rlang
assertthat, caret, deldir, digest, distances, dplyr (>=
1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr,
ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats,
stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr
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, Matrix,
graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods,
ggplot2
AnnotationDbi, ape, circlize, clusterProfiler, ComplexHeatmap,
ggplot2, ggtree, magrittr, org.Hs.eg.db, ReactomePA, scales
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, ggrepel, BiocParallel, utils, rgl,
rlang
gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats, magrittr,
SummarizedExperiment
AnnotationDbi, gplots, graphics, stats, utils
testthat, VennDiagram, pamr, methods, DESeq2, edgeR, limma,
Biobase, SummarizedExperiment, plyr, foreach, utils, sSeq,
xtable
GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
maaslin3, 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
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,
GenomeInfoDb, 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, 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
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
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, utils, MsCoreUtils (>= 1.23.8)
ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges,
MsCoreUtils, methods, stats, data.table
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
softImpute, methods, stats, graphics, pdist, reticulate,
scran, data.table, FNN, matrixStats, limma, mvtnorm, tidyr,
dplyr
data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr,
org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils
QFeatures, limma, SummarizedExperiment, magrittr, rlang,
dplyr, purrr, stats, tidyr, stringr, ggplot2, ggseqlogo,
heatmaply, readr, rstatix, tibble, ggpubr, imputeLCMD
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite,
BiocFileCache
stats, methods, lme4, purrr, BiocParallel, Matrix, MASS,
limma, SummarizedExperiment, MultiAssayExperiment, codetools,
matrixStats, ggplot2, assertthat, dplyr, grDevices, utils,
rlang
MSstatsConvert, data.table, checkmate, MASS, htmltools, limma,
lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel,
gplots, plotly, marray, stats, grDevices, graphics, methods,
statmod, parallel, rlang
arrow, DBI, dplyr, MSstats, MSstatsConvert, readr, sparklyr,
utils
httr, jsonlite, r2r, tidyr, htmlwidgets, grDevices, stats,
text2vec, stopwords, xml2, rentrez
data.table, log4r, methods, checkmate, utils, stringi, Rcpp,
parallel
dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
MSstatsConvert, data.table, Biostrings, MSstatsPTM (>= 2.12.0),
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 (>= 1.19.1), MSstats, data.table,
Rcpp, Biostrings, checkmate, ggrepel, plotly, htmltools, rlang
BiocParallel, ggplot2, dplyr, stats, parallel, data.table
shiny (>= 1.5.0), shinyBS, shinyjs, shinybusy, dplyr, ggplot2,
plotly, data.table, Hmisc, shinyFiles, MSstats,MSstatsBig,
MSstatsTMT, MSstatsPTM, MSstatsConvert, gplots, marray, DT,
readxl, ggrepel, uuid, utils, stats, htmltools, methods, tidyr,
grDevices, graphics, mockery, MSstatsBioNet, shinydashboard,
arrow, tools, MSstatsResponse, stringr, httr
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
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
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
methods, S4Vectors, data.table, grid, dplyr, tidyr,
matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize,
mashr, grDevices
stringr, readr, WGCNA, magrittr, dplyr, reshape2, data.table,
patchwork, scales, igraph, flashClust, ggplot2, dcanr, cowplot,
ggrepel, methods, SummarizedExperiment, ggraph, tidyr
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
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
BiocGenerics, Biostrings, BSgenome, data.table, dplyr,
GenomicRanges, ggplot2, here, IRanges, ggdendro, magrittr,
methods, plyranges, rlang, S4Vectors, Seqinfo, stringr,
SummarizedExperiment, tidyr, VariantAnnotation
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST,
ComplexHeatmap, stats, utils
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
BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes,
grDevices, IRanges, methods, pheatmap, RColorBrewer, stats,
utils
DESeq2, mgcv(>= 1.8-24), BiocParallel, genefilter, methods,
stats,
graph, KEGGgraph, methods, RBGL, RCy3, R.oo
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,
R.utils
glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust,
parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer
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
BiocGenerics, BiocParallel, dplyr, futile.logger, methods,
openxlsx, S4Vectors, scales, stringr, tidyr, utils
BiocGenerics, BiocParallel, broom, dplyr, methods, notame,
stats, tibble, tidyr, utils
BiocGenerics, cowplot, devEMF, dplyr, ggbeeswarm, ggdendro,
ggrepel, grDevices, limma, methods, notame, pcaMethods, qpdf,
Rtsne, scales, stringr, stats, tibble, tidyr, utils
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
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, Matrix, S4Vectors, SummarizedExperiment,
DelayedArray, MatrixGenerics, BiocSingular, BiocParallel,
beachmat, ggplot2, methods, QFeatures
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
htmltools, shinydashboard, 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
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
biomaRt, grDevices, graphics, utils, methods,
Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
smatr, ggplot2, ggrepel, stringr
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
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, repmis, ggtree, tools, magrittr
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
data.table, methods, openxlsx, R.utils, vcfR,
VariantAnnotation, SummarizedExperiment, BiocGenerics,
GenomeInfoDb
stats, utils, dplyr, rlang, iterators, parallel, foreach,
doParallel, qvalue, rtracklayer, ggplot2, GenomicRanges,
S4Vectors
circlize, clusterProfiler, ComplexHeatmap, dplyr, fgsea,
ggplot2, ggraph, ggrepel, grid, igraph, patchwork, 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
lattice, grDevices, cowplot, methods, reshape2, stats, Matrix,
DelayedMatrixStats, DelayedArray, beachmat (>= 2.21.1),
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
tidyr, dplyr (>= 1.1.2), IRanges, GenomicRanges, tidyselect,
purrr, readr (>= 2.1.2), tibble (>= 3.2.1), rlang, stringr,
here, stats, Seqinfo
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
ggplot2, protolite, Biobase, GEOquery, 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,
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
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
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, bsplus, colourpicker,
data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra,
htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast,
scattermore, shiny, 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
Hmisc, igraph, patchwork, scales, utils, cluster, umap, tsne,
kernlab, vegan, dbscan, grDevices, stats, methods,
SummarizedExperiment, ggplot2
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
ggplot2, ggpubr, grid, gridExtra, lmerTest, mixOmics,
performance, scales, stats, Rdpack
Seqinfo, BiocGenerics, GenomicRanges, IRanges, S4Vectors,
rlang, dplyr, tibble, tidyselect, methods, utils
methods, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0),
rtracklayer, GenomicAlignments, Seqinfo, Rsamtools, S4Vectors
(>= 0.23.10), utils
dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect,
vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods
stats, impute, pcaMethods, missForest, ggplot2, methods,
SummarizedExperiment, S4Vectors, matrixStats, grDevices,
reshape2, utils
dplyr (>= 1.1.0), shiny, bslib, shinyFiles, plotly,
rtracklayer, reshape2, ggseqlogo, ggplot2, seqinr, magrittr,
rlang, utils, stringr, BiocFileCache
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
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
Biostrings, ggplot2, methods, assertthat, glue, magrittr,
dplyr, rlang, ShortRead, readr, shiny, purrr
dplyr, plyr, Biostrings, data.table, gridExtra, seqinr,
R.utils, reshape2, vioplot, stringr, plotrix, gplots, ggplot2,
ggrepel, anota2seq, memes, GenomicRanges, IRanges, WriteXLS,
randomForest, igraph, Boruta, ROCR, caret, msigdb,
ExperimentHub, AnnotationHub, GSEABase, fgsea, org.Hs.eg.db,
org.Mm.eg.db, RColorBrewer, httr2, rvest, umap, clusterProfiler
(>= 4.18.4), gage, withr, grDevices, graphics, methods, stats,
utils, tools, BiocFileCache, curl
cubature, doParallel, evmix, foreach, magrittr, methods,
parallel, purrr, stats, truncdist, vegan, VGAM
pheatmap, ggplot2, RColorBrewer, grDevices,
SummarizedExperiment, limma
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
Biobase, QFeatures, SummarizedExperiment, S4Vectors, corrplot,
dplyr, data.table, ggfortify, ggplot2, gridExtra, grDevices,
lazyeval, lubridate, limma, magrittr, matrixStats, methods,
pheatmap, preprocessCore, purrr, pvca, RColorBrewer, reshape2,
rlang, scales, stats, sva, tidyr, tibble, tools, utils,
viridis, wesanderson, WGCNA
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, utils, methods, BiocGenerics, SummarizedExperiment,
S4Vectors, extraDistr
SingleCellExperiment, methods, cluster, stats, limma, NMF,
ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2,
viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2,
cowplot, ggrepel, umap, tsne
bnlearn, reshape2, sva, stats, utils, Biobase
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
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
MASS, pscl, arrangements, hitandrun, assertthat, dplyr,
BiocParallel
Biostrings, graphics, gtools, methods, stats, utils, HMMcopy,
rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges,
limma, Seqinfo, BiocGenerics, grDevices, zoo, BiocParallel,
S4Vectors
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
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
dplyr, glmnet, graphics, magrittr, Matrix, matrixStats, rlang,
Seurat, stats, SummarizedExperiment
curl, jsonlite, lifecycle, paws.storage, R.utils, utils
dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools,
BiocManager, BiocParallel, rawrr (>= 1.15.5), rlang, reshape2,
scales, shiny (>= 1.5), stats, utils
Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach,
grDevices, stats, utils
EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats
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
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
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
AnnotationDbi, enrichplot, enrichit, 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
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, data.table, GenomicRanges, httr, Matrix,
methods, R.utils, rtracklayer, S4Vectors, sessioninfo, tools,
utils
WGCNA, ica, moments, clusterProfiler, msigdbr, RColorBrewer,
car, lme4, lmerTest, pheatmap, biomaRt, stats, grDevices,
BiocParallel, ggplot2, patchwork, BiocGenerics, S4Vectors
askpass, httr2, jsonlite, jsonvalidate, keyring, readxl,
rlang, stringr, tibble, tidyr, validate, yaml
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
Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5,
cluster, data.table, GenomeInfoDb, GenomicRanges, glmnet,
ggplot2, gridExtra, IRanges, lsa, MutationalPatterns, nnls,
parallel, reshape2, S4Vectors, RhpcBLASctl, survival
ggplot2, limma, methods, pROC, ranger, stats,
SummarizedExperiment, sva, AnnotationDbi, umap, scales, utils,
S4Vectors, digest, mgcv, Matrix, glmnet, xgboost, patchwork
utils, Seqinfo, data.table, IRanges, GenomicRanges, parallel,
Rsamtools
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
dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors,
tidyr, tools, yaml
Rsamtools, IRanges, S4Vectors, baySeq, Seqinfo, seqLogo
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
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
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
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr,
magrittr, rlang, edgeR, foreach, mice
GenomicRanges, IRanges, Rsamtools, foreach, zoo, ggplot2,
dplyr, magrittr, tidyr, ComplexHeatmap, circlize, dendextend,
DescTools, ggpubr, MASS, SummarizedExperiment, BiocParallel
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
Rcpp, stats, Biobase, methods, BiocParallel, lme4, survival
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
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
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, SKAT,
CompQuadForm, survey
Rcpp, BiocGenerics, BiocParallel, MatrixGenerics, methods,
S4Vectors, scuttle, SingleCellExperiment, SummarizedExperiment
rJava, Biostrings, IRanges, utils, stats, cluster, binom
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
Biostrings, pwalign, GenomicRanges, IRanges, data.table,
BiocParallel, methods, Seqinfo, S4Vectors, ggplot2, stats,
stringi, utils, graphics, grid, seqLogo, cowplot
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
stats, utils, methods, Matrix, BiocGenerics, S4Vectors,
SummarizedExperiment, MatrixGenerics, SparseArray,
DelayedArray, beachmat, BiocNeighbors, BiocSingular,
BiocParallel, rlang, ggbeeswarm, viridis, Rtsne, RColorBrewer,
RcppML, uwot, pheatmap, ggrepel, ggrastr
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
stats, boot, utils, scales, lifecycle, rlang, tidyselect,
magrittr, crayon, cli, fansi, dplyr, tidyr, purrr, tibble,
ggplot2, ggrepel, patchwork, forcats, readr, stringr, glue,
SingleCellExperiment
igraph, stats, SummarizedExperiment, BiocParallel, Rgraphviz
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 (>= 3.1),
stats, utils, MASS, IRanges, GenomicRanges, GenomeInfoDb,
Rsamtools, rtracklayer
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, umap, ggplot2, irlba, viridis,
BiocParallel, matrixStats, Matrix, sparseMVN, coop
SingleCellExperiment, methods, isotree, FNN, igraph, ggplot2,
GGally, ggridges, SummarizedExperiment, ranger, transport,
cramer, rlang, bluster, scales, MASS, stringr, Matrix,
grDevices
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
BiocGenerics, cluster, corrplot, DESeq2, dplyr, factoextra (>=
2.0.0), ggplot2, ggpubr, ggrepel, gtools, Matrix, mclust,
methods, pheatmap, plotly, rlang, rstatix, S4Vectors, stringr,
SummarizedExperiment (>= 1.34.0), tidyr, vegan
matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph,
Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils,
methods, survival
glmnet (> 2.0), caret (>= 6.0), ggplot2 (>= 2.2.1),
fastcluster, dplyr, Rcpp, RcppArmadillo, RcppParallel,
grDevices, graphics, stats, utils, DESeq2, locfit
BiocBaseUtils, BiocParallel (>= 1.30.0), doParallel, doRNG,
GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, distributions3, dplyr, grDevices,
graphics, httr, igraph, jsonlite, methods, parallel,
reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors,
graph, mpath
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, SpatialPack, ggplot2, stats,
pheatmap, plotly, shiny, igraph, janitor, knitr, methods,
utils, isoband, S4Vectors, grDevices, dbscan, hexDensity,
hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba
geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr,
furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2,
splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr,
tidyselect, broom.mixed, Rcpp
dplyr, ggplot2, henna, methods, paletteer, rlang, S4Vectors,
SeuratObject, SingleCellExperiment, stats, SummarizedExperiment
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
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
IHW, ggplot2, ggrepel, matrixStats, metapod, methods,
MsCoreUtils, MultiAssayExperiment, nipals, RColorBrewer,
S4Vectors, SingleCellExperiment, SummarizedExperiment, stats,
utils
stats, methods, assertthat, tibble, dplyr, purrr, stringr,
Rdpack, matrixStats, BiocParallel, elasticnet, sparsepca,
cluster, kernlab, origami, RSpectra, coop, Matrix,
DelayedArray, ScaledMatrix, MatrixGenerics
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), S4Vectors, SparseArray,
DelayedArray, BiocNeighbors (>= 1.99.0), 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, desc, DBI, DT, fs, GenomicRanges, GenomeInfoDb,
ggdendro, ggforce, ggnewscale, 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
DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment,
SummarizedExperiment, BiocSingular
Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
emdbook, magrittr, utils
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
dplyr, forcats, ggplot2, stringr, openxlsx, viridis,
patchwork, utils, httr2
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
S4Vectors, seriation, circlize, methods, randomcoloR, stats,
grid, grDevices, matrixStats
Rsamtools, IRanges, Seqinfo, graphics, grDevices, utils, abind
BiocGenerics, Biostrings, GenomeInfoDb, AnnotationDbi,
ggplot2, ggrepel, VariantAnnotation, GenomicRanges,
GenomicFeatures, data.table, methods, scales, S4Vectors, stats,
rlang, stringi, universalmotif, Rcpp, ggtree
nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
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
BiocSingular, checkmate, data.table, future.apply, Matrix,
MatrixGenerics, purrr, Rcpp, RcppHNSW, RSpectra, zeallot
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
dplyr, MASS, Matrix, SingleCellExperiment (>= 1.30.1), stats,
tidygraph, rlang, utils
BiocParallel, Matrix, DESeq2, S4Vectors, data.table, edgeR,
openxlsx, pheatmap, stats, circlize, methods, sva
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, data.table
Rcpp, enviGCMS, stats, mzR, rmarkdown, methods,
SummarizedExperiment, S4Vectors
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
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, 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)
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, VariantAnnotation
quadprog (>= 1.5-5), methods, Biobase, BSgenome (>= 1.46.0),
VariantAnnotation (>= 1.24.5), Biostrings, GenomeInfoDb,
GenomicRanges, rtracklayer, SummarizedExperiment, graphics,
stats, utils
mzR, ggplot2, grid, reshape2, grDevices, stats, utils
dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges,
Rsamtools, parallel, graphics, stats, utils, methods
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, 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
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)
SummarizedExperiment, BiocParallel, DelayedArray, methods,
utils, Matrix, S4Vectors, stats
methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges,
DelayedArray
stats, utils, methods, ggplot2, matrixTests, matrixStats,
foreach, BulkSignalR, grid, ComplexHeatmap, circlize
methods, Matrix, BiocGenerics, S4Vectors, DelayedArray, stats,
utils, Rcpp, beachmat (>= 2.27.3)
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
S4Vectors, stats, utils, BiocGenerics, GenomeInfoDb, MASS,
IRanges, GenomicRanges
RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree,
graphics, grDevices, gridExtra, methods, parallel, seqinr,
stats, tidytree, utils
Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase,
methods, rsvd, SingleCellExperiment, SummarizedExperiment,
stats
graphics, grDevices, igraph, matrixStats, methods, S4Vectors,
SingleCellExperiment, SummarizedExperiment
magrittr (>= 1.5), dplyr, stats, tidyr, utils, data.table,
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
jsonlite, GenomicRanges, rtracklayer, stringr, BiocFileCache,
S4Vectors
R6, httr, rlang, purrr, jsonlite, assertthat, data.table,
Matrix, magrittr, methods, stringr, stats, IRanges,
GenomicRanges, SummarizedExperiment
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, RColorBrewer,
circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis
ggplot2, Matrix, parallel, quadprog, httr, methods, memoise,
BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie,
SpatialExperiment
edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran,
SeuratObject, SingleCellExperiment, SpatialExperiment, stats,
SummarizedExperiment, S4Vectors, utils, BiocParallel,
BiocSingular
Rcpp, stats, Matrix, SpatialExperiment, SummarizedExperiment,
BiocParallel (>= 1.0)
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, GenomeInfoDb, ggplot2,
gridExtra, reshape2, RhpcBLASctl
ggplot2, methods, stats, dplyr, spatstat.geom,
spatstat.random, SpatialExperiment, SummarizedExperiment, RANN
SpatialExperiment, SummarizedExperiment, S4Vectors, scuttle,
dplyr, terra, stats, methods
grDevices, stats, utils, graphics, SeuratObject, Biobase,
GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
rjson, grDevices, magick, utils, S4Vectors,
SummarizedExperiment, BiocGenerics, BiocFileCache
dplyr, ggplot2, parallel, patchwork, purrr, refund,
SpatialExperiment, spatstat.explore, spatstat.geom,
SummarizedExperiment, methods, stats, fda, tidyr, graphics,
ExperimentHub, scales, S4Vectors, mgcv
S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML,
scattermore, dplyr, pbapply, data.table, readxl, magick,
grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats,
utils, methods, ggtext, tools, RBioFormats
limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods,
stats, grDevices, graphics
ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>=
1.23.6), graphics, grDevices, stats, tools, utils, fs,
BiocGenerics, MetaboCoreUtils, data.table
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges, utils
Spectra (>= 1.5.6), MsCoreUtils, methods
Spectra (>= 1.19.9), IRanges, S4Vectors, MsCoreUtils,
ProtGenerics, methods, data.table, snakecase
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
stats, methods, graphics, grDevices, huge (>= 1.3.2), pulsar
(>= 0.3.11), MASS, VGAM, Matrix (>= 1.5), glmnet, phyloseq
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
data.table, BiocFileCache, BiocParallel, Biostrings,
GenomicRanges, SummarizedExperiment, biomaRt, IRanges, PFAM.db,
dplyr, ggplot2, ggpubr, patchwork, pwalign, rtracklayer,
scales, stats, tidyr, tools, utils, magrittr, methods,
S4Vectors
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
graphics, ggplot2, seqLogo, Biostrings, pwalign, biomaRt,
GenomicAlignments, GenomicRanges, GenomicFeatures, Gviz,
IRanges, S4Vectors, Seqinfo, utils, plyr,stringr, methods,
BSgenome.Mmusculus.UCSC.mm9, googleVis
concaveman, dbscan, dplyr, FNN, ggplot2, limma, magrittr,
Matrix, methods, patchwork, purrr, rlang, scales, Seurat, sf,
SingleCellExperiment, SpatialExperiment, splines, stringr,
SummarizedExperiment, tibble, 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, Matrix, 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
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
GenomicRanges, IRanges, S4Vectors, methods, tibble, dplyr,
ggplot2, progress, GenomeInfoDb, Rcpp, data.table, purrr,
rtracklayer, tidyr, rlang, MASS
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
dplyr, janitor, purrr, rlang, stringr, tidyr, flowCore,
flowWorkspace, glue, tibble
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
BiocGenerics, dplyr, Seqinfo, GenomicAlignments,
GenomicRanges, gridExtra, IRanges, grid, methods, reshape2,
rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene,
tidyselect
png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots,
hash, plotrix
methods, datasets, graphics, stats, utils, knitr,
SummarizedExperiment, S4Vectors, httr2, jsonlite
methods, BiocGenerics, XVector, stringr, stringi, crayon,
grDevices
ggplot2, ggthemes, grid, gridExtra, httr, jsonlite, methods,
scales, sp, stats, limma
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
stats, utils, graphics, ggplot2, BiocParallel
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
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, AnnotationDbi, 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
data.table, reshape2, ggplot2, stats, grDevices, graphics,
utils, biomaRt, methods
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), rlang, utils, methods, dplyr
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
downloader (>= 0.4), grDevices, biomaRt, dplyr, graphics,
tibble, GenomicRanges, XML (>= 3.98.0), data.table, jsonlite
(>= 1.0.0), plyr, knitr, methods, ggplot2, stringr (>= 1.0.0),
IRanges, rvest (>= 0.3.0), stats, utils, S4Vectors, R.utils,
SummarizedExperiment (>= 1.4.0), TCGAbiolinksGUI.data (>=
1.15.1), readr, tools, tidyr, purrr, xml2, httr (>= 1.2.1)
AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb,
GenomicFeatures, GenomicRanges, GenomicDataCommons, glue,
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
AnnotationHub, apeglm, biomaRt, dplyr, doParallel, DESeq2,
foreach, magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats,
utils
graphics, grDevices, stats, utils, tools, S4Vectors,
GenomicRanges, IRanges, parallel, pastecs, ggplot2 (>= 4.0),
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
S4Vectors, Seqinfo, GenomicRanges, Biobase (>= 2.15.1)
DESeq2, KEGGREST, stats, utils, dplyr, plotly, htmlwidgets,
biomaRt, methods
utils, igraph, methods, graphics, stats, BiocParallel
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
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, tibble, ggplot2, ggrastr,
dplyr, fansi, pillar, rlang, scales, cli, purrr, vctrs, stats
BiocFileCache, broom, cluster, dplyr, DT, factoextra, fenr,
ggplot2 (>= 3.4.0), ggpubr, ggrepel, Hmisc, httr, igraph,
jsonlite, limma, MASS, methods, mixOmics, naniar, purrr, readr,
RGCCA, rlang, S4Vectors, scales, shiny, stats, stringr,
SummarizedExperiment, tibble, tidybulk, tidyr, utils
Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang,
stats, stringr, tibble, tidyr
tidySummarizedExperiment, tidySingleCellExperiment,
tidySpatialExperiment, tidyseurat, plyranges, purrr, rlang,
stringr, cli,
magrittr, tidyr, tibble, dplyr, purrr, pillar, S4Vectors,
stringr, cli, vctrs, SummarizedExperiment, methods, rlang,
fansi, pkgconfig
dplyr, tidyr, SummarizedExperiment, tibble, ggplot2, magrittr,
rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors,
tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi,
Matrix, stats
SummarizedExperiment, SingleCellExperiment, BiocGenerics,
S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr,
ggplot2 (>= 4.0.0), 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,
plyxp
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
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
BiocFileCache, httr2, IRanges, jsonlite, methods, purrr,
readr, S4Vectors, xml2, yaml
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
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
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, GenomicAlignments,
GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2,
graphics, grDevices, IRanges (>= 2.11.15), pROC, reshape2,
Rsamtools, rtracklayer, S4Vectors, stats, utils
BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>=
0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0),
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 (>=
4.0.0), IRanges, jsonlite, matrixStats, methods, parallel,
patchwork, scales, stats, S4Vectors, SummarizedExperiment,
VariantAnnotation
RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
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
methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel,
BiocNeighbors, SingleCellExperiment, SummarizedExperiment
methods, stats, httr, jsonlite, S4Vectors (>= 0.47.6)
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, 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
methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp,
Biostrings, BiocGenerics, S4Vectors, rlang, grid,
MatrixGenerics
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
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), curl
GDSArray (>= 1.11.1), DelayedDataFrame (>= 1.6.0), tools,
utils, stats, methods, gdsfmt, SNPRelate, SeqArray,
DelayedArray, Biostrings, IRanges
Rsamtools (>= 1.31.2), BiocGenerics, Biostrings, parallel,
GenomicFeatures (>= 1.31.3), Matrix, rtracklayer (>= 1.39.7),
BiocParallel, GenomeInfoDb, BSgenome, Biobase
tools, GenomicRanges, VariantAnnotation (>= 1.29.3),
GenomicFiles (>= 1.17.3), S4Vectors (>= 0.19.19), Rsamtools
BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix,
methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
stats, SummarizedExperiment, utils
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
dplyr, DT, ggplot2, grid, gridExtra, magrittr, methods,
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
igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm,
ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb,
ggrepel, textstem, tidygraph, stats, scales, ggraph
AnnotationDbi, cli, clusterProfiler, colorspace, DESeq2,
dplyr, edgeR, forcats, ggplot2, ggrepel, GGally, ggpubr, grid,
matrixStats, methods, msigdbr, limma, purrr, rlang, S4Vectors,
scales, stringr, SummarizedExperiment, tibble, tidyr,
tidyselect, viridis
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
Rcpp (>= 1.0.1), arm (>= 1.10-1), eva, BiocFileCache (>=
2.6.0), BiocParallel, SingleCellExperiment, parallel, methods,
stats
multtest, qvalue, stats, utils, BiocManager
methods, utils, stats, grDevices, assertthat, S4Vectors,
DelayedArray, DelayedMatrixStats, BiocParallel, BiocGenerics,
limma, topconfects, dplyr, purrr, ggplot2, rlang, scales,
reshape2, splines, Ckmeans.1d.dp, glm2, RhpcBLASctl
dplyr, ggplot2 (>= 2.2.0), GenomicRanges, rtracklayer,
cowplot, assertthat, purrr, S4Vectors, IRanges, GenomeInfoDb
utils, methods, cli, Biobase, SummarizedExperiment, config,
golem, shiny, DT, ggplot2, dplyr, rlang, stringr,
shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer,
logging
limma, matrixStats, locfit, stats, graphics
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
BiocGenerics, genefilter, graphics, grDevices, gtools,
methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta,
siggenes
methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
methods, utils, stats, tools, BiocGenerics, S4Vectors, IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
stats, tools, BiocGenerics, S4Vectors, IRanges, S4Arrays, Rarr
(>= 1.11.33)
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
cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib
Rcpp, RcppArmadillo, RcppProgress, RcppSpdlog, Rhtslib,
stringfish
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rcpp, Biostrings, IRanges, S4Vectors, XVector
Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings
Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
Rcpp, assorthead (>= 1.5.16), beachmat, BiocNeighbors,
Rigraphlib
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
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
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, 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
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
BiocStyle, dplyr, tidyr, graph, mia, KEGGREST, testthat (>=
3.0.0), knitr, rmarkdown
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
batchelor, BiocStyle, bluster, knitr, magick, matrixStats,
patchwork, RcppArmadillo, rmarkdown, scater, scran, Seurat,
splatter, testthat (>= 3.0.0), UpSetR
BiocStyle, biomformat, devtools, glmnet, knitr, rmarkdown,
testthat, usethis
BiocFileCache, BiocStyle, knitr, processx, rhdf5 (>= 2.52.1),
rmarkdown, S4Vectors, Seurat, SeuratObject,
SingleCellExperiment, spelling, SummarizedExperiment, testthat
(>= 3.0.0), vctrs, withr, yaml
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.Drerio.UCSC.danRer10.refGene,
TxDb.Drerio.UCSC.danRer11.refGene,
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.Mmusculus.UCSC.mm39.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Rnorvegicus.UCSC.rn5.refGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene,
TxDb.Rnorvegicus.UCSC.rn7.refGene
BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest
AnVIL, AnVILAz, AnVILGCP, BiocStyle, GCPtools, knitr,
rmarkdown, testthat (>= 3.0.0), tinytest
AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr
DESeq2, airway, knitr, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran,
sparseMatrixStats, testthat
ALLMLL, CCl4, BiocStyle, knitr, rmarkdown
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, formatR, rmarkdown, magick, devtools
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
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
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, rmarkdown, testthat, scRNAseq, magick
testthat, BiocStyle, knitr, rmarkdown, scran, scater,
bluster, scRNAseq
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD
BiocStyle, knitr, markdown, rmarkdown, SpatialExperiment,
SpatialExperimentIO, VisiumIO, ggplot2, pheatmap, pals,
OSTA.data, tidyr, STexampleData, testthat (>= 3.0.0),
codetools, grid, tools
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, Matrix
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, knitr
testthat, BiocStyle, knitr, rmarkdown, pander, seewave
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
BiocStyle, knitr, rmarkdown, sessioninfo, testthat
BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>=
3.0.0)
testthat, BiocStyle, knitr, rmarkdown, GenomicAlignments,
scales, Gviz, xlsx, GGally, patchwork, viridis, ggplotify,
SummarizedExperiment, DESeq2, ggpointdensity, ggrastr, ashr,
txdbmaker, ggrepel, stringr
BiocStyle, RCurl, biomaRt, knitr, knitcitations,
knitrBootstrap, testthat, ggplot2, rmarkdown
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
BiocFileCache, BiocStyle, GenomicFeatures, GenomeInfoDbData,
knitr, httr2, rmarkdown, rvest, tinytest, txdbmaker,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, ggplot2,
tidyr, stringr
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
Matrix, DelayedArray, beachmat, BiocParallel, testthat,
BiocStyle, knitr, rmarkdown
airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1),
GOSemSim, Hmisc, knitr (>= 1.43), org.Hs.eg.db, reactome.db,
rmarkdown, spelling, testthat (>= 3.1.5), 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)
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
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, httptest2, knitr, mockery, rmarkdown, testthat (>=
3.0.0), withr
testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),
rmarkdown (>= 0.7), SummarizedExperiment, S4Vectors, tibble,
rhdf5
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
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl
knitr, rmarkdown, testthat (>= 3.2.3), covr, tradeSeq, scran,
slingshot, tools, ami, reshape2, plyr, fs, sparseMatrixStats,
ggVennDiagram, uwot, BiocStyle, DelayedMatrixStats, limma
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
knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
lifecycle, tidyverse, 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
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
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
knitr, rmarkdown, testthat, BiocStyle, txdbmaker,
TENxBUSData, TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86
BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat
(>= 3.1.6)
knitr, rmarkdown, BiocStyle, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm9.knownGene
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
BiocStyle, knitr, msqc1, RefManageR, rmarkdown, sessioninfo,
testthat, vdiffr
BiocStyle, foreach, knitr, pcaMethods, rmarkdown, testthat,
VGAM
BiocStyle, testthat, knitr, rmarkdown, emmeans, lme4,
lmerTest
knitr, rmarkdown, testthat, RcppML, BiocStyle
RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0),
sessioninfo
BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto,
rmarkdown, testthat, uwot
fossil, interp, knitr, BiocStyle, tictoc
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown,
withr, BiocStyle, 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, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle
limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
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
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
testthat (>= 3.0.0), covr, withr, rmarkdown, knitr,
BiocStyle, scater, scRNAseq
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
airway, kableExtra, knitr, org.Hs.eg.db, rmarkdown, testthat
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14),
devtools (>= 2.3.0), BiocStyle, testthat
ChemmineR, BiocStyle, knitr, knitrBootstrap, BiocManager,
rmarkdown,RUnit,codetools
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
testthat, roxygen2, devtools, knitr, lintr
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat
ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle,
gridExtra (>= 2.2), testthat
clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram,
knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown,
testthat, TxDb.Hsapiens.UCSC.hg38.knownGene
BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene,
BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19),
testthat, knitr (>= 1.1.0), rmarkdown, mzR (>= 2.41.4),
MsBackendMetaboLights (>= 1.3.1), pheatmap, vdiffr, IRanges,
RColorBrewer
testthat, knitr, markdown, rmarkdown, BiocStyle, Signac,
future, igraph, bluster, httr
AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown,
rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown,
BiocStyle
BiocStyle, knitr, rmarkdown, testthat, webshot
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
RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2
knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle
Biobase, ComplexHeatmap, clusterProfiler, TCseq,
org.Mm.eg.db, circlize, knitr, monocle, pheatmap, rmarkdown,
Seurat, WGCNA, utils, BiocManager, S4Vectors, pheatmap,
testthat (>= 3.0.0)
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, BiocManager, DOSE, ggtangle, readr,
org.Hs.eg.db, quarto, 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, ggrepel, patchwork, htmlwidgets
knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2,
patchwork, dplyr, scattermore
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat,
BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Ggallus.UCSC.galGal3
minet, Rgraphviz, RUnit, BiocGenerics, igraph
BiocStyle, knitr, rmarkdown, testthat, XVector
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
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
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
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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, RUnit
knitr, BiocStyle, rmarkdown, testthat, Seurat
BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra,
magick, Cairo, limma
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 (>= 3.2.0), proto, spelling, knitr, ragg, Cairo,
conflicted, data.table, gsubfn, R.utils, tidyverse, rmarkdown,
htmlwidgets, MASS, Rtsne, plotly, BiocStyle, cowplot, qpdf,
GEOquery, sf, torch, S4Vectors
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
rstatix, MASS, mgcv, ggplotify, ggpubr, ggrepel, ggtree,
glmnet, Matrix, microbiome, phyloseq, vegan, gt, testthat (>=
3.0.0), BiocManager, devtools, knitr, rmarkdown, BiocStyle,
curatedMetagenomicData, xgboost
BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat
(>= 3.0.0), knitr, rmarkdown
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
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, GenomicFeatures, knitr, rmarkdown, readxl,
rtracklayer, sangerseqR, testthat, VariantAnnotation
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
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
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
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
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
XML, grImport, grImport2, BiocStyle, knitr, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
BSgenome.Hsapiens.UCSC.hg19
testthat, curl, knitr, htmltools, rmarkdown, BiocStyle,
bookdown, org.Dm.eg.db
BiocStyle, fields, knitr, rmarkdown, RColorBrewer, scater,
scRepertoire, DelayedMatrixStats, slingshot, testthat
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, devtools, testthat (>= 3.0.0)
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
macrophage, knitr, BiocStyle, apeglm, mosdef, org.Hs.eg.db,
topGO, clusterProfiler, DEFormats, ExperimentHub, scater,
muscat, 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)
corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL,
rrcov, Rgraphviz, NCIgraph
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
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
BiocStyle, knitr, rmarkdown, testthat, ggplot2, patchwork
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
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, 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,
MASS
msigdbr, org.Hs.eg.db, org.Mm.eg.db, minfi, knitr, rmarkdown,
GO.db, KEGGREST, testthat,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, BiocStyle, RUnit
knitr, RUnit, BiocGenerics, rmarkdown, bookdown, BiocStyle,
betareg, rtracklayer, BSgenome.Hsapiens.UCSC.hg38
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
BiocStyle, airway, tidyverse, knitr, rmarkdown, testthat (>=
3.0.0), dominatRData
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
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
AnnotationDbi, BiocStyle, biocthis, codemetar, devtools,
here, httptest2, jsonlite, knitr, rmarkdown, testthat (>=
3.0.0), tidyverse, usethis
RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT,
EnsDb.Hsapiens.v86
Biobase, mia, BiocGenerics, magrittr, BiocManager, cluster,
devtools, DT, e1071, foreach, ggtext, intergraph, knitr,
optparse, plyr, preprocessCore, qpdf, remotes, rmarkdown,
ShortRead, testthat (>= 3.0.0), vegan, viridis
BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0)
knitr, UpSetR, BiocStyle, rmarkdown, testthat (>= 3.0.0)
limma, convert, GEOquery, dyebiasexamples, methods
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
jsonlite, knitr, Matrix, nanoparquet, readr, rhdf5,
SeuratObject, splines, AnnotationDbi, Biobase, BiocStyle,
org.Hs.eg.db, S4Vectors, 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
RUnit, ggrastr, BiocGenerics, knitr, DESeq2, pasilla, airway,
org.Hs.eg.db, gridExtra, magrittr, rmarkdown
GenomeInfoDb, 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
testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter,
RColorBrewer
AnnotationDbi, clusterProfiler, europepmc, ggarchery,
ggforce, ggHoriPlot, ggplotify, ggridges, ggstar, ggtreeExtra,
ggupset, glue, grDevices, gridExtra, gson, org.Hs.eg.db,
quarto, scales, tibble, tidyr
BiocStyle, knitr, rmarkdown, ggplot2, scatterpie, ggtangle,
ggrepel, testthat, ggnetwork, 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
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, scMultiome
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)
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
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
BiocStyle, BiocCheck, knitr, rmarkdown, withr, testthat (>=
3.0.0)
apeglm, BiocStyle, SimpleUpset, 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
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown, pkgdown,
XVector, ggplot2, dplyr, tidyr, scales
BiocFileCache, BiocStyle, ggtree, 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)
shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown,
testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi,
GOSemSim
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
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, ComplexHeatmap
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
ragg, covr, testthat (>= 3.0.0), knitr, rmarkdown (>= 1.14),
BiocStyle
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, rmarkdown, 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, gDRtestData (>= 1.7.1), gDRstyle (>= 1.7.1),
knitr, purrr, 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, 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, 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
GenomeInfoDb, Biobase, AnnotationDbi, annotate, Biostrings
(>= 2.77.2), SummarizedExperiment (>= 1.39.1), Rsamtools,
GenomicAlignments, BSgenome, GenomicFeatures, UCSC.utils,
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.plantsmart51,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
rmarkdown, BiocStyle
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
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, rmarkdown, stringr, testthat (>=
3.0.0)
airway, BiocStyle, knitr, org.Hs.eg.db, rmarkdown, testthat,
vdiffr
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, OSTA.data, VisiumIO, arrow,
STexampleData, BumpyMatrix, scater, scran, uwot, testthat,
patchwork
emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,
prettydoc, rmarkdown, igraph, 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
BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC,
rmarkdown, survival, testthat, VennDiagram, withr
GO.db, golubEsets, hu6800.db, vsn, Rgraphviz
vsn, golubEsets, KEGGREST, hu6800.db, Rgraphviz, GO.db,
lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS,
boot, rpart, mstate
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown,
zellkonverter
knitr, BiocStyle, rmarkdown, markdown, testthat (>= 3.0.0)
GenomeInfoDb, RUnit, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19,
LungCancerLines
testthat, knitr, rmarkdown, pasillaBamSubset, BiocStyle,
BiocManager, GenomeInfoDb
BiocStyle, knitr, rmarkdown, testthat, org.Dr.eg.db
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, 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
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, clipper, codetools,
hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db,
parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat,
topologyGSA (>= 1.4.0)
BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene
MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate,
org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR,
BiocStyle
hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools,
testthat, BiocStyle, knitr, RUnit
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
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff
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
BiocStyle, knitr, qs2, rmarkdown, scater, scRNAseq, scuttle,
testthat (>= 3.0.0), withr
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
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)
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
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
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rgl,
HiContactsData, HiContacts, plotly, callr
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
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
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
anndataR, BiocStyle, imageFeatureTCGA, ggplot2, knitr, paws,
rhdf5, rmarkdown, sfdep, spdep, SpatialFeatureExperiment,
tinytest
BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown,
Peptides, randomForest, rmarkdown, scRepertoire, spelling,
testthat, tidygraph, viridis
BiocManager, BiocStyle, knitr, mockery, spelling, rmarkdown,
testthat (>= 3.0.0), withr
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT
BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
testthat (>= 3.0.0), ggfortify, shinyWidgets, pROC, tuneR,
knitr, curl, readxl, reshape2, vroom, here, enrichR, rmarkdown
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
testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite,
processx, attempt, BiocStyle, httr
gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat
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
BiocFileCache, BiocStyle, bsseq, ggplot2, ggridges, knitr,
microbenchmark, rmarkdown, GenomicRanges, IRanges, Rsamtools,
SummarizedExperiment, S4Vectors, testthat (>= 3.0.0)
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, GenomeInfoDb, testthat (>= 3.0.0)
BiocStyle, igraph, knitr, rmarkdown, testthat (>= 3.0.0)
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
BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
BSgenome.Hsapiens.UCSC.hg19, BiocStyle, Cairo, rmarkdown,
knitr, R.utils, tinytest, GenomeInfoDb, GenomicRanges, IRanges,
MutationalPatterns, magick
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
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, 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,
BiocStyle, devtools, knitr, roxygen2, rmarkdown, testthat (>=
3.0.0), S4Vectors,
parallel, XVector, testthat, knitr, BiocStyle, rmarkdown
knitr, rmarkdown, Seurat, parallelDist, uwot, NMF, fpc,
dendextend, cluster, Rtsne, scRNAseq, Matrix
LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2,
testthat
ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat,
Biobase
knitr, testthat (>= 2.1.0), rmarkdown, markdown
knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra,
SummarizedExperiment, TreeSummarizedExperiment
knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown,
markdown
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors
knitr, rmarkdown, kableExtra, RUnit, TBX20BamSubset,
BiocGenerics, BiocStyle
BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo,
testthat (>= 3.0.0)
devtools, markdown, renv, testthat, BiocManager, knitr,
rmarkdown, roxygen2, mockery, covr, magick, BiocStyle
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
knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(>
6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF,
TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer,
BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr
BiocManager, BiocStyle, clusterProfiler, ComplexHeatmap,
depmap, enrichplot, ggrepel, ggvenn, Glimma, 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
testthat, knitr, rmarkdown, fgsea, BiocManager
knitr, rmarkdown, BiocStyle, HDCytoData, flowCore, testthat
(>= 3.0.0)
covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer,
derfinder, GenomeInfoDb, tools, RefManageR, testthat
testthat, knitr, rmarkdown, BiocManager, BiocStyle,
BiocParallel, Matrix, microbiome
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, MsDataHub, BiocStyle, rmarkdown, plotly,
shiny, shinyjs, msentropy, DT, microbenchmark, mzR
BiocStyle, testthat, knitr, rmarkdown, robustbase
BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown,
structToolbox, testthat, pmp, grid, png
BiocStyle, knitr, rmarkdown, DT, ggraph, tidyverse, testthat
(>= 3.0.0)
BiocGenerics, RUnit, knitr, BiocStyle, rmarkdown
annotate, BiocGenerics, biomformat, knitr, gss, testthat (>=
0.8), vegan, IHW, SparseArray
BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr
(>= 1.48), testthat (>= 3.2.1.1)
BiocStyle, knitr, rmarkdown, RUnit, methylInheritance
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
covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0),
rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache,
msPurity, rsvg, metabolomicsWorkbenchR, KEGGREST, plyr, magick,
structToolbox, ggVennDiagram, patchwork, XML, GO.db, tidytext,
tidyr, tidyselect, ComplexUpset, jsonlite, openxlsx, ggplotify,
cowplot
biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2,
BiocStyle, miaViz, vegan, scater, phyloseq, magick
ade4, BiocStyle, biomformat, dada2, knitr, mediation,
miaTime, miaViz, microbiomeDataSets, NMF, patchwork, philr,
phyloseq, reldist, rhdf5, rmarkdown, scuttle, 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, ggpubr, knitr, maaslin3, mediation, miaTime, patchwork,
rmarkdown, rstatix, shadowtext, testthat, vegan, vipor
BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat
clusterProfiler (>= 4.5.2), 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, ggalluvial (>= 0.11.1), forcats, phyloseq,
aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext,
DirichletMultinomial, ggpp, BiocManager, rhdf5
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
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
knitr, rmarkdown, RUnit, ggplot2, BiocStyle
BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml,
kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0),
xgboost
stringi, testthat (>= 2.1.0), HGNChelper,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Biobase, BiocStyle, 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, airway
GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz,
GOstats, graph, limma, mouse4302.db, reactome.db
MMDiffBamSubset, MotifDb, knitr, BiocStyle,
BSgenome.Mmusculus.UCSC.mm9
testthat, BiocStyle, knitr, rmarkdown, magrittr, vegan,
phyloseq, curatedMetagenomicData, genefilter
knitr, devtools, rmarkdown, BiocGenerics, RUnit, epiNEM,
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, devtools, roxygen2,
png, edgeR
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
RUnit, seqLogo, BiocStyle, knitr, rmarkdown, formatR,
markdown
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm39,
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 (>= 1.13.3), ggdendro, knitr, MASS, MotifDb,
rmarkdown, rtracklayer, SimpleUpset, 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, MsDataHub, rmarkdown, microbenchmark, mzR
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest, rlang
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, MsDataHub, MsBackendSql (>= 1.3.2),
RSQLite
testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2,
tinytest
knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown,
BiocStyle
MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
msPurityData, CAMERA, RPostgres, RMySQL
stringr, ExploreModelMatrix, kableExtra, ComplexHeatmap,
scater, multcomp, gridExtra, knitr, BiocStyle, RefManageR,
sessioninfo, rmarkdown, testthat, tidyverse, tidyr, plotly,
MsDataHub, MSnbase, MsCoreUtils, covr, arrow, data.table,
ggcorrplot, iq
BiocStyle, knitr, rmarkdown, tinytest, covr, markdown,
mockery, kableExtra
data.table, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0),
mockery, MSstatsConvert, shiny
BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
knitr, rmarkdown, tinytest, covr, mockery, arrow, testthat
(>= 3.0.0)
MSstats, MSstatsTMT, tidyverse, boot, purrr, gridExtra,
knitr, rmarkdown, BiocStyle, testthat
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
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)
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
TCGAbiolinks, shinyBS, shinyalert, shinybusy, shinydashboard,
shinyjs, shinyjqui, sortable, testthat, BiocStyle, knitr,
rmarkdown, survival, XVector, qpdf, covr, shinyWidgets,
cowplot, withr
BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3),
TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>=
2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR
(>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr,
rmarkdown
testthat (>= 3.0.0), BiocStyle, knitr, Biostrings, pwalign,
plotly, scattermore, BiocManager
binom, BiocManager, BiocStyle, bs4Dash,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, car,
colorspace, dendsort, doBy, DT, ExperimentHub, fmsb, fs,
ggrepel, gtools, htmltools, httr, knitr, lme4, magick,
MutSeqRData, openxlsx, packcircles, patchwork, RColorBrewer,
reticulate, rmarkdown, scales, shiny, testthat (>= 3.0.0),
trackViewer, withr, yaml, xml2
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
MsDataHub, RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML,
rmarkdown
biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf
grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly,
rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
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
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
BiocStyle, fpc, igraph, knitr, missForest, notameViz,
notameStats, pcaMethods, RUVSeq, testthat
BiocStyle, car, knitr, lmerTest, missForest, mixOmics, MuMIn,
MUVR2, notameViz, PERMANOVA, PK, randomForest, rmcorr, testthat
batchCorr, BiocStyle, igraph, knitr, notameStats, testthat
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,
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
knitr, dplyr, testthat, BiocGenerics, BiocStyle, graphics,
grDevices
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, SBMLR, sigmajs,
smoof, testthat
RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis,
desc, testthat (>= 3.0.0)
testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
flowWorkspaceData, knitr, rmarkdown, markdown, testthat,
utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2),
MASS
airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2,
gridExtra, knitr, Matrix, rmarkdown, scales, testthat
txdbmaker, GenomeInfoDbData, Homo.sapiens, Rattus.norvegicus,
BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs,
rtracklayer, biomaRt, RUnit, RMariaDB, BiocStyle, knitr
remotes, knitr, BiocStyle, markdown, rmarkdown, testthat (>=
3.0.0), piggyback, magick, GenomeInfoDbData, ape, phytools,
rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
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
BiocStyle, knitr, optparse, rmarkdown, testthat (>= 3.0.0),
waldo
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle, rmarkdown
AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite,
knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0)
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat, scran, BiocGenerics, knitr, Biobase, GEOquery,
hgu133a.db, ggplotify, RMTstat, ggforce, concaveman, DESeq2,
airway, org.Hs.eg.db, magrittr, rmarkdown, airway
testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr,
HDF5Array
testthat (>= 3.0.0), tidyverse, rmarkdown, styler, cli,
lintr, rtracklayer, knitr, devtools, ggplot2, BiocStyle,
BiocManager, usethis, utils, AnnotationHub, GenomeInfoDb
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
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
BiocStyle, testthat, knitr, rmarkdown, Seurat,
SingleCellExperiment, aricode, mclust, viridis, magick,
ggrepel, dplyr
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)
knitr, BiocStyle, testthat, rmarkdown, irlba, GenomeInfoDb
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
SummarizedExperiment, TreeSummarizedExperiment, vegan, knitr,
rmarkdown, BiocStyle, testthat, badger, pheatmap, Biobase
tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings,
BiocParallel, GenomeInfoDb, scales, HiContactsData,
rtracklayer, BiocStyle, covr, knitr, rmarkdown, sessioninfo,
testthat (>= 3.0.0), RefManageR
knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0),
HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19,
pasillaBamSubset, covr, ggplot2
devtools, knitr, rmarkdown, testthat, airway, IRanges, here
testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra,
magick
BiocStyle, knitr, seqLogo, rmarkdown, testthat (>= 3.0.0)
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
testthat (>= 3.0.0), knitr, rmarkdown, ddPCRclust
BiocStyle, covr, ggraph, ggtext, knitr, patchwork, plotly,
tidyverse, testthat (>= 2.3.2)
testthat, devtools, DNABarcodes, knitr, rmarkdown, tibble,
tidyr, BiocStyle, RefManageR, sessioninfo, DBI, chunked,
RSQLite, dbplyr
knitr, rmarkdown, BiocStyle, pdftools, magick, testthat (>=
3.0.0)
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
BiocStyle, cowplot, ggplotify, knitr, rmarkdown, devtools,
gtable, roxygen2, testthat (>= 3.0.0), spelling, HDF5Array
testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr,
tibble, limma, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle
BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools,
knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
MsDataHub, rpx, mzID, mzR, SummarizedExperiment, BiocStyle,
rmarkdown, knitr, factoextra, vdiffr (>= 1.0.0), testthat
xml2, testthat, knitr, BiocStyle, Biostrings
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
devtools, DESeq2, knitr, rmarkdown, testthat, BiocStyle
BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle,
knitr, rmarkdown, BiocManager, MASS
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
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
BiocStyle, knitr, rmarkdown, SingleCellExperiment, testthat
(>= 3.0.0)
markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>=
3.0.0)
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), withr,
ZarrArray
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
knitr, BiocStyle, knitcitations, sessioninfo, rmarkdown,
testthat, covr
testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse,
tinytex
BiocStyle, testthat, knitr, rmarkdown, base64enc, graph
BiocStyle, knitr, rmarkdown, igraph, grDevices
clusterProfiler, knitr, rmarkdown, org.Hs.eg.db, prettydoc,
testthat
testthat, igraph, XML, BiocManager, RCurl, bookdown,
rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows
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, lobstr, RefManageR,
rmarkdown, testthat, recount
knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf
knitr, rmarkdown, testthat, biocViews, BiocCheck, BiocStyle,
airway
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
testthat, BiocStyle, knitr, rmarkdown, BiocSingular
BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2,
corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl
GEOquery, Biobase, edgeR, uwot, BiocStyle, knitr,
org.Hs.eg.db, rmarkdown, DESeq2, MASS, matrixStats,
BiocGenerics, fastshap, caret, testthat (>= 3.0.0), covr
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
bench, BiocParallel, BiocStyle, bit64, curl, dplyr, ggplot2,
knitr, rmarkdown, testthat, withr
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, testthat, rhdf5 (>= 2.47.7)
BiocStyle, knitr, rmarkdown, tinytest, mockery
knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0)
DescTools, devtools, knitr, rmarkdown, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), plyranges,
plotgardener, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene,
tibble
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
readxl, knitr, rmarkdown, reshape2, pander, testthat
BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr,
testthat (>= 3.0.0)
doParallel, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0),
PupillometryR, matrixStats, RColorBrewer, scales, tibble,
patchwork, ConsensusClusterPlus
BiocStyle, knitr, rmarkdown, GSEABenchmarkeR,
EnrichmentBrowser, preprocessCore, DESeq2
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)
BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
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
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, rmarkdown, testthat, covr, BiocStyle, AnnotationHub,
ensembldb, edgeR, DEXSeq, stageR, DelayedArray
knitr, rmarkdown, mclust, scater, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, BiocSingular,
DelayedMatrixStats
BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown,
rmarkdown, rhdf5, HDF5Array
future, RUnit, knitr, markdown, rmarkdown, BiocStyle
BiocStyle, DelayedMatrixStats, snifter, densvis, cowplot,
biomaRt, knitr, scRNAseq, robustbase, rmarkdown, testthat,
Biobase, scattermore
BiocStyle, knitr, testthat, cluster, SingleCellExperiment
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown,
loo, prettydoc, SeuratObject, tidyseurat,
tidySingleCellExperiment, bayesplot, posterior
knitr, Matrix, rmarkdown, BiocStyle, VGAM, ontoProc,
MerfishData, doParallel, scuttle, SingleCellExperiment, scran,
testthat (>= 3.0.0)
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, rvinecopulib, knitr, rmarkdown, testthat (>=
3.0.0), RefManageR, sessioninfo, BiocStyle
AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
SingleR, celldex, scuttle, scater, dplyr, ComplexHeatmap, grid,
testthat (>= 3.0.0)
AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
scuttle, SeuratObject, testthat, vdiffr
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
Seurat (>= 5.0.0), igraph, knitr, rmarkdown, BiocStyle,
testthat, scRNAseq
testthat, knitr, rmarkdown, BiocStyle, MASS,
SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot
Matrix (>= 1.2), testthat, knitr, parallel, rmarkdown,
RColorBrewer, ReactomePA, clusterProfiler, cowplot,
org.Hs.eg.db, reshape2, xlsx, dendextend, networkD3, Rtsne,
BiocParallel, e1071, WGCNA, devtools, DOSE
AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot,
fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db,
org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA,
rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0),
knitr, rmarkdown, tidyverse, magick, celldex, SingleR,
TENxPBMCData, scater, GenomeInfoDb, GenomicRanges,
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
covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba,
rlang, magick, igraph, scater, gtable, ggpubr, viridis,
bluster, cluster, circlize, speedglm, rmarkdown, gridExtra,
BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel,
BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0),
testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment
BiocStyle, knitr, qs2, rmarkdown, scater, scRNAseq, Seurat,
testthat (>= 3.0.0)
BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales,
proxy, testthat, badger
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
BiocStyle, BiocGenerics, MsDataHub (>= 1.3.3), impute, knitr,
patchwork, preprocessCore, rmarkdown, scater, scpdata, sva,
testthat, vdiffr, vsn, uwot
Seurat, SingleCellExperiment, SummarizedExperiment, knitr,
rmarkdown, testthat (>= 3.0.0)
DelayedMatrixStats, sparseMatrixStats, testthat (>= 2.1.0),
covr, knitr, rmarkdown, BiocStyle, ggplot2, ggpubr, splatter,
SingleCellExperiment, microbenchmark
testthat, BiocStyle, knitr, rmarkdown, DelayedMatrixStats,
HDF5Array, scRNAseq, dynamicTreeCut, ResidualMatrix,
ScaledMatrix, DESeq2, pheatmap, scater, scrapper
testthat, knitr, rmarkdown, BiocStyle, Matrix, IRanges,
SummarizedExperiment, SingleCellExperiment, scRNAseq,
org.Mm.eg.db, scater, 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
airway, BiocStyle, curl, DESeq2, knitr, rmarkdown, S4Vectors,
SingleCellExperiment, SummarizedExperiment, testthat (>= 3.0.0)
knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s,
metagenomeSeq, epivizrStandalone, GenomeInfoDb
testthat (>= 3.0.0), transformGamPoi (>= 1.8.0), glmGamPoi
(>= 1.14.3), anndata (>= 0.8.0), SummarizedExperiment (>=
1.32.0), igraph (>= 2.1.1), Seurat, SingleCellExperiment,
knitr, rmarkdown, BiocStyle, BiocManager, SeuratObject, ggpubr,
rlang, stringr, tibble
BiocStyle, knitr, scRNAseq, rmarkdown, testthat,
sparseMatrixStats, DelayedMatrixStats, scran
knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
knitr, rmarkdown, BiocStyle, devtools, testthat (>= 3.0.0),
IRanges, BSgenome.Hsapiens.UCSC.hg38,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Hs.eg.db
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
BiocStyle, box, dplyr, future, ggplot2, harmony, knitr, MASS,
patchwork, rmarkdown, scater, scuttle, SingleCellExperiment,
sparseMatrixStats, stringr, TENxPBMCData, testthat (>= 3.0.0),
tibble
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
BiocStyle, caret, glmnet, corrplot, ggplot2, ggraph, knitr,
methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat,
SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext,
testthat (>= 3.0.0)
testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions,
covr
knitr, data.table, BiocStyle, ggplot2, MsCoreUtils, testthat
(>= 3.0.0)
BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite,
testthat (>= 3.0.0)
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi,
knitr
BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx
IRanges, BSgenome.Hsapiens.UCSC.hg19, BiocStyle, knitr,
rmarkdown
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
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
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
testthat, knitr, rmarkdown, BiocStyle, BiocParallel,
SingleCellExperiment, scrapper (>= 1.5.16), scRNAseq, ggplot2,
pheatmap, grDevices, gridExtra, viridis, celldex
pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
BiocStyle, devtools, knitr, magick, rmarkdown, testthat
BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat
BiocGenerics, BiocStyle, clusterExperiment,
DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl,
rmarkdown, testthat, uwot, covr
BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater,
splatter, testthat (>= 3.0.0), tibble, 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)
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest,
ggfortify, tidyr, testthat (>= 3.0.0)
data.table, devtools, knitr, cowplot, rjson, rmarkdown,
BiocStyle, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap
testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown,
covr, BiocStyle, scater, Seurat (>= 5.0.0), patchwork, ggforce,
ggnewscale, tensorflow
FNN, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
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
BiocStyle, knitr, rmarkdown, BiocCheck, ggplot2, patchwork,
testthat (>= 3.0.0)
testthat, knitr, rmarkdown, qpdf, Seurat
knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix,
DropletUtils, VisiumIO
stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), stringi,
qpdf, pheatmap, viridis, cowplot, vdiffr, sf
testthat (>= 3.0.0), STexampleData, ggplot2, knitr
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), MsDataHub, 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, MsDataHub, roxygen2, rmarkdown, knitr, S4Vectors,
BiocStyle, mzR
testthat, quarto, MsBackendMgf, MsDataHub, mzR, knitr,
BiocStyle
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)
parallel, boot, igraph, batchtools, testthat, covr, knitr,
BiocStyle, rmarkdown, RefManageR, sessioninfo, magick
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
devtools, testthat (>= 3.0.0), knitr, rmarkdown, cowplot,
stringr, readr, tibble, BiocStyle, clusterProfiler,
AnnotationDbi, msigdbr, org.Hs.eg.db, org.Mm.eg.db
testthat, knitr, rmarkdown, ggplot2, tidyr
igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.refGene,
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
BiocStyle, knitr, rmarkdown, SeuratObject, testthat (>=
3.0.0)
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
testthat (>= 3.0.0), knitr, rmarkdown, devtools
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq, testthat
knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr,
ggrepel, cluster, testthat (>= 3.0.0)
flowAI, ggplot2, gt, knitr, openCyto, ggcyto, rmarkdown,
data.table, here, testthat (>= 3.0.0), BiocStyle
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
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
devtools, MutationalPatterns, RUnit, BiocManager,
BiocGenerics, BiocStyle, knitr, rmarkdown
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)
flowCore, knitr, rmarkdown, usethis, testthat (>= 3.0.0),
BiocSingular, bluster, scater, scran, Seurat,
SingleCellExperiment, BiocStyle, magick, qs2
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, org.Hs.eg.db, ggplot2,
devtools, testthat (>= 2.1.0), roxygen2, knitr, BiocStyle,
plyranges, circlize, tictoc, IRanges, stats,
SummarizedExperiment, rmarkdown
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
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
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, mia, rmarkdown,
SummarizedExperiment, testthat
jpeg, png, BiocStyle, rmarkdown, devtools, maftools,
parmigene, c3net, minet, Biobase, affy, testthat, sesame,
AnnotationHub, ExperimentHub, pathview, clusterProfiler,
Seurat, ComplexHeatmap, circlize, ConsensusClusterPlus, igraph,
limma, edgeR, sva, EDASeq, survminer, genefilter, gridExtra,
survival, doParallel, parallel, ggrepel (>= 0.6.3), scales,
grid, DT
AnnotationHub, Bioc.gff, BiocFileCache, BiocStyle,
curatedTCGAData, ComplexHeatmap, devtools, dplyr, httr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr,
magrittr, miRNAmeConverter, org.Hs.eg.db, RColorBrewer, readr,
rmarkdown, RTCGAToolbox, rtracklayer, R.utils, testthat,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene
BiocStyle, GenomeInfoDb, bslib, ggplot2, ggpubr, plotly,
rmarkdown, shiny, knitr, testthat (>= 3.0.0)
apeglm, BiocStyle, knitr, rmarkdown, testthat
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, fastmatch,
functional, survminer, tidySummarizedExperiment, markdown,
uwot, matrixStats, preprocessCore, igraph, EGSEA, IRanges,
here, glmmSeq, pbapply, pbmcapply, lme4, glmmTMB, MASS,
pkgconfig, enrichplot, patchwork, airway
tidySummarizedExperiment, plyranges,
TxDb.Mmusculus.UCSC.mm10.knownGene, AnnotationHub,
GenomicFeatures, BiocStyle, hues, knitr, rmarkdown,
sessioninfo, testthat (>= 3.0.0)
BiocStyle, circlize, curl, densityClust, DiagrammeR,
dynamicTreeCut, edgeR, forcats, ggh4x, ggnewscale, ggraph,
ggridges, ggsci, ggvenn, grid, gridExtra, impute, janitor,
knitr, matrixStats, mice, mirt, missForest, MOFA2, nipalsMCIA,
openxlsx, patchwork, reticulate, rmarkdown, testthat (>=
3.0.0), tidygraph, tidyHeatmap, tidytext, tidyverse
BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown,
sessioninfo, testthat (>= 3.0.0)
utils, tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr
(>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6),
nullranges, tidybulk, plyinteractions
knitr, rmarkdown, BiocStyle, airway, pasilla, testthat (>=
3.0.0)
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, rbibutils, prettydoc
BiocStyle, testthat, knitr, markdown, scater, igraph,
cowplot, DropletUtils, tidySummarizedExperiment
BiocStyle, testthat, knitr, markdown, rmarkdown, plotly,
rbibutils, prettydoc, airway
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
ALL, hgu95av2.db, hgu133a.db, genefilter, multtest,
Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown
BiocStyle, DFplyr (>= 1.5.0), knitr, rmarkdown, testthat (>=
3.0.0)
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)
knitr, rmarkdown, testthat, covr, clusterExperiment,
DelayedMatrixStats
BiocNeighbors, DelayedArray, DelayedMatrixStats,
BiocParallel, testthat, knitr, BiocStyle, rmarkdown
BiocStyle, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg19.knownGene, testthat, e1071
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, edgeR, extraChIPs,
InteractionSet, knitr, readr, rmarkdown, rtracklayer,
SimpleUpset, testthat (>= 3.0.0)
testthat, roxygen2, knitr, BiocStyle, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
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
mcbiopi, splines, logicFS (>= 1.28.1), KernSmooth,
VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
BiocGenerics, shinycssloaders, tidyverse, BiocManager,
Biostrings, xtable, rlist, motifStack, knitr, rmarkdown,
testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
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
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow,
limma, edgeR (>= 4.9.2), 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
knitr, rmarkdown, BiocStyle, org.Hs.eg.db,
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
SC3, knitr, testthat, reticulate, rmarkdown
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
testthat, knitr, rmarkdown, markdown, BiocStyle
RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>=
1.21.3), TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
SeqArray, BiocStyle, BiocManager, testthat, knitr, rmarkdown
breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), markdown,
RColorBrewer, rstudioapi
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager, stats, utils,
grDevices, processx
testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore,
knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr
airway, BiocStyle, circlize, ComplexHeatmap, DT,
EnhancedVolcano, ggpointdensity, ggridges, ggalluvial,
ggcorrplot, ggrain, ggvenn, enrichplot, knitr, magrittr,
patchwork, org.Hs.eg.db, org.Mm.eg.db, quarto, rmarkdown, yaml,
writexl, testthat (>= 3.0.0), uwot, xCell2
GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
testthat, covr, knitr, rmarkdown, pkgdown
knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr,
magick
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat, hexbin
knitr, devtools, testthat, roxygen2, rprojroot, rmarkdown,
scater
knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR,
EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi,
ComplexHeatmap, patchwork, testthat (>= 2.1.0)
knitr, rmarkdown, biomaRt, GenomicFeatures, testthat,
ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi,
AnnotationFilter, arrow
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, knitr, rmarkdown, digest, mtbls2, testthat
paws.storage, HDF5Array, testthat, knitr, rmarkdown,
BiocStyle
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
celldex, future, SingleR, SummarizedExperiment, tricycle,
terra
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