a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 3.6), adductData, ExperimentHub, AnnotationHub
R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata
R (>= 2.10),methods,Biobase,limma,affy (>=
1.22),preprocessCore,affycoretools
methods, stats, zCompositions, lattice, latticeExtra
R (>= 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 (>= 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 (>= 1.5.1)
R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy
methods, grDevices, stats, utils, parallel, edgeR, limma,
AnnotationDbi
R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R(>= 4.1), SummarizedExperiment(>= 1.1.6), S4Vectors(>=
0.22.1), BSgenome, IRanges
R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc
R (>= 3.4), stats, utils, methods, rmarkdown, knitr,
prettydoc, yaml
R (>= 3.4), Biostrings, GenomicAlignments, caTools,
GenomicRanges, grDevices, graphics, stats, utils
R (>= 4.3.0), SummarizedExperiment, S4Vectors, GenomicRanges
R (>= 1.8.0), Biobase (>= 2.5.5), multtest, GSEABase, GO.db
R (>= 3.3), wateRmelon (>= 1.25.0), gdsfmt (>= 1.0.4),
methods, minfi (>= 1.21.0), Biobase, methylumi
R (>= 4.0.0), methods, utils, graphics, stats, generics
R (>= 4.0), reticulate, methods, SummarizedExperiment
R (>= 2.1.0), methods, MVCClass, Biobase, graph, Rgraphviz
R (>= 3.5.0), igraph (>= 2.0.1.1), poweRlaw, latex2exp,
RSpectra, Rdpack
ROntoTools, GSA, PADOG, limma, graph, stats, utils, parallel,
Biobase, metafor, methods
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
GenomicRanges
R (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 3.5), GenomicRanges, cowplot, breakpointRdata
R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5),
SummarizedExperiment (>= 1.19.5)
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
R (>= 3.5), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23),
GenomeInfoDb, GenomicRanges, foreach, iterators, methods,
parallel, locfit
R (>= 2.14.0), Biobase, binom, methods, stats
R (>= 4.4), BiocParallel, BiocGenerics, ProtGenerics,
S4Vectors, methods, stats, stats4
R (>= 4.4), BiocParallel, matter, ontologyIndex
methods, stats4, BiocGenerics, AnnotationDbi, Biobase, Matrix
R (>= 4.5.0), AnVIL (>= 1.19.5), MultiAssayExperiment
R (>= 3.3.0), stats, methods, CCP, PROMISE, Biobase, GSEABase,
utils
R (>= 3.6), SingleCellExperiment, magrittr, methods, stats,
tibble, utils
R (>= 4.1), Seurat (>= 4.0.1), SingleCellExperiment
R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML,
ggplot2, rmarkdown
R (>= 2.10), methods, Biobase (>= 2.5.5), marray
R (>= 2.0.0), impute(>= 1.8.0), DNAcopy (>= 1.6.0), methods,
Biobase, CGHbase (>= 1.15.1), snowfall
R (>= 3.3), minfi, ChAMPdata (>= 2.6.0),DMRcate,
Illumina450ProbeVariants.db,IlluminaHumanMethylationEPICmanifest,
DT, RPMM
R (>= 4.2), ggplot2, SingleCellExperiment
Biostrings, GenomicRanges, IRanges, Gviz, S4Vectors,
ensembldb, AnnotationFilter, data.table
R (>= 3.5.0), methods, BiocGenerics (>= 0.1.0), S4Vectors (>=
0.17.25), IRanges (>= 2.13.12), GenomicRanges (>= 1.31.8),
ShortRead
R (>= 2.10.0), methods, BiocGenerics, S4Vectors (>= 0.9.25)
stats, utils, graphics, grDevices, datasets, base, biomaRt,
GenomicRanges, R (>= 3.1.0)
R (>= 4.1.0), generics, methods, S4Vectors,
MultiAssayExperiment, BiocParallel, survival
R (>= 3.5.0), BSgenome.Drerio.UCSC.danRer7, methods
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>=
1.15.4), BiocGenerics
R (>= 3.6), stats, utils, graphics, infotheo, lattice,
latticeExtra, httr, jsonlite
R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats,
utils
R (>= 3.5.0), methods, utils, stats, graphics, parallel,
GenomicRanges
R (>= 2.10), methods, tools, stats, genefilter
brglm, doParallel, foreach, GenomicRanges, methods,
splitstackshape
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 (>= 3.5.0), methods, grid, graphics, stats, grDevices
R (>= 4.1), methods, AnnotationFilter, S4Vectors
R (>= 4.1), BiocGenerics, SummarizedExperiment
R (>= 3.3), mvtnorm, igraph, gsl, Biobase, stats,
LaplacesDemon, Matrix
R (>= 3.5.0), GenomicFeatures, GSEABase (>= 1.24.0)
R (>= 2.15.0), S4Vectors, IRanges, GenomeInfoDb, GenomicRanges
R (>= 3.5.0), GenomicRanges, SummarizedExperiment
R (>= 4.0), EBImage, SingleCellExperiment, methods
R (>= 2.14.0), limSolve, pcaMethods, ggplot2, grid
MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7)
SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6)
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
R (>= 3.6.0), parallel, Rcpp (>= 1.0.0), SummarizedExperiment,
knitr, KernSmooth, matrixcalc, rmarkdown, DSS, dendextend,
psych, sva
R (>= 3.5), GenomicRanges, IRanges, S4Vectors (>= 0.23.10)
R (>= 4.3.0), variancePartition (>= 1.33.11),
SingleCellExperiment, ggplot2
R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel
blockmodeling, gplots, testthat, R (>= 3.0.0)
R (>= 3.6.0), methods, grid, ComplexHeatmap (>= 2.11.0),
GenomicRanges
R (>= 3.5.0), methods, Biobase, S4Vectors, IRanges,
GenomicRanges, SummarizedExperiment
R (>= 3.4), methods, epivizrServer (>= 1.1.1), Biobase
R (>= 3.6), SummarizedExperiment, MultiAssayExperiment,
cluster (>= 2.0.9), fpc (>= 2.2-3), randomForest (>= 4.6.14),
flexmix (>= 2.3.15), RSKC (>= 2.4.2), sparcl (>= 1.0.4)
R (>= 3.5.0), SGSeq, Matrix, SummarizedExperiment
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.3.6),
BiocFileCache (>= 1.5.1)
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
methods, LiquidAssociation, parallel, doParallel, stats,
Hmisc, utils
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), Ckmeans.1d.dp (>= 4.3.0), GenomicRanges,
biomaRt, ggplot2
R (>= 3.5), S4Vectors (>= 0.7.21), GenomicRanges, methods,
BiocGenerics (>= 0.13.8)
R (>= 3.6), Biobase, NanoStringNCTools, S4Vectors
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(>= 3.3.0),stats,utils,graphics, grDevices, diagram, plotrix,
base,GenomicRanges
R (>= 4.3.0), shiny, shinydashboard, shinydashboardPlus,
dashboardthemes, shinyWidgets, shinymeta, tidyverse,
operator.tools, maftools
R (>= 3.4), grid, stats, graphics, Biobase (>= 2.22.0)
Biobase, AnnotationDbi, GO.db, CompQuadForm, stringr
shiny, sp, gplots, ggplot2, reshape2, RColorBrewer, rhdf5,
R(>= 2.10.0)
R (>= 3.5.0), Biobase, SummarizedExperiment
R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures,
AnnotationDbi
R (>= 3.1.2), grid, IRanges, GenomicRanges
R (>= 3.5.0), GenomicRanges, BiocGenerics
R (>= 4.5), methods, rhdf5, BiocGenerics, SparseArray
R(>= 4.3), QFeatures, S4Vectors, Spectra
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
R (>= 4.4.0), SummarizedExperiment (>= 1.1.6), GenomicRanges,
IRanges, S4Vectors
R (>= 3.6), utils, curl, rhdf5, R6, grid
InteractionSet, GenomicRanges, SummarizedExperiment, R (>=
4.1.0)
R (>= 4.1), igraph (>= 1.0.1), AnnotationHub(>= 2.6.5),
MultiAssayExperiment(>= 1.4.9), SummarizedExperiment(>= 1.8.1)
R (>= 3.5.0), Biostrings, pwalign, GenomicAlignments,
BiocParallel, hiAnnotator
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
R (>= 2.10), methods, Biobase, annotate, plotrix
R (>= 3.5.0), GenomicRanges, methods, shiny
R (> 3.0.0),GenomicFeatures, ggplot2, IVAS
R (>= 2.14.0), plyr, ggbio, GenomicRanges
R (>= 3.5.0), methods, BiocGenerics, grid
R (>= 4.1), mclust, BiocParallel, survival
R (>= 3.5.0), methods, AnnotationDbi (>= 1.43.1),
AnnotationHub
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2),
S4Vectors (>= 0.45.2)
R(>= 4.2.0), Matrix, parallel, BiocParallel,
SummarizedExperiment, BiocGenerics, lme4, nnls
R (> 3.0.0),GenomicFeatures, ggplot2, Biobase
R (>= 2.13.2), methods, graphics, fdrtool
R (>= 4.0), ggplot2, parallel, stats, S4Vectors
R (>= 3.5.0), S4Vectors, SingleCellExperiment,
SummarizedExperiment, methods, rhdf5, BiocIO
R (>= 4.1), ExperimentHub, AnnotationHub
R (>= 4.3.0), stats, methods, utils, SummarizedExperiment,
SingleCellExperiment, BiocGenerics
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(>= 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 (>= 4.1.0), methylclockData, devtools, quadprog
R (>= 3.5.0), methods, grDevices, graphics, stats, utils,
GenomicRanges, SummarizedExperiment (>= 0.2.0), Rsamtools
Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
R(>= 4.4.0), MultiAssayExperiment, TreeSummarizedExperiment,
SummarizedExperiment, BiocGenerics
R (>= 4.0), MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, TreeSummarizedExperiment (>= 1.99.3)
R (>= 4.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0),
SummarizedExperiment, TreeSummarizedExperiment
R (>= 4.3.0), SummarizedExperiment, stats
R (>= 4.1), MultiAssayExperiment (>= 1.8.3)
R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,
ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats,
cluster, marray, mclust, RColorBrewer, colorspace, igraph,
Rgraphviz, graph, annotate, Hmisc, fastICA, JADE
methods, BiocGenerics (>= 0.15.3), GenomicRanges,
SummarizedExperiment (>= 1.1.6), Biostrings, bumphunter (>=
1.1.9)
R (>= 3.2), Biobase (>= 2.22.0), miRcompData
R (>= 3.6.0), IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICv2anno.20a1.hg38
R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
R (>= 4.0), SummarizedExperiment, topGO, stats
data.table, parallel, utils, stats, R (>= 4.1)
Biostrings, GenomicRanges, ggplot2 (>= 3.5.0), R (>= 4.3.0),
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
limma
SummarizedExperiment (>= 1.3.81), R (>= 3.5.0)
QTLExperiment, SummarizedExperiment, ComplexHeatmap,
data.table, collapse
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.2.1), GenomicFeatures, txdbmaker
R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods,
minet, mclust, reshape2
R (>= 4.2.0), igraph, reticulate, pandaR, yarn, matrixcalc
R(>= 3.5.0), keras, limma, e1071, SingleCellExperiment,
kableExtra
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
dplyr, optimalFlowData, rlang (>= 0.4.0)
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 (>= 3.5.0), cn.mops, methods, utils, stats, graphics
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2, Hmisc
R (>= 4.1.0), SummarizedExperiment (>= 1.3.81)
R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 3.5.0), methods, Rsamtools (>= 1.99.1), GenomicRanges
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
BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)
R (>= 3.5.0), methods, BiocGenerics, Biostrings
R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
R (>= 3.2.1), stats, methods, Rmpfr, gmp
R (>= 3.2), Biobase, rcellminerData (>= 2.0.0)
R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2,
multtest, Biostrings, BSgenome, ChIPpeakAnno
R (>= 4.4.0), SummarizedExperiment, methods
R (>= 2.11.0), Biostrings, IRanges, BSgenome, methods, seqLogo
R (>= 2.6.0), methods, utils, graph, grid
R (>= 4.0.0), GenomicRanges, IRanges, methods
R (>= 3.0.2), methods, GenomicRanges, abind
R (>= 4.0.0), ggplot2, RnaSeqSampleSizeData
R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25),
GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2),
gplots, grid, gridExtra, limma, matrixStats, methods,
illuminaio, methylumi, plyr
R (>= 3.6.0), Biobase, ggplot2, limma, methods
boot, SummarizedExperiment, fission, knitr, methods
methods, graph, boot, KEGGREST, KEGGgraph, Rgraphviz
R (>= 3.1.1), affy, BiocGenerics, BiocStyle, methods,
rmarkdown
methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.31.8),
Biostrings (>= 2.47.6), R (>= 3.5.0)
foreach, doParallel, parallel, Biostrings, methods, utils
R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>=
0.45.2), S4Vectors, IRanges
R (>= 4.0.0), methods, utils, stats, stats4, BiocGenerics (>=
0.53.2)
R (>= 2.4.0), AnnotationDbi, Biobase, methods, SparseM
R (>= 4.0.0), stringr, ape, Biostrings, pwalign, DECIPHER,
parallel, reshape2, sangerseqR, gridExtra, shiny,
shinydashboard, shinyjs, data.table, plotly, DT, zeallot,
excelR, shinycssloaders, ggdendro, shinyWidgets, openxlsx,
tools, rmarkdown (>= 2.9), knitr (>= 1.33), seqinr, BiocStyle,
logger
R (>= 3.5.0), Biostrings, pwalign, stringr
R (>= 4.3), RaggedExperiment, GenomicRanges
R (>= 3.4), smoothie, GenomicRanges, IRanges,
SummarizedExperiment
R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment
methods, SCArray (>= 1.13.1), SeuratObject (>= 5.0), Seurat
(>= 5.0)
R (>= 4.0), S4Vectors, 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 (>= 4.2), GenomicRanges, IRanges, S4Vectors
BiocGenerics (>= 0.23.3), BiocParallel, Biostrings (>=
2.47.6), Rsamtools (>= 1.31.2), GenomicAlignments (>= 1.15.6)
R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db
R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 4.3.0), SummarizedExperiment, CATALYST
GenomicFeatures (>= 1.17.13), GenomicAlignments (>= 1.1.22),
Rgraphviz (>= 2.3.7)
R (>= 3.3), Biobase, igraph, limma, GSEABase, gtools, splines,
GeneNet (>= 1.2.13), longitudinal (>= 1.1.12), FIs
R (>= 4.0), ggplot2, ggridges, SummarizedExperiment,
BiocGenerics
R (>= 3.6.0),SummarizedExperiment, methods, Rcpp
R (>= 3.5.0), methods, Rsamtools, Biostrings, reshape,
ggplot2, RColorBrewer, stats
R (>= 4.0.0), methods, MatrixGenerics (>= 1.1.3),
GenomicRanges (>= 1.55.2), Biobase
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
Rsamtools (>= 1.31.2), Biostrings, ShortRead (>= 1.37.1),
methods
methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.13.5),
Rsamtools, hwriter
R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment
R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.4.0)
SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7)
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.6), EpiDISH, limma, nnls, quadprog
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R (>= 3.5.0), 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
Biostrings, BSgenome, GenomicRanges, R (>= 4.1)
R (>= 4.3.0), ggplot2, limma (>= 3.62.1), BiocParallel
R (>= 4.0), GenomicRanges, IRanges, ggplot2
R (>= 3.0.0), graph, GenomicRanges, gwascat, doParallel,
foreach
R (>= 3.5.0), Biobase, limma, methods, matrixStats, methylumi,
lumi, ROC, IlluminaHumanMethylation450kanno.ilmn12.hg19,
illuminaio
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, 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
checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS,
Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment,
stats, SummarizedExperiment, utils
AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest
(>= 1.6.0), stats (>= 2.1.0)
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils
affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi,
ggplot2, gplots, oligoClasses, ReportingTools, hwriter,
lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma
affxparser (>= 1.16.0), affy, graphics, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi,
BiocManager, R2HTML, xtable
stats, methods, S4Vectors, SummarizedExperiment,
SingleCellExperiment, Matrix, tibble, rlang
SingleCellExperiment, SummarizedExperiment, S4Vectors, scater,
stats, smurf, apeglm (>= 1.13.3), emdbook, mclust, clue,
dynamicTreeCut, matrixStats, dplyr, plyr, ggplot2,
ComplexHeatmap, forestplot, RColorBrewer, rlang, lpSolve, grid,
grDevices, graphics, utils, pbapply
alabaster.matrix, alabaster.ranges, alabaster.se,
alabaster.sce, alabaster.spatial, alabaster.string,
alabaster.vcf, alabaster.bumpy, alabaster.mae
alabaster.schemas, methods, utils, S4Vectors, rhdf5 (>=
2.47.6), jsonlite, jsonvalidate, Rcpp
methods, rhdf5, Matrix, BiocGenerics, S4Vectors, IRanges
methods, alabaster.se, S4Vectors, jsonlite, rhdf5
methods, BiocGenerics, S4Vectors, DelayedArray (>= 0.33.3),
S4Arrays, SparseArray (>= 1.5.22), rhdf5 (>= 2.47.1),
HDF5Array, Matrix, Rcpp
methods, S4Vectors, BiocGenerics, IRanges, GenomeInfoDb, rhdf5
methods, alabaster.ranges, alabaster.matrix, BiocGenerics,
S4Vectors, IRanges, GenomicRanges, jsonlite
methods, utils, grDevices, S4Vectors, alabaster.sce, 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
rjsoncons (>= 1.0.1), DBI, duckdb (>= 0.9.1), rlang, curl,
BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats,
tools, methods, whisker, ggplot2
callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT,
MultiAssayExperiment, circlize, curatedTCGAData, foreach,
glmnet, httr, limma, matrixStats, readr, reshape2, tibble,
rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2,
gridExtra, utils
stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack,
doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest,
multcomp, nloptr, parallel, utils
igraph, Biobase, survival, MASS, stats, RColorBrewer
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, httr,
yaml, dplyr
stats, utils, methods, futile.logger, jsonlite, httr,
rapiclient (>= 0.1.3), yaml, tibble, tidyselect, tidyr, rlang,
shiny, DT, miniUI, htmltools, BiocBaseUtils
AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods,
rjsoncons, tibble, utils
httr, httr2, dplyr, jsonlite, methods, tibble
methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr,
dplyr, lubridate, plotly, ggplot2
AnVILBase, BiocBaseUtils, dplyr, httr, jsonlite, methods,
rlang, stats, tibble, tidyr, utils
AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite,
rmarkdown, yaml, readr, whisker, tools, utils, stats
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
graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
affy, affyPLM (>= 1.27.3), beadarray, Biobase, genefilter,
graphics, grDevices, grid, gridSVG (>= 1.4-3), Hmisc, hwriter,
lattice, latticeExtra, limma, methods, RColorBrewer, setRNG,
stats, utils, vsn (>= 3.23.3), XML, svglite
AnnotationDbi, bit64, circlize, cluster, corrplot, data.table,
dplyr, getopt, ggdendro, ggplot2, gplots, ggrepel, graphics,
grDevices, grid, limma, MSstats, openxlsx, org.Hs.eg.db,
pheatmap, plotly, plyr, RColorBrewer, scales, seqinr, stats,
stringr, tidyr, UpSetR, utils, VennDiagram, yaml
BiocParallel, ggplot2, glmnet, grDevices, gridExtra, methods,
mvtnorm, PepsNMR, plyr, quadprog, ropls, stats,
SummarizedExperiment, utils, Matrix, zoo
GenomicRanges, GenomicFeatures, BiocGenerics, IRanges,
GenomicAlignments, Gviz, S4Vectors, Rsamtools, BiocStyle,
igraph, htmltools, data.table, UpSetR, tidyr, DT, MASS, grid,
graphics, pbmcapply, txdbmaker
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
methods, stats, Matrix, BiocGenerics, MatrixGenerics,
BiocParallel, S4Vectors, IRanges, GenomicFeatures,
GenomicRanges, GenomicAlignments, Rsamtools, GenomeInfoDb,
SQUAREM, sparseMatrixStats, AnnotationHub, matrixStats, cli
BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table,
ggplot2, grDevices, graphics, grid, motifStack, rappdirs,
stats, testthat, utils, lifecycle
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
DelayedArray, DelayedMatrixStats, data.table, graphics,
grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats,
SummarizedExperiment, BiocGenerics, utils
abind, BiocFileCache, BiocGenerics, bit64, cluster,
codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce,
ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma,
magrittr, matrixStats, methods, MultiAssayExperiment, parallel,
RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats,
stringi, SummarizedExperiment, survival, tidyr, tidyselect,
tools, utils, vsn
GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy,
reshape2, scales, coda, foreach, ggplot2, methods, utils,
graphics, stats
BiocGenerics, BiocParallel, data.table, dplyr, tidyr,
GenomeInfoDb, GenomicAlignments, GenomicFeatures,
GenomicRanges, stats, Rsamtools, methods, Rcpp, xgboost
methods, BiocGenerics, Rcpp (>= 0.10.6), IRanges,
GenomicRanges, zlibbioc
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr,
knitr, methods, BiocParallel, robustbase, BiocStyle,
ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils,
grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>=
0.19-4)
cowplot, circlize, dplyr, ggplot2, ggdendro, ggridges,
graphics, grDevices, magrittr, plyr, proxy, RColorBrewer,
rlang, scales, shiny, stats, SummarizedExperiment, S4Vectors,
tibble, tidyr, vegan, viridis, utils
ggplot2, stringr, XML, raster, dplyr, data.table, tidyr,
magrittr, DT, lazyeval, ShortRead
Biobase, BiocGenerics, coda, cowplot, ggExtra, ggplot2,
graphics, grDevices, MASS, methods, Rcpp (>= 0.11.3),
S4Vectors, scran, scuttle, stats, stats4, SummarizedExperiment,
viridis, utils, Matrix (>= 1.5.0), matrixStats, assertthat,
reshape2, BiocParallel, posterior, hexbin
methods, glmGamPoi, scran, scuttle, stats, utils,
SingleCellExperiment, SummarizedExperiment, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), rstantools (>= 2.1.1)
utils, methods, parallel, dir.expiry, basilisk.utils (>=
1.15.1)
SummarizedExperiment, S4Vectors, BiocGenerics, Rcpp, stats,
methods, utils, igraph, BiocNeighbors, BiocSingular, Matrix,
SparseArray, DelayedArray (>= 0.31.5), DelayedMatrixStats,
BiocParallel, scuttle, ResidualMatrix, ScaledMatrix, beachmat
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
methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics,
Matrix, Rcpp
methods, beachmat, HDF5Array, DelayedArray, Rcpp
methods, beachmat, tiledb, TileDBArray, DelayedArray, Rcpp
BeadDataPackR, limma, AnnotationDbi, stats4, reshape2,
GenomicRanges, IRanges, illuminaio, methods, ggplot2
futile.logger, Rdpack, Matrix, data.table (>= 1.11.8), Rcpp,
abind, stats, graphics, utils, methods, dixonTest, ids
cli, edgeR, BiocParallel, methods, progressr, stats,
SummarizedExperiment, utils
cluster, comprehenr, foreach (>= 1.5.2), invgamma, iterators
(>= 1.0.14), janitor (>= 2.2.0), limma (>= 3.46.0), logging (>=
0.10-108), sva (>= 3.38.0), SummarizedExperiment, methods,
BiocParallel
stats, ggplot2, scales, methods, pROC, foreach, doParallel,
parallel, cowplot, dplyr, tidyr, tidyselect, stringr, utils
dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6),
tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid,
methods, cowplot, Hmisc, sortable, shinyjqui, grDevices,
scales, DT, SummarizedExperiment, S4Vectors
R.utils, data.table, curl, RCurl, digest, methods, stats,
utils, dplyr, RSQLite, graph, Biobase, zellkonverter, anndata,
HDF5Array, bread
stats, utils, GEOquery, graphics, BiocGenerics, illuminaio
R.oo, R.methodsS3, DT (>= 0.3), dplyr (>= 0.7.2), tidyr, shiny
(>= 1.0.5), AlgDesign (>= 1.1.7.3), import (>= 1.1.0), methods,
AnnotationDbi, shinythemes, Biobase, geNetClassifier,
org.Hs.eg.db, org.Bt.eg.db, DOSE, clusterProfiler, reactome.db,
ReactomePA, DiagrammeR(<= 1.01), visNetwork, htmlwidgets, plyr,
tibble, GO.db
BiocGenerics, available, cli, glue, gert, gh, gitcreds, httr,
usethis, dplyr, purrr, tibble, methods, rprojroot, stringr,
yaml, tools, utils, rlang, quarto, renv
BiocBaseUtils, BiocFileCache, BiocManager, biocViews, callr,
cli, codetools, graph, httr2, knitr, methods, rvest,
stringdist, tools, utils
DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils,
methods, BiocBaseUtils
methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl,
httr
Rgraphviz, geneplotter, graph, BiocGenerics, methods
AnnotationHub, ExperimentHub, DT, htmlwidgets, rclipboard,
S4Vectors, shinyAce, shinyjs, shinythemes, shinytoastr, utils
stats, utils, futile.logger, parallel, snow, codetools
BiocFileCache, BiocManager, biocViews, tibble, magrittr,
methods, rlang, stringr, stats, rvest, dplyr, xml2, readr,
httr, htmltools, DT, tools, utils, igraph, jsonlite, gh, RBGL,
graph, rorcid
methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO,
AnnotationDbi, KEGGREST, ontologyIndex, tidyr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>=
2.21.1)
bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1)
Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit, BiocManager
BiocStyle, bookdown, git2r, httr, knitr, rmarkdown,
rstudioapi, stringr, tools, utils, usethis
BiocFileCache, R6, RCurl, RSQLite, Rcpp, XML, chk, git2r,
jsonlite, lgr, lifecycle, methods, openssl, plyr, progress,
rappdirs, stats, stringr, tools, withr, yaml
ggplot2, graphics, Rcpp, SummarizedExperiment, animation,
rlang, biocViews, sessioninfo, BiocStyle
utils, AnnotationDbi, progress, stringr, httr2, digest,
BiocFileCache, rappdirs, xml2, curl
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
Biobase, methods, e1071, grDevices, graphics,
MultiAssayExperiment, MultiDataSet, randomForest, ropls, stats,
SummarizedExperiment, utils
methods, utils, grDevices, stats, crayon
igraph, cluster, psych, stringr, GenomicRanges, MASS, scran
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics,
BiocParallel, SummarizedExperiment, limma
beadarray(>= 2.0.0), Biobase(>= 2.0.0), Rcpp (>= 0.12.8),
BiocGenerics, grDevices, stats, graphics
SummarizedExperiment, ExperimentHub, methods, grid, graphics,
stats, grDevices, circlize, testthat, ComplexHeatmap(>=
1.99.8), ggplot2, matrixStats, gtools, reshape2,
preprocessCore, randomcoloR, V8, limma
stats, methods, utils, cluster, Matrix, Rcpp, igraph,
S4Vectors, BiocParallel, BiocNeighbors
Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb,
S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage,
utils, HiCBricks
CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
dplyr, NbClust, ggplot2, ggbio, grDevices, stats, tidyr,
GenomicRanges, ggforce, stringr, plyranges, methods, utils,
magrittr
doParallel, snow, purrr, plyr, foreach, gamlss, gamlss.dist,
bsseq, methods, DSS, R.utils, utils, stats, ggplot2, cowplot,
dplyr, rlang, GenomicRanges
assertthat, methods, MASS, doParallel, parallel, e1071, earth,
foreach, randomForest, stats, IRanges, S4Vectors, data.table,
graphics, truncnorm, mvtnorm, Rcpp (>= 0.12.14), matrixcalc,
magrittr, kernlab, ggplot2, cowplot, BiocStyle
methods, utils, grDevices, stats, S4Vectors, GenomeInfoDb (>=
1.12.3), IRanges, Rsamtools, GenomicAlignments, ggplot2,
BiocGenerics, gtools, doParallel, foreach
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
GenomicRanges, methods, rlang, S4Vectors, utils
IRanges (>= 2.23.9), GenomeInfoDb, scales, stats, parallel,
tools, graphics, Biobase, locfit, gtools, data.table (>=
1.11.8), S4Vectors (>= 0.27.12), R.utils (>= 2.0.0),
DelayedMatrixStats (>= 1.5.2), permute, limma, DelayedArray (>=
0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils,
HDF5Array (>= 1.19.11), rhdf5, beachmat (>= 2.23.2)
BiocFileCache, httr, DBI, RSQLite, cli, curl, dplyr, 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, biomaRt, BiocGenerics,
Biostrings, BSgenome, dplyr, ensembldb, GenomeInfoDb,
GenomicFeatures, GenomicRanges, ggplot2, IRanges, magrittr,
Matrix, methods, plyranges, Rcpp, S4Vectors, stats, stringr,
tibble, tidyr, utils, zeallot
SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
grDevices, methods, stats, utils
doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi,
MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats,
SummarizedExperiment
ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges,
IRanges, reshape2, methods, BioNERO
ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr,
DT, MesKit, maftools, data.table, utils, stats, methods, tidyr
GSEABase, tkrplot, geNetClassifier, RUnit, Formula, rpart,
survival, Biobase, phenoTest, circlize, plyr, tidyr, dplyr,
graphics, stats, utils, grDevices, R.oo, R.methodsS3
CardinalIO, Biobase, EBImage, graphics, grDevices, irlba,
Matrix, matter (>= 2.7.10), nlme, parallel, utils
readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson,
rmarkdown
circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel,
ggridges, graphics, grDevices, grid, gridExtra, Matrix,
matrixStats, methods, nnls, purrr, RColorBrewer, reshape2,
Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29),
methods, grDevices, utils
Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma,
reshape2, rdist, igraph, geometry, Rfast, data.table, abind,
pheatmap, EBImage, S4Vectors, SeuratObject,
SingleCellExperiment, SpatialExperiment, Matrix, methods,
SummarizedExperiment, msigdbr
BiocFileCache, RColorBrewer, cBioPortalData, genefilter,
gplots, grDevices, stats, utils, openxlsx, zip
BiocBaseUtils, BiocFileCache (>= 1.5.3), digest, dplyr,
GenomeInfoDb, GenomicRanges, httr, IRanges, methods, readr,
RaggedExperiment, RTCGAToolbox (>= 2.19.7), S4Vectors,
SummarizedExperiment, stats, tibble, tidyr, TCGAutils (>=
1.9.4), utils
ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7),
patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot,
reshape2, ggforce, dplyr, tidyr, stringr, depmap,
ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist,
purrr, pvclust, stats, rlang
utils, DT, htmltools, vroom, plyr, dplyr, magrittr, jsonlite,
rapportools, basilisk, reticulate, shinyBS, shinycssloaders,
rintrojs, rlang, markdown
Rcpp, sparseMatrixStats, stats, BiocParallel, irlba,
SingleCellExperiment, Matrix, SummarizedExperiment
plyr, tidyr, dplyr, ggplot2, forcats, ggraph, igraph,
scatterpie, circlize, ComplexHeatmap, tibble, grid, ggbump,
stringr, ggtext, ggh4x, patchwork, RColorBrewer, scales,
viridis, grDevices, graphics, stats, methods
matrixStats, Seurat, SeuratObject, stats, BiocParallel,
ggplot2, reshape2, grDevices, ggsci, SingleCellExperiment,
SummarizedExperiment, methods
MAST, ggplot2, Matrix, dplyr, magrittr, stats, utils, rlang,
BiocGenerics, S4Vectors, readr, tibble, DelayedArray
methods, stats, Rcpp (>= 1.0.5), data.table (>= 1.12.6), plyr,
ggplot2, stringr, magrittr, ShortRead (>= 1.48.0), Biostrings
(>= 2.58.0), egg, Ckmeans.1d.dp, utils, S4Vectors, seqinr,
Rsamtools
methods, jsonlite, httr, data.table, pbapply, tidyr, R.utils,
Rsamtools, BiocParallel, foreach, utils, parallel, doParallel
assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr,
rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr,
tidyselect, lubridate
Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater,
stringr, irlba, data.table, glue, pbapply, umap, Rtsne,
reticulate, fastmatch, matrixStats, ggplot2, BiocParallel,
SummarizedExperiment, fgsea
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
tiff, graphics, stats, utils, reshape2, parallel, doParallel,
grDevices, matrixStats, FME, SpatialTools, sp, vioplot,
FactoMineR, Hmisc
BiocNeighbors, ggplot2, scater, viridis, cowplot,
SummarizedExperiment, SingleCellExperiment, tidyr, magrittr,
dplyr, ggridges, stats, purrr, methods, BiocParallel,
BiocGenerics
BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats,
ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv,
reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
httr, curl, utils, tools, cli, shiny, DT, rjsoncons
methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid,
ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler,
fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools,
pracma, intergraph, grDevices, utils, network, matrixStats,
ggdendro, gridExtra, gtable, fastcluster
BiocParallel, broom.mixed, dirmult, dplyr, edgeR,
fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp,
purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment,
survival, tibble, tidyr, utils
DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors,
methods, SingleCellExperiment, SummarizedExperiment, ggplot2,
rlang, grDevices, patchwork, reshape2, BiocParallel, stats,
dplyr, purrr
furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr,
future, stats
Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges,
magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats,
rlang
tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb,
GenomicRanges, BiocGenerics, stats, utils, dplyr (>= 0.8.3),
stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1),
Rsamtools (>= 2.4.0), rlang (>= 0.4.0),
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.NCBI.GRCh38
Rcpp, utils, GenomicRanges, basilisk, R.utils, stats,
cfToolsData
Biobase, CGHbase, CGHcall, methods, stats, utils
prettydoc,Hmisc,globaltest,sva,illuminaio,rmarkdown,IlluminaHumanMethylation450kmanifest,IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
limma, DNAcopy, preprocessCore,impute, marray, wateRmelon,
plyr,goseq,missMethyl,kpmt,ggplot2,
GenomicRanges,qvalue,isva,doParallel,bumphunter,quadprog,shiny,shinythemes,plotly
(>= 4.5.6),RColorBrewer,dendextend, matrixStats,combinat
BiocGenerics, zlibbioc, Rcpp (>= 0.11.0)
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
shiny, plotly, pheatmap, bioDist, dendextend, cowplot,
corrplot, grDevices, stats, graphics, reshape2, S4Vectors,
SummarizedExperiment
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
methods, stats, lattice, BiocGenerics, IRanges, GenomicRanges,
ShortRead
Biostrings, fBasics, GenomicRanges, IRanges (>= 2.5.14),
graphics, grDevices, HilbertVis, ShortRead, stats, timsac,
utils
IRanges, XVector, Biostrings, ShortRead, graphics, methods,
stats, utils
graphics, stats, utils, methods, survival
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
stats, tools, utils, R.utils, methods, S4Vectors, rlang,
magrittr, dplyr, tidyr, ggplot2, BiocGenerics, Biostrings,
IRanges, ShortRead, Rsamtools, Rbowtie2, Rhisat2, shiny,
shinyFiles, shinyjs, plotly, parallel, htmltools
SingleCellExperiment (>= 1.8.0), SummarizedExperiment (>=
1.16.0), Matrix, mixtools, cowplot, ggplot2, gridExtra, grid,
dbscan, uwot, Rtsne, S4Vectors (>= 0.24.0), igraph, scales,
scran (>= 1.14.6), graphics, methods, stats, utils, reshape2,
ggridges, randomForest, pheatmap, ggraph, grDevices, rhdf5,
rlang, Rcpp, compositions
grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2
(>= 3.0.0), ggpubr, reshape2, ggupset
BSgenome, GenomicRanges, seqinr, e1071, Biostrings,
GenomeInfoDb, IRanges, utils, stringr, stats, S4Vectors
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
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop,
slam, matrixStats, methods
FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach,
dplyr, fpc, mice, modeest, flock, networkD3, methods,
ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices,
ggplot2, grid, stats, utils, pbapply
methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats,
limma, locfdr, matrixStats, graphics, parallel, BiocSingular,
kernlab, stringr, S4Vectors, grDevices, DelayedArray (>=
0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales,
zinbwave, phylobase, pracma, mbkmeans
methods, igraph, ggplot2, scales, BiocParallel, graphics,
stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat,
SeuratObject, SingleCellExperiment, ggdendro
AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3),
GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph,
magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils,
yulab.utils (>= 0.1.6)
methods, pracma, princurve (>= 2.0.5), scatterplot3d,
RColorBrewer, grDevices, graphics, utils, stats
cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang,
scales, stringr, tibble, tidyr, stats, methods,
SingleCellExperiment, SummarizedExperiment, SeuratObject,
matrixStats, S4Vectors, proxy, httr, utils
blaster, future, future.apply, grDevices, igraph, methods,
Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils,
posterior, visNetwork
methods, rhdf5, data.table, flowCore, SummarizedExperiment,
matrixStats
BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb,
S4Vectors
dplyr, stats, utils, grDevices, plotly, karyoploteR,
CopyNumberPlots, GenomicRanges, magrittr, DT, scales, graphics
GenomicRanges, IRanges, S4Vectors, BiocParallel, methods,
magrittr, stats, pheatmap, gridExtra, grDevices, rBeta2009
BiocGenerics, S4Vectors, grDevices, stats, utils, NOISeq,
IRanges, Rsamtools, foreach, ggplot2, plyr, GenomeInfoDb,
gplots, reshape2, stringr, testthat, graphics, methods, shiny,
shinyFiles, shinyjs, grid, openxlsx
BiocGenerics, BiocParallel, GDSArray, GenomeInfoDb, IRanges,
S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR,
gdsfmt, grDevices, lattice, limma, methods, plyr, qqman,
rappdirs, reshape2, stats, utils
BiocGenerics, S4Vectors, IRanges, data.table, ggplot2,
Biobase, stats, methods, ComplexHeatmap, MIRA, tidyr, grid,
grDevices, simpleCache, fitdistrplus
BiocParallel, cluster, methods, gplots, graphics, grDevices,
RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tools, utils, rhdf5, dplyr, fgsea,
forcats, ggplot2
methods, class, gplots, mclust, amap, apcluster, foreach,
parallel, doParallel, fastcluster, corrplot, biwt, Biobase,
reshape2, stringr, tibble, tidyr, dplyr, devtools
utils, graphics, stats, methods, reshape2, ggplot2, scales,
ggtree, patchwork, igraph, rlang, ggbeeswarm, jsonlite,
Biostrings
BiocManager, rmarkdown, GenomeInfoDb, S4Vectors,
AnnotationDbi, graphics, stats, utils, methods, magrittr,
ggplot2, TxDb.Mmusculus.UCSC.mm9.knownGene
grDevices, graphics, grid, stats, utils, ComplexHeatmap (>=
2.5.4), matrixStats, GetoptLong, circlize (>= 0.4.7),
GlobalOptions (>= 0.1.0), clue, parallel, RColorBrewer,
cluster, skmeans, png, mclust, crayon, methods, xml2,
microbenchmark, httr, knitr (>= 1.4.0), markdown (>= 1.6),
digest, impute, brew, Rcpp (>= 0.11.0), BiocGenerics, eulerr,
foreach, doParallel, doRNG, irlba
methods, ggplot2, reshape2, dplyr, gridExtra, plotly,
circlize, rlang, GenomicRanges, IRanges, foreach, BiocParallel,
GenomeInfoDb, scales, RColorBrewer, tidyr, S4Vectors, utils,
Matrix, grid, stats, SummarizedExperiment, plyr, Gviz
ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>=
1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices,
graphics, methods, SummarizedExperiment
AnnotationHub, BiocParallel, bumphunter, ExperimentHub,
GenomicRanges, IRanges, lmerTest, methods, stats, utils
methods, Rcpp, data.table, RColorBrewer, scales, grid, plyr,
knitr, abind, clue, grDevices, utils, pdist, magrittr,
reshape2, dplyr, tidyr, rlang, BiocStyle, rmarkdown, foreach,
coda
knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots,
gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr,
modeest, edgeR, limma, vioplot, methods, stats, utils, ape,
phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny,
shinydashboard
AnnotationDbi, BiocGenerics, Biostrings, Rsamtools, parallel,
grDevices, gplots, IRanges, GenomicFeatures, XVector,
methylPipe, GO.db, S4Vectors, GenomeInfoDb
circlize (>= 0.4.14), GetoptLong, colorspace, clue,
RColorBrewer, GlobalOptions (>= 0.1.0), png, digest, IRanges,
matrixStats, foreach, doParallel, codetools
BiocGenerics, ChemmineR, tibble, jsonlite, dplyr, DBI, dbplyr,
RSQLite, Biobase, ProtGenerics (>= 1.35.3), xml2, IRanges,
Spectra (>= 1.15.10), MsCoreUtils, MetaboCoreUtils,
BiocParallel, stringi
data.table, dplyr, forcats, ggplot2, magrittr, purrr, tidyr,
rlang, stringr, shiny, DT, RColorBrewer, VennDiagram, rio,
scales, shinydashboard, shinyjs, stats, tibble, grid
stats, base, ggplot2, plotly, magrittr, ggpubr, gridExtra,
utils, data.table
BiocGenerics, BiocNeighbors, BiocParallel, bluster, cli,
DelayedArray, Matrix, methods, purrr, rlang,
SingleCellExperiment, sparseMatrixStats, SpatialExperiment,
SummarizedExperiment
slingshot (>= 1.9), mgcv, RANN, stats, SingleCellExperiment,
SummarizedExperiment, utils, magrittr, dplyr (>= 1.0), Ecume
(>= 0.9.1), methods, pbapply, matrixStats, BiocParallel,
TrajectoryUtils, igraph, distinct
matrixStats, gplots, grDevices, methods, graphics, stats,
utils
Biobase, ALL, graphics, stats, utils, cluster
Biobase, GSVA (>= 1.50.0), gdata, genefu, limma, matrixStats,
randomForest, stats, utils, methods, BiocParallel
fastICA (>= 1.2.1), sm, org.Hs.eg.db, GO.db, stats,
SummarizedExperiment, BiocParallel, graph, ggplot2, methods,
Rfast, pheatmap, survival, topGO, graphics, grDevices
methods, stats, 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
CARNIVAL, dorothea, dplyr, GSEABase, igraph, progress, purrr,
rlang, stringr, utils, visNetwork, decoupleR
stats, plyr, dplyr, methods, grDevices, Matrix, ggplot2,
ggrepel, ggthemes, graphics, parallel, parallelly, tibble,
tidyr, BiocSingular, PCAtools, parallelDist, ComplexHeatmap,
circlize, grid, scales, RColorBrewer, utils, rlang, Rfast,
stringr, Seurat, umap, dendextend, zeallot, assertthat, withr,
SingleCellExperiment, SummarizedExperiment, S4Vectors
parallel, genefilter, grDevices, stats, graphics
methods, corpcor, BiocParallel, ggplot2, plyr
splines, graphics, nor1mix, stats, quantreg
DT, shiny, grid, ComplexHeatmap, InteractiveComplexHeatmap,
graphics, stats, ggplot2, plotly, shinyWidgets,
shinycssloaders, shinyjqui, dittoSeq, matrixStats,
colourpicker, shinyjs, circlize, PCAtools, utils, grDevices,
htmlwidgets, methods
BiocGenerics, Biostrings, GenomicRanges, graphics, IRanges,
S4Vectors, stringr
BiocGenerics, Biostrings, BSgenome, crisprBase (>= 0.99.15),
GenomeInfoDb, GenomicRanges, IRanges, Rbowtie, readr, stats,
stringr, utils
BiocGenerics, BSgenome, crisprBase (>= 0.99.15), GenomeInfoDb,
Rbwa, readr, stats, stringr, utils
basilisk (>= 1.9.2), basilisk.utils (>= 1.9.1), 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,
GenomeInfoDb, GenomicRanges, dplyr, keras, mltools
BiocGenerics, Biostrings, BSgenome, crisprBase, crisprDesign,
crisprScore, crisprViz, DT, GenomeInfoDb, htmlwidgets, methods,
pwalign, S4Vectors, shinyBS, shinyjs, utils, waiter
AnnotationDbi, BiocParallel, Biostrings, methods,
GenomeInfoDb, GenomicAlignments, GenomicRanges, grDevices,
grid, gridExtra, IRanges, reshape2, Rsamtools, S4Vectors (>=
0.9.38), utils
BiocManager, cli, crisprBase, crisprBowtie, crisprScore,
crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils
BiocGenerics, Biostrings, BSgenome, GenomeInfoDb,
GenomicFeatures, GenomicRanges, grDevices, Gviz, IRanges,
methods, S4Vectors, txdbmaker
Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods,
S4Vectors, IRanges, GenomeInfoDb, stats, BiocParallel, metapod,
utils
WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache
BiocGenerics, ComplexHeatmap, grid, SummarizedExperiment,
GenomicRanges, IRanges, dplyr, tidyr, tibble, ggplot2, rlang,
grDevices, stats, circlize, ggrepel, SingleCellExperiment,
MatrixGenerics
AnnotationDbi, AnnotationHub, binr, cowplot, data.table,
dplyr, DT, fastmatch, fgsea, ggplot2, ggrepel, graphics,
highcharter, htmltools, httr, limma, methods, parallel,
pbapply, purrr, qs, R.utils, readxl, reshape2, rhdf5, rlang,
scales, shiny (>= 1.7.0), shinycssloaders, stats, tibble,
tools, utils
ccaPP, ggplot2, limma, reshape2, shiny, stats, stringr, utils
stats, pscl, qvalue, BiocParallel, methods, knitr,
SpatialExperiment, SummarizedExperiment
dplyr, SummarizedExperiment, SingleCellExperiment, purrr (>=
1.0.0), BiocGenerics, glue, HDF5Array, DBI, tools, httr, cli,
assertthat, SeuratObject, Seurat, methods, rlang, stats,
S4Vectors, tibble, utils, dbplyr (>= 2.3.0), duckdb, stringr
AnnotationHub, RSQLite, XML, utils, ChemmineR, methods, stats,
rappdirs, BiocFileCache
Biobase, flowCore, flowDensity, flowClust, cytometree,
ggplot2, GGally, graphics, grDevices, methods, mrfDepth, stats,
utils
viridis, methods, shiny, graphics, stats, grDevices, utils,
BiocGenerics, S4Vectors, BiocParallel, SummarizedExperiment,
flowCore, Biobase, Rcpp, BiocNeighbors
doParallel, dplyr, glmnet, rpart, rpart.plot, stats,
flowCore,grDevices, graphics, utils
CATALYST, flowCore, e1071, EZtune, gbm, ggplot2, hrbrthemes,
matrixStats, randomForest, rmarkdown, SingleCellExperiment,
stats, SummarizedExperiment, ssc, S4Vectors, graphics, methods
stats, methods, BiocParallel, RColorBrewer, cowplot,
doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr,
mbest, pheatmap, stringr, strucchange, tibble, ggrepel, MASS,
logging, Matrix, tidyr, caret, rlang, grDevices
Rcpp, SummarizedExperiment, utils, methods, ComplexHeatmap,
circlize, ashr, data.table, BiocParallel, dplyr, stats,
magrittr, rlang, S4Vectors
SpatialExperiment, S4Vectors, BiocParallel, HDF5Array,
DelayedArray, RColorBrewer, viridis, utils,
SummarizedExperiment, tools, graphics, raster, grDevices,
stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny,
shinydashboard, matrixStats, rhdf5, nnls
methods, stats, rlang, pracma, withr, flowCore, reshape2,
ggplot2, ggrepel, ggforce, patchwork, transport, smacof,
BiocParallel, CytoPipeline
gplots, tools, flowCore, grDevices, stats, utils, matrixStats,
methods
cytolib(>= 2.3.10), flowCore (>= 1.99.10), flowWorkspace (>=
4.1.8), openCyto (>= 1.99.2), XML, data.table, jsonlite, RBGL,
Rgraphviz, Biobase, methods, graph, graphics, utils, jsonlite,
dplyr, grDevices, methods, ggcyto (>= 1.11.4), yaml, stats,
tibble
methods, stats, utils, withr, rlang, ggplot2 (>= 3.4.1),
ggcyto, BiocFileCache, BiocParallel, flowCore, PeacoQC, flowAI,
diagram, jsonlite, scales
shiny, shinydashboard, utils, colourpicker, shinycssloaders,
svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite,
EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors,
SummarizedExperiment
pheatmap, Biostrings, UniProt.ws, BiocGenerics, utils,
biomaRt, motifStack, httr
AnnotationDbi, Biostrings, ComplexHeatmap, dplyr, edgeR,
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggbio, ggplot2,
goseq, magrittr, patchwork, plyranges, reshape2, rlang,
Rsamtools, Rsubread, stats, stringr, tidyr, utils
Biobase, MSnbase, DAPARdata (>= 1.30.0), utils, highcharter,
foreach
cli, ComplexHeatmap, crayon, dplyr, generics, ggplot2, glue,
gplots, heatmaply, magrittr, methods, mia, phyloseq, purrr,
readr, rlang (>= 0.4.11), scales, stringr, tibble, tidyr,
UpSetR, waldo
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
MCMCpack, matrixStats, robustbase, aod, e1071
Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice,
BiocGenerics
plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore,
flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks
CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr,
matrixStats, methods, patchwork, parallel, pbapply, reshape2,
rlang, scattermore, stats, statmod, survey, tibble, viridisLite
methods, rJava, BiocParallel, stats, Biobase,
SummarizedExperiment, corpcor, geometry, NMF, nnls, DMwR2,
pcaPP, apcluster, graphics
methods, DBI, S4Vectors, IRanges, XVector
tensorflow, CatEncoders, matlab, rcdk, stringdist, tokenizers,
webchem, purrr, ttgsea, PRROC, reticulate, stats
fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats,
grDevices, graphics, depmap, readr, dplyr
GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats,
graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges,
BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Hs.eg.db, utils
Rcpp (>= 1.0.2),GenomicFeatures, txdbmaker, parallel, foreach,
S4Vectors, doParallel, Rsamtools (>= 1.31.2),
GenomicAlignments, heatmaply, data.table, stats, ggplot2,
GenomicRanges, IRanges, plyr, plotly, utils,viridis
graphics, grDevices, methods, stats, utils
methods, sparseMatrixStats (>= 1.13.2), Matrix (>= 1.5-0),
S4Vectors (>= 0.17.5), IRanges (>= 2.25.10), SparseArray (>=
1.5.19)
methods, utils, S4Arrays, SparseArray, DelayedArray (>=
0.31.8), HDF5Array, BiocSingular, rTensor, DelayedRandomArray
(>= 1.13.1), irlba, Matrix, einsum,
matrixStats, stats, truncdist, base64enc, ggplot2
stats, MASS, Matrix, ggplot2, gridExtra, methods
Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba
caret, data.table, dplyr, fmsb, ggplot2, grDevices, pROC,
PRROC, readr, stats, BiocFileCache, utils
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
derfinder (>= 1.1.0), GenomeInfoDb (>= 1.3.3),
GenomicFeatures, GenomicRanges (>= 1.17.40), ggbio (>=
1.13.13), ggplot2, graphics, grDevices, IRanges (>= 1.99.28),
limma, methods, plyr, RColorBrewer, reshape2, S4Vectors (>=
0.9.38), scales, utils
methods, graphics, grDevices, grid, utils, stats, Matrix, Rcpp
(>= 0.10.3), RcppEigen, RSpectra (>= 0.14-0), irlba,
pcaMethods, Biobase, BiocGenerics, SummarizedExperiment,
SingleCellExperiment, ggplot2, ggplot.multistats, rlang, tidyr,
tidyselect, ggthemes, VIM, knn.covertree, proxy, RcppHNSW,
smoother, scales, scatterplot3d
Biobase, GEOquery, impute, limma, pheatmap, plyr, scales,
snpStats, sva, swamp, stats, methods, utils, bnstruct,
RColorBrewer, grDevices
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
grDevices, stats, methods, Matrix, MASS, checkmate, expm,
igraph, Rcpp, RcppArmadillo, RcppParallel, plyr, precrec
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
parallel, Rcpp, RcppRoll, betareg, grDevices, graphics,
methods, stats, utils
AnnotationHub, ExperimentHub, bsseq, GenomeInfoDb, limma,
edgeR, minfi, missMethyl, GenomicRanges, plyr, Gviz, IRanges,
stats, utils, S4Vectors, methods, graphics,
SummarizedExperiment, biomaRt, grDevices
Matrix, MASS, RcppRoll,GenomicRanges, IRanges, GenomeInfoDb,
methods, mvtnorm, stats, parallel
dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods,
Rcpp (>= 0.11.2), BH
bamsignals, GenomicRanges, IRanges, Rsamtools,
GenomicAlignments, BiocBaseUtils, S4Vectors, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg38.knownGene, BiocGenerics
biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid,
igraph, Matrix, methods, plyr, stats, utils
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, SummarizedExperiment, utils
methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy,
limma, stringr, ggplot2, graphics, grDevices, calibrate,
corrgram, gridExtra, DT, shiny, shinydashboard, readxl,
prodlim, matrixStats
AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>=
2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils
(>= 0.1.6)
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
edgeR, SummarizedExperiment, DelayedMatrixStats,
sparseMatrixStats, MatrixGenerics, Matrix, methods, purrr,
GSEABase, data.table, zenith (>= 1.1.2), mashr (>= 0.2.52),
ashr, dplyr, BiocParallel, ggbeeswarm, S4Vectors, IRanges,
irlba, limma, metafor, remaCor, broom, tidyr, rlang,
BiocGenerics, S4Arrays, SparseArray, DelayedArray, gtools,
reshape2, ggrepel, scattermore, Rcpp, lme4 (>= 1.1-33), MASS,
Rdpack, utils, stats
utils, stats, MASS, GenomicRanges, IRanges, S4Vectors,
BiocGenerics, methods, BiocParallel, limma, edgeR, ggplot2,
reshape2
utils, stats, methods, Matrix, Rcpp, BiocGenerics, S4Vectors,
IRanges, GenomicRanges, SummarizedExperiment, BiocParallel,
SparseArray (>= 1.5.18), DelayedArray (>= 0.31.9),
DelayedMatrixStats, HDF5Array, rhdf5, edgeR, R.utils, dqrng,
beachmat, scuttle
utils, RSQLite, UniProt.ws, biomaRt,ensembldb,
BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors
zoo, ggplot2, purrr, reshape2, parallel, IRanges, S4Vectors,
rlang, grDevices, stats, utils
BiocParallel, SummarizedExperiment, utils, ggplot2, dplyr,
tidyr, RColorBrewer, magrittr, gganimate, purrr, aricode
clusterProfiler, dplyr, forcats, ggplot2, magrittr, rlang,
stats, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, vctrs (>=
0.6.4), BiocStyle
Biobase (>= 2.64.0), BiocFileCache (>= 2.12.0), BiocGenerics
(>= 0.50.0), BiocParallel (>= 1.38.0), biomaRt (>= 2.60.1),
Biostrings (>= 2.72.1), edgeR (>= 4.2.1), GenomeInfoDb (>=
1.40.1), genomeIntervals (>= 1.60.0), GenomicAlignments (>=
1.40.0), GenomicRanges (>= 1.56.1), SummarizedExperiment (>=
1.34.0), graphics, IRanges (>= 2.38.1), LSD (>= 4.1-0),
methods, parallel, rappdirs (>= 0.3.3), Rsamtools (>= 2.20.0),
S4Vectors (>= 0.42.1), ShortRead (>= 1.62.0), utils
Biobase, cluster, graphics, grDevices, lattice, methods, stats
BiocGenerics (>= 0.7.1), graphics, grDevices, stats, abind,
tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils,
htmltools, htmlwidgets, RCurl
methods, graphics, BiocGenerics, IRanges (>= 1.13.9),
aroma.light, Rsamtools (>= 1.5.75), biomaRt, Biostrings,
AnnotationDbi, GenomicFeatures, GenomicRanges, BiocManager
methods, splines, sva, qvalue(>= 1.99.0), MASS
gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo,
igraph, plyr, MASS, RCurl, methods
PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0),
limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5),
hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0),
safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap,
grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1),
htmlwidgets, plotly, DT
graphics, stats, GenomicRanges, S4Vectors, IRanges, limma,
edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics,
utils
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
survivalROC, glmnet, rms, mboost, Matrix, igraph, methods,
survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache
BiocGenerics, Rgraphviz, clusterProfiler, hash, S4Vectors,
dplyr, ggplot2, graph, magrittr, methods, pheatmap, graphics,
utils, purrr, tidyr, stats
matrixStats, stats, GetoptLong, Rcpp, utils, locfit, circlize
(>= 0.4.5), IRanges
AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db,
KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR,
graphite, hwriter, limma, methods, pathview, safe
aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7),
ggnewscale, ggplot2, ggrepel (>= 0.9.0), ggtangle (>= 0.0.5),
graphics, grid, igraph, methods, plyr, purrr, RColorBrewer,
reshape2, rlang, stats, utils, scatterpie, GOSemSim (>=
2.31.2), magrittr, ggtree, yulab.utils (>= 0.1.6)
gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE,
methods
stats, methods, utils, data.table, BiocGenerics,
GenomicRanges, Rcpp
MASS, e1071, quadprog, parallel, stats, matrixStats, stringr,
locfdr, Matrix
BiocGenerics, MCMCpack, Rsamtools, parallel, GenomeInfoDb,
beadarray
AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table,
doParallel, doSNOW, downloader, dplyr, ELMER.data,
ExperimentHub, foreach, GenomeInfoDb, GenomicFeatures,
GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges,
limma, methods, parallel, plyr, progress, R.matlab,
RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats,
SummarizedExperiment, tibble, tidyr, utils
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
scran, ComplexHeatmap, Matrix, SummarizedExperiment,
checkmate, circlize, clusterProfiler, ggplot2, ggraph, igraph,
lifecycle, patchwork, reshape2, scales, scater, stats
GenomicRanges, SummarizedExperiment, BiocGenerics, S4Vectors,
IRanges, graphics, plotrix, grDevices, stats, methods
BiocParallel, data.table, matrixStats, stats, survival,
igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid,
bigmemory, graphics, utils
methods, utils, httr, xml2, curl, rex, GenomicFeatures,
txdbmaker, GenomicRanges, GenomeInfoDb, BiocGenerics,
BiocFileCache, S4Vectors, IRanges, RSQLite, DBI, Biostrings,
tRNAdbImport
epivizrServer (>= 1.1.1), epivizrData (>= 1.3.4),
GenomicRanges, S4Vectors, IRanges, bumphunter, GenomeInfoDb
epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson,
methods, BiocGenerics
S4Vectors, GenomicRanges, SummarizedExperiment (>= 0.2.0),
OrganismDbi, GenomicFeatures, GenomeInfoDb, IRanges, ensembldb
git2r, epivizrServer, GenomeInfoDb, BiocGenerics,
GenomicFeatures, S4Vectors
edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr,
qvalue, reshape2, ROCR, scales, stringr, knitr
AUCell, BiocParallel, grDevices, dplyr, ggdist, ggplot2,
ggpointdensity, GSEABase, GSVA, SingleCellExperiment, ggridges,
msigdbr, stats, reshape2, patchwork, MatrixGenerics, utils,
SummarizedExperiment, UCell, stringr, methods, SeuratObject,
Matrix
SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang,
SummarizedExperiment
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2,
ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class,
prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0)
GenomicFeatures, stringr, GenomeInfoDb, igraph, MASS, nnls,
limma, matrixStats, RBGL, prodlim, graph, methods, utils,
stats, doParallel, foreach, affxparser, GenomicRanges,
S4Vectors, IRanges, qvalue, cobs, rhdf5, BSgenome, Biostrings,
glmnet, abind, iterators, lpSolve, poibin, speedglm, tximport,
fgsea
stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2,
reshape2, limma, stringr, HGNChelper, Matrix, parallel,
SingleCellExperiment, SummarizedExperiment, DelayedArray,
BiocParallel, orthogene (>= 0.99.8), data.table
methods, ExperimentHub, BiocManager, DBI, httr, curl
shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr,
magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales,
tibble, MASS, limma, S4Vectors, shinyjs
methods, graphics, grDevices, stats, utils
BiocParallel, brio, cli, curl (>= 5.0.0), data.table, httr2
(>= 1.0.0), MCMCpack, methods, openEBGM, rlang (>= 1.1.0),
rvest, tools, utils, vroom, xml2
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2,
rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex,
tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT,
clusterProfiler, org.Hs.eg.db
methods, shiny, stats, IRanges, Biostrings, ShortRead, DT,
S4Vectors, graphics, htmltools, shinyBS, Rcpp (>= 0.12.12)
ape, data.table, dynamicTreeCut, methods, R.utils, rJava,
stats, stringr, utils
tcltk, graphics, grDevices, stats, utils
SingleCellExperiment, methods, stats, utils, irlba, TSCAN,
SC3, matrixStats
openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes,
forcats, RColorBrewer, RCy3, utils, stats
methods, igraph, Matrix, KEGGREST, plyr, stats, graphics,
utils
tools, methods, assertthat, rlang, dplyr, tidyr, tidyselect,
tibble, purrr, readr, stringr, httr2, rvest, progress,
BiocFileCache, shiny, ggplot2
Biobase, BiocGenerics, affy, lumi, methylumi, sfsmisc
graph, stats, e1071, methods, gRbase, jsonlite, BiocFileCache,
curl, igraph
igraph (>= 0.6), hwriter, R.utils, XML, plotrix, reshape2,
RColorBrewer, png, methods, stats, utils, graphics, grDevices
Rcpp, data.table, BiocParallel, stats, ggplot2 (>= 2.2.0),
cowplot, grid, fastmatch, Matrix, scales, utils
foreach, doParallel, GenomicRanges, IRanges, Rsamtools,
parallel, S4Vectors
Biobase, BiocParallel, parallel, stats, SummarizedExperiment,
survival, utils
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
NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db,
dplyr, stringr
pls, matrixStats, minfi, methods,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb,
grDevices, graphics, stats
psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster,
fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest,
methods, SummarizedExperiment, stats, S4Vectors
Biostrings, stats, GenomicRanges, IRanges, Rcpp, RcppRoll,
data.table, GenomeInfoDb, S4Vectors, ggplot2, cowplot,
progress, ggseqlogo, viridis, ggpointdensity
AnnotationDbi, BiocGenerics, dplyr, DT, GenomeInfoDb,
openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny,
shinyjs, tidyr, shinythemes
DaMiRseq, MLSeq, stats, methods, SummarizedExperiment
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
data.table, igraph, BioNet, plyr, methods, XML, sna,
intergraph, network, GGally, grid, ggplot2, mwcsr, pryr,
htmlwidgets, htmltools, shinyCyJS (>= 1.0.0)
stats, utils, methods, ggplot2, tidyr, expm, Rcpp,
RcppParallel, gdsfmt
BiocGenerics, GenomeInfoDb, S4Vectors, IRanges, Biostrings,
BSgenome, GenomicRanges, Rsamtools, GenomicAlignments,
matrixStats, MASS, splines, grDevices, graphics, stats, methods
Biobase, limma, RobustRankAggreg, ggplot2,
SummarizedExperiment, grid, rmarkdown, grDevices, graphics,
methods, ComplexHeatmap, stats, utils, parallel
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
methods, BiocGenerics, BiocParallel, matrixStats, Biostrings,
S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, GenomicFiles,
GenomicAlignments, GenomicFeatures, Rsamtools, AnnotationHub,
RColorBrewer, AnnotationDbi, bitops, plotrix,
SummarizedExperiment, grDevices, graphics, stats, utils, cli
BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils
(>= 1.5.6), MultiAssayExperiment, purrr, stringr, S4Vectors,
SummarizedExperiment, data.table
assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx,
data.table, futile.logger, gDRutils (>= 1.3.17), magrittr,
methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats,
stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml,
openxlsx
BiocCheck, BiocManager, checkmate, desc, git2r, lintr (>=
3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild, withr
BiocParallel, BumpyMatrix, checkmate, data.table, drc,
jsonlite, jsonvalidate, methods, MultiAssayExperiment,
S4Vectors, stats, stringr, SummarizedExperiment
tools, S4Vectors (>= 0.17.34), SNPRelate, SeqArray
GOSemSim, Matrix, shiny, shinyWidgets, bs4Dash, rintrojs,
utils, DT, dplyr, shinyBS, STRINGdb, igraph, visNetwork,
shinycssloaders, fontawesome, grDevices, parallel, stats,
ggplot2, plotly, GeneTonic, RColorBrewer, scales, readxl,
ggdendro, ComplexHeatmap, BiocNeighbors, tm, wordcloud2, tools,
BiocParallel, BiocFileCache, cluster, circlize
tcltk, ggplot2, methods, stats, grDevices, graphics, utils
dplyr, grDevices, ggplot2, magrittr, mixtools, scales,
pbmcapply, parallel, stats, utils
magrittr, glue, memoise, jsonlite, data.table, rlang,
lubridate, utils, stringr, SummarizedExperiment, Biobase,
tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat,
digest, R.utils, base64enc
graphics, grDevices, methods, stats, tcltk, utils, xtable
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, BiocGenerics, BiocParallel, GenomeInfoDb,
GenomicRanges, IRanges, matrixStats, XVector, dplyr,
data.table, parallel, doParallel, foreach, methods, S4Vectors,
stats, numbers, utils
stats, stats4, utils, UCSC.utils, GenomeInfoDbData
methods, utils, stats, BiocGenerics, S4Vectors, IRanges,
GenomicRanges, Biostrings, Rsamtools, BiocParallel
stats, httr, xml2, jsonlite, utils, rlang, readr,
GenomicRanges, IRanges, dplyr, rappdirs, tibble, tidyr
data.table, ggplot2, reshape2, methods, utils, Biostrings,
plyr, dplyr, scales, broom, GenomeInfoDb, stats
AnnotationDbi, graph, GO.db, GenomicRanges, GenomicFeatures,
GenomeInfoDb, methods, IRanges, RBGL, S4Vectors
grDevices, stats, utils, plyr, gridExtra, lsr, parallel,
ggbio, S4Vectors, IRanges, GenomeInfoDb, Rdpack
stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache,
IRanges (>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub,
rhdf5, DelayedArray, HDF5Array
ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr,
dplyr, plotly, BiocFileCache, grid, flextable, irlba
methods, BiocGenerics (>= 0.21.2), Rcpp (>= 0.11.2), IRanges
(>= 2.19.13), data.table, stats4, stats, utils
tensorflow, word2vec, DeepPINCS, ttgsea, CatEncoders,
reticulate, stats
Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods,
graphics, stats, testthat, GeomxTools, NanoStringNCTools
xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
BiocGenerics, GenomeInfoDb, GenomicRanges, graphics,
grDevices, grid, htmlwidgets, igraph, InteractionSet, IRanges,
MASS, Matrix, methods, plotrix, rgl, rjson, S4Vectors, scales,
stats, trackViewer
BiocGenerics, rjson, readxl, EnvStats, reshape2, methods,
utils, stats, data.table, lmerTest, dplyr, stringr, grDevices,
graphics, GGally, rlang, ggplot2, SeuratObject
readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr,
limma, curl, rentrez, R.utils, stringr, SummarizedExperiment,
S4Vectors, rvest, httr2
utils, data.table, plyr, cqn, topconfects, stats,
SummarizedExperiment, methods
repo (>= 2.1.1), foreach, stats, utils, GSEABase, methods,
Biobase, XML, rhdf5, digest, iterators
grDevices, graphics, methods, stats, utils, dbscan,
fastcluster, matrixStats
bslib (>= 0.6.0), BiocStyle, ComplexHeatmap, dplyr, DT,
ggbeeswarm, ggplot2, htmltools, magrittr, shiny,
SummarizedExperiment, tibble, tidyselect, tidyr
plyr, scales, hexbin, data.table, RColorBrewer, gridExtra,
rlang
BiocFileCache, GetoptLong, 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, ggalt, ggforce, dplyr, R4RNA, grDevices,
seqmagick, grid, methods, statebins, ggtree (>= 1.17.1)
Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2,
grDevices, grid, methods, rlang, scattermore, stats, Seurat,
SingleCellExperiment, SummarizedExperiment, tidydr, tidyr,
tibble, utils, RColorBrewer, yulab.utils, scales
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
ggside, grid, ggrepel, RColorBrewer, scales, grDevices,
methods, stats
ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods,
purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr,
tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, scales, stats,
cli
ggplot2, utils, rlang, ggnewscale, stats, ggtree, tidytree (>=
0.3.9), cli, magrittr
interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools,
rlang, tibble, tidyr, tidyselect, stats
KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise,
cachem, jsonlite, rvest
BiocParallel, biomaRt, OmnipathR, edgeR, ggplot2, ggridges,
gtools, MultiAssayExperiment, plyr, stringi, stringr,
SummarizedExperiment, methods, stats, reshape2, randomForest,
limma, org.Hs.eg.db, org.Mm.eg.db, BiocGenerics,
GenomicFeatures, ReactomePA, clusterProfiler, dplyr,
AnnotationDbi, TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, shiny, GenomicRanges,
ggtree, shinydashboard, plotly, DT, MASS,
InteractiveComplexHeatmap, ComplexHeatmap, visNetwork,
shiny.gosling, ggvenn, RColorBrewer, utils, grDevices, callr,
circlize
DBI, RMariaDB, RSQLite, numDeriv, RColorBrewer, parallel,
stats, methods, graphics, grDevices, xtable, tools, brew,
stringr, RJSONIO, ggplot2, ggrepel, tidyr, utils, RCurl, XML
Rcpp, beachmat, DelayedMatrixStats, matrixStats,
MatrixGenerics, SparseArray (>= 1.5.21), DelayedArray,
HDF5Array, Matrix, SummarizedExperiment, SingleCellExperiment,
BiocGenerics, methods, stats, utils, splines, rlang, vctrs
biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2,
glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet,
Matrix, MultiAssayExperiment, SummarizedExperiment, survminer,
TCGAutils, utils
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel,
mvnfast, SingleCellExperiment, rlang
AnnotationDbi, ape, bnlearn, Category, DT, doParallel,
foreach, gRbase, GSEABase, gRain, GOstats, org.Hs.eg.db,
org.Mm.eg.db, shiny, WGCNA, data.table, grDevices, graphics,
reshape2, stats, utils
DT, fontawesome, shinycssloaders, cBioPortalData, shinyjs,
reshape2, RColorBrewer, survival, survminer, stats,
compareGroups, rpart, partykit, DescTools, car, rstatix,
fabricatr, shinylogs, magrittr
Rcpp (>= 0.11.5), mapplots (>= 1.5), gtools (>= 3.5.0),
GenomicRanges (>= 1.28.4), IRanges, AnnotationDbi, utils,
grDevices, graphics, stats,
AnnotationDbi, dendextend, doParallel, foreach, parallel,
org.Hs.eg.db, GO.db, Rcpp, stats, graphics,
MultiAssayExperiment, IRanges, S4Vectors
AnnotationDbi, DBI, digest, GO.db, methods, rlang, R.utils,
stats, utils, yulab.utils (>= 0.1.6)
clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats,
stringr
AnnotationDbi, biomaRt, GO.db, graphics, memoise, stats, utils
methods, stats, stats4, AnnotationDbi (>= 0.0.89), GO.db (>=
1.13.0), RBGL, annotate (>= 1.13.2), AnnotationForge, Rgraphviz
parallel, ggplot2, ggrepel, plyr, vegan, DT, shiny, shinyBS,
stats, utils, grDevices
stats, utils, graphics, ggplot2, plotly, zlibbioc, scales,
RColorBrewer, dplyr, grDevices, GenomicRanges, shiny, cowplot,
ggpubr, stringr, rlang
cowplot, e1071, epiR, dplyr, dtangle, ggplot2, ggplotify,
grDevices, limSolve, magrittr, MASS, nnls, parallel, pheatmap,
purrr, rlang, stats, tibble, tidyr, utils
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats,
utils, graphics, rlang, purrr
graphics, grDevices, reshape2, stats, utils
SummarizedExperiment, nloptr, fGarch, methods, BiocParallel,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel,
edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics,
KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods,
S4Vectors, stats, utils
dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud,
stringr, gridExtra, rlang, grDevices, graphics, stats, methods
cluster, doParallel, foreach, matchingR, nsga2R, survival,
proxy, stats, methods,
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, stats, utils, graphics, S4Vectors, IRanges, Biobase,
SummarizedExperiment, GSEABase, Matrix (>= 1.5-0), parallel,
BiocParallel, SingleCellExperiment, SpatialExperiment,
sparseMatrixStats, DelayedArray, DelayedMatrixStats, HDF5Array,
BiocSingular, cli
circlize (>= 0.4.8), GetoptLong, grDevices, utils
Biostrings, pwalign, CRISPRseek, ChIPpeakAnno, data.table,
matrixStats, BSgenome, parallel, IRanges (>= 2.5.5), S4Vectors
(>= 0.9.6), stringr, multtest, GenomicAlignments (>= 1.7.3),
GenomeInfoDb, Rsamtools, hash, limma,dplyr, GenomicFeatures,
rio, tidyr, tools, methods, purrr, ggplot2, openxlsx,
patchwork, rlang
graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
quantsmooth, data.table
utils, httr2, jsonlite, parallel, filelock, rappdirs
stats, tools, rhdf5filters, S4Vectors, IRanges, S4Arrays
rhdf5, reshape, S4Vectors, IRanges, Biostrings, Rsamtools (>=
2.13.1), methods, GenomicRanges, abind, BiocParallel,
BatchJobs, h5vcData, GenomeInfoDb
Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel,
methods, matrixStats
httr, jsonlite, dplyr, tibble, tidyr, readr, BiocFileCache,
tools, utils, digest, shiny, miniUI, DT
utils, stats, tools, Matrix, rhdf5filters, BiocGenerics (>=
0.51.2), S4Vectors, IRanges, S4Arrays (>= 1.1.1)
dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices,
stats, MsCoreUtils
methods, grDevices, graphics, stats, Biostrings,
GenomicRanges, IRanges, KernSmooth, plotrix, Matrix, EBImage,
RColorBrewer, BiocGenerics, GenomeInfoDb
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
ggplot2, viridis, RColorBrewer, scales, reshape2, stringr,
data.table, GenomeInfoDb, GenomicRanges, stats, IRanges,
grDevices, S4Vectors, digest, tibble, jsonlite, BiocParallel,
R.utils, readr, methods
data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet,
GenomicRanges, IRanges, S4Vectors, BiocParallel, 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, GenomeInfoDb
InteractionSet, strawr, GenomeInfoDb, GenomicRanges, IRanges,
S4Vectors, BiocGenerics, BiocIO, BiocParallel, methods, rhdf5,
Matrix, vroom, dplyr, stats
InteractionSet, SummarizedExperiment, GenomicRanges, IRanges,
GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO,
BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr,
stringr, ggplot2, ggrastr, scales, stats, utils
BiocIO, S4Vectors, GenomicRanges, IRanges, InteractionSet,
vroom, basilisk, reticulate, rmarkdown, rmdformats, plotly,
dplyr, stringr, sessioninfo, utils
methods, utils, png, grDevices, circlize (>= 0.3.3), IRanges,
GenomicRanges, polylabelr, Rcpp
R2jags, abind, cowplot, grid, forcats, stringr, GenomicRanges,
S4Vectors, XVector, Biostrings, GenomicFeatures,
BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices,
stats, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp
coin, stats, limma, grDevices, utils, graphics,
preprocessCore, servr, DelayedArray, matrixStats, methods,
S4Vectors, ggplot2, ggpubr, dplyr, tibble, visNetwork,
reshape2, MetBrewer
ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap,
dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment,
ggrepel
sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl,
methods
dplyr, httr2, jsonlite, S4Vectors, stats, 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
available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager,
utils
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, graphics, preprocessCore, grDevices, randomForest,
affy, limma, parallel, GeneSelectMMD, rgl, MASS, lmtest,
scatterplot3d, utils
fields, ggplot2, truncnorm, tidyr, data.table, dplyr,
grDevices, graphics, stats, utils, rlang
shiny (>= 0.9.1.9008), shinydashboard, shinyBS, reshape2,
ggplot2 (>= 3.4.0), scales, ROCR, dplyr, DT, limma, methods,
UpSetR, markdown, utils, rlang
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, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel
(>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0),
SummarizedExperiment, tidyr
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
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, stats,
ggfortify, grDevices, methods, Matrix, utils, graphics,
gridExtra, grid, lattice, Rsamtools, survival, BiocParallel,
GenomicAlignments, parallel
S4Vectors, stats, utils, SummarizedExperiment, methods,
pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind,
BiocParallel, viridis, dplyr, magrittr, DT, igraph,
SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph,
tidygraph, ggplot2, data.table, sf, concaveman, tidyselect,
distances, MatrixGenerics, rlang, grDevices
STRINGdb, pwalign, igraph, graphics, utils, seqinr
hash, httr, keras3, magrittr, matrixStats, methods,
reticulate, rvest, SingleCellExperiment, stats, stringi,
stringr, tensorflow, utils
methods, stats, graphics, grid, lattice, grDevices
stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
xml2, maps, rlang
SummarizedExperiment, GenomicRanges (>= 1.24.1), stats, WGCNA,
grDevices, graphics, survival, igraph, Pigengene (>= 1.19.26),
Homo.sapiens, glmnet, caret, gplots, minfi, matrixStats, Rfast,
tidyr, tidyselect, utils
graphics, grDevices, RColorBrewer, gplots, futile.logger,
stats, utils, methods, ape, phyclust, Matrix, fastcluster,
parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin,
caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus,
future, foreach, doParallel, Seurat, BiocGenerics,
SummarizedExperiment, SingleCellExperiment, tidyr, parallel,
coda, gridExtra, argparse
stats, grDevices, utils, graphics, pbapply, matlab, png,
raster, grid, uwot, gtools, Biobase, generics, parallel,
methods, xgboost
AnnotationDbi,batchtools,Biobase,Biostrings,BSgenome,cleanUpdTSeq,
depmixS4,dplyr,flock,future,future.apply,GenomeInfoDb,GenomicRanges,
GenomicFeatures, ggplot2, IRanges, limma,
magrittr,methods,parallelly, plyranges, preprocessCore,
readr,reshape2, RSQLite, stats,S4Vectors, utils
SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2
methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12),
IRanges, GenomeInfoDb
grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>=
0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils,
svglite, htmltools, clisymbols, jsonlite, RColorBrewer,
fontawesome
interactiveDisplayBase (>= 1.7.3), shiny, RColorBrewer,
ggplot2, reshape2, plyr, gridSVG, XML, Category, AnnotationDbi
config, golem, shiny, DT, shinydashboard, shinyFiles,
shinycssloaders, data.table, fs, dplyr, tidyr, circlize,
colourpicker, dendextend, factoextra, ggplot2, plotly, plyr,
shinyFeedback, shinyalert, tibble, umap, visNetwork,
wordcloud2, readxl, htmlwidgets, colorspace, signal, scales,
htmltools, ComplexHeatmap, grDevices, stats, tools, utils,
biomaRt, rlang, fmsb, igraph
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
rhdf5, dplyr, magrittr, tidyr, ShortRead, Biostrings, ggplot2,
methods, BiocGenerics, XVector, tibble, stats, BiocParallel,
bit64, stringr, utils
Rcpp (>= 1.0.5), matrixStats, ggpubr, ggplot2, survminer,
stats
Biostrings, GenomicRanges, RSQLite, DBI, IRanges, stats,
assertthat
utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs,
lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools,
grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib,
DT
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2,
ggrepel, colourpicker, igraph, vipor, mgcv, graphics,
grDevices, viridisLite, shinyWidgets, listviewer,
ComplexHeatmap, circlize, grid
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
grDevices, methods, miaViz, S4Vectors, shiny, mia,
shinyWidgets, SingleCellExperiment, SummarizedExperiment,
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
graphics, grDevices, stats, survival, utils
doParallel, lme4, BiocGenerics, GenomicRanges, IRanges,
foreach, AnnotationDbi, S4Vectors, GenomeInfoDb, ggfortify,
grDevices, methods, Matrix, BiocParallel,utils, stats
shiny, survival, survminer, hwriter, plotly, ggplot2,
S4Vectors, graphics, stats, utils, UpSetR
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
stringr, methods, ggplot2 (>= 3.3.0), jsonlite, kernlab,
rlist, rmarkdown, reshape2, e1071, randomForest, caret, XML,
praznik, R.utils, httr, sva (>= 3.30.1), edgeR (>= 3.24.3),
limma (>= 3.38.3), grDevices, graphics, stats, utils, Hmisc (>=
4.4.0), gridExtra
sesameData, dplyr, methods, rlang, GenomicRanges, IRanges,
reshape2, S4Vectors, stats, stringr, utils, ggplot2, ggrepel,
tibble, wheatmap, magrittr
curl, igraph, foreach, doParallel, sortable, dplyr, forcats,
data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast,
stats, SummarizedExperiment, utils, purrr, stringi, stringr,
Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs,
data.table, htmltools, htmlwidgets, bsplus, shinyvalidate,
shiny, shinythemes, shinyFiles, shinyjs, shinyBS,
shinydashboard, biomaRt, callr, logr, ggplot2, svglite
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
coin, MASS, ggplot2, S4Vectors, stats, methods, utils, dplyr,
testthat, tibble, tidyr, forcats, stringr, ggtree,
BiocGenerics, ape, ggrepel, mia, purrr, tidyselect, treeio
stats, utils, irlba, methods, SingleCellExperiment,
SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0),
glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix,
DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats,
Rcpp, harmony (>= 1.2.0), limma, BiocNeighbors
grDevices, graphics, stats, utils, methods, statmod
methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot,
xtable, utils
ggplot2, stringr, plyr, ggrepel, reshape2, grDevices,
graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci,
tidyverse, methods, stats, SummarizedExperiment, S4Vectors
limma, stringr, qvalue, utils, stats, BiocParallel,
basilisk.utils, S4Vectors, dplyr
scales, cluster, graphics, ggpubr, gridExtra, vegan, rio,
MultiAssayExperiment, emmeans, reshape2, data.table
Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan,
mclust, apcluster, ggplot2, ellipse, limma, utils, statmod,
MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo,
stats, amap, Rtsne, gmodels
data.tree, reshape2, networkD3, stringdist, purrr, ape,
cowplot, ggnewscale, stringr, dplyr, rlist, pheatmap,
Biostrings, pwalign, IRanges, BiocGenerics(>= 0.36.1), ggtree
methods, stats, utils, data.table, S4Vectors, rlang, dplyr,
tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD,
magrittr
Biobase, graphics, grDevices, methods, stats
ggplot2, class, concaveman, grid, BiocParallel,
spatstat.explore, spatstat.geom, BiocGenerics, S4Vectors,
methods, spicyR, purrr, stats, data.table, dplyr, tidyr,
SingleCellExperiment, SpatialExperiment, SummarizedExperiment,
pheatmap, spatstat.random, lifecycle, simpleSeg, rlang,
pheatmap, wordcloud, RColorBrewer, data.table, methods,
grDevices, stats, graphics, GenomicRanges, BiocParallel,
S4Vectors
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
reshape2, utils, stats, methods
DelayedArray, GenomicRanges, HDF5Array, Matrix, stats,
stringr, utils
methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase
BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures,
GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv,
KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS,
graphics, stats, stats4, methods
S4Vectors, Biobase, scran, dplyr, ggplot2
data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
Biostrings, phangorn, stringdist, UpSetR
ggplot2, Matrix, doSNOW, cluster, parallel, foreach,
doParallel, matrixcalc, Rtsne, corpcor, umap
RColorBrewer, gplots, bbmle, statmod, grDevices, graphics,
stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods,
scater
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, pbapply, lmerTest, parallel, lme4, optparse, logging,
multcomp, ggplot2, RColorBrewer, patchwork, scales, rlang,
tibble, ggnewscale, survival, methods, BiocGenerics,
SummarizedExperiment, TreeSummarizedExperiment
BiocParallel, DelayedArray, WGCNA, ff, data.table,
dynamicTreeCut, Maaslin2, plyr, stats, psych, xml2, httr,
RJSONIO, logging, methods, utils
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
utils, reticulate, S4Vectors, methods, basilisk,
ExperimentHub, AnnotationHub
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy, pheatmap
caret, parallel, doParallel, foreach, e1071, future.apply,
future, missForest, pcaMethods, tidyverse, stats, utils,
methods, SummarizedExperiment, S4Vectors
flowCore, Biobase, stringr, uwot, iCellR, igraph, ggplot2,
RColorBrewer, Rfast, ComplexHeatmap, circlize, glmnetUtils,
e1071, xgboost, parallel, pbapply, reshape2, gtools, utils,
stats, cowplot, methods, grDevices, graphics
methods, S4Vectors, BiocGenerics, BiocManager, GenomicRanges,
InteractionSet, data.table, stats, rlang, glue, assertthat,
plyranges, magrittr, dbscan, purrr, progress, GenomeInfoDb,
strawr (>= 0.0.91), DelayedArray, HDF5Array, abind,
BiocParallel, IRanges, SummarizedExperiment, rhdf5,
plotgardener, RColorBrewer, colourvalues, utils, grDevices,
graphics, grid
Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr,
magrittr, rlang, S4Vectors
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, SingleCellExperiment,
stats, SummarizedExperiment, tidyr, utils
BiocGenerics, ProtGenerics, digest, irlba, stats, stats4,
graphics, grDevices, parallel, utils
methods, magrittr, phyloseq, limma, lme4, lmerTest, pheatmap,
rmarkdown, cluster, dplyr, ggplot2, gridExtra, ruv, sva,
tibble, tidyr, vegan, stats, utils, Matrix
methods, DelayedArray, Rcpp, S4Vectors, SingleCellExperiment,
SummarizedExperiment, ClusterR, benchmarkme, Matrix,
BiocParallel
Biobase, graphics, methods, utils, grDevices
stats, graphics, utils, limma (>= 3.30.13),
SummarizedExperiment (>= 1.10.0), preprocessCore (>= 1.36.0),
BiocFileCache, rappdirs, xml2, RCurl, ggplot2, PairedData,
rmarkdown
MatrixEQTL, dplyr, ggplot2, readxl, stringr, tidyr,
metagenomeSeq, pheatmap, broom, graphics, stats, methods
BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db,
org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA
biomaRt, fgsea, GenomicFeatures, GenomicRanges, ggplot2,
graphics, grDevices, Gviz, IRanges, limma, methods, parallel,
S4Vectors, stats, SummarizedExperiment, utils
GenomicAlignments, GenomicRanges, IRanges, Biostrings,
DNAcopy, Rsamtools, parallel, stringr
GenomicRanges, limma, vegan, BiocGenerics, minfi, IRanges,
S4Vectors, methods, parallel, ggplot2 (>= 2.0.0), permute,
Gviz, missMethyl, isva, SummarizedExperiment, SmartSVA,
graphics, stats, utils, matrixStats
impute (>= 1.58), dynamicTreeCut (>= 1.63), glmnet (>= 2.0),
grDevices, graphics, stats, utils, stringr, tibble, RPMM (>=
1.25), minfi (>= 1.30), dplyr, SummarizedExperiment, wateRmelon
e1071, edgeR, scater, stats, wrswoR, SummarizedExperiment,
SingleCellExperiment
xfun, utils, fs, GenomicRanges, readr, cmdfun, dplyr, magrittr
data.table, parallel, ROCR, matrixcalc, mclust, ggplot2,
doParallel, foreach, MCMCpack, cowplot, magrittr, mvtnorm,
truncnorm, assertthat, BiocStyle, stats, utils
Biostrings, dplyr, cmdfun (>= 1.0.2), GenomicRanges, ggplot2,
ggseqlogo, magrittr, matrixStats, methods, patchwork, processx,
purrr, rlang, readr, stats, tools, tibble, tidyr, utils,
usethis, universalmotif (>= 1.9.3), xml2
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, DOSE, enrichplot, GOSemSim (>= 2.31.2),
methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5)
markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils,
fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite
methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape
(>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges,
circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3),
ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors
dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils,
rlang, graphics, matrixStats, tidyr
BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics,
methods, S4Vectors, Spectra (>= 1.13.2), BiocParallel,
SummarizedExperiment, QFeatures, AnnotationHub, graphics,
CompoundDb
utils, MsCoreUtils, BiocParallel, methods, stats
data.table, httr, jsonlite, methods, MultiAssayExperiment,
struct, SummarizedExperiment, utils
optimx, Formula, plyr, multtest, BiocParallel, ggplot2
KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75,
stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi,
MWASTools, mygene
flowCore (>= 1.4),tidyr (>=
0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices,
graphics, stats, utils
parallel, matrixStats, foreach, Matrix, gplots, graphics,
grDevices, stats, utils, Wrench
grDevices, graphics, methods, stats (>= 3.4), utils (>= 3.4),
Matrix (>= 1.2), matrixStats (>= 0.54), beanplot (>= 1.2),
gplots (>= 3.0.1), RColorBrewer (>= 1.1.2),
SummarizedExperiment (>= 1.12), SingleCellExperiment, igraph,
dplyr, tidyr, tibble, ggplot2
utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats,
clusterProfiler, RecordLinkage, RCy3
Rcpp (>= 0.12.4.5), methods, utils, grDevices, stats,
GenomeInfoDb, IRanges, Biostrings, reshape2, minpack.lm,
data.table
Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase,
grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0),
methods, RColorBrewer, shiny, stats, SummarizedExperiment,
utils
Biobase, GenomicRanges, IRanges, S4Vectors, dplyr, magrittr,
minfi, bsseq, quadprog, plyranges, stats, utils, bumphunter,
genefilter, methods, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
Rcpp (>= 1.0.6), ExperimentHub, dplyr, impute,
PerformanceAnalytics, Biobase, ggpmisc, tidyverse, ggplot2,
ggpubr, minfi, tibble, RPMM, stats, graphics, tidyr, gridExtra,
preprocessCore, dynamicTreeCut, planet
RobustRankAggreg, ggplot2, stringr, stats, clusterProfiler,
missMethyl, org.Hs.eg.db, reactome.db, BiocParallel, GO.db,
AnnotationDbi, shiny,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
BiocParallel, parallel, stats, methods, corpcor,
SummarizedExperiment, utils
foreach, RPMM, RColorBrewer, ggplot2, RCurl, impute,
data.table, limma, R.matlab, digest
marray, gplots, IRanges, BiocGenerics, Gviz,
GenomicAlignments, Biostrings, parallel, data.table,
GenomeInfoDb, S4Vectors
shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings,
pwalign, Rfast, grDevices, graphics, stats, utils, tools,
methods, shinyFiles, data.table, SummarizedExperiment
bsseq, DelayedArray, DelayedMatrixStats, DSS, IRanges,
GenomeInfoDb, GenomicRanges, methods, parallel, stats,
S4Vectors
BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
SummarizedExperiment, Biobase, graphics, lattice, annotate,
genefilter, AnnotationDbi, minfi, stats4, illuminaio,
GenomicFeatures
dplyr, methods, httr, scales, ggthemes, ggplot2, utils, rlang,
cowplot, stats
methods, stats, ggplot2, Rcpp, dplyr, ggmcmc, MCMCpack,
MCMCglmm, coda, magrittr, tibble, Biobase
mia, ape, dplyr, httr, methods, plyr, reshape2, S4Vectors,
urltools, utils, tidyjson
ape, BiocGenerics, BiocParallel, Biostrings, bluster,
DECIPHER, decontam, DelayedArray, DelayedMatrixStats,
DirichletMultinomial, dplyr, IRanges, MASS, MatrixGenerics,
mediation, methods, rbiom, rlang, S4Vectors, scater, scuttle,
stats, tibble, tidyr, utils, vegan
SummarizedExperiment, deSolve, stats, poweRlaw,
MatrixGenerics, S4Vectors
ape, BiocGenerics, BiocParallel, DelayedArray,
DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggplot2,
ggraph, ggtree, methods, rlang, scater, S4Vectors,
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
clusterProfiler (>= 4.5.2), config, DT, enrichplot, golem,
gson, methods, magrittr, shiny (>= 1.6.0), shinyWidgets,
shinycustomloader, htmltools, ggplot2, graphics, stats, utils,
yulab.utils
ape, tidyr, ggplot2, magrittr, dplyr, Biostrings, ggrepel,
vegan, zoo, ggtree, tidytree (>= 0.4.2), MASS, methods, rlang,
tibble, grDevices, stats, utils, coin, ggsignif, patchwork,
ggstar, tidyselect, SummarizedExperiment, foreach, treeio (>=
1.17.2), pillar, cli, plyr, dtplyr, ggtreeExtra, data.table,
ggfun (>= 0.1.1)
BiocParallel, ggplot2, ggside, grid, rlang, stats, stringr,
TreeSummarizedExperiment
TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2,
ggpubr, ggridges, glue, S4Vectors, dirmult
BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>=
1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods,
igraph, irlba, utils, cowplot, BiocParallel, BiocSingular,
limma, ggplot2, tibble, matrixStats, ggraph, gtools,
SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel,
ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv
methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
biganalytics, stringr, Hmisc, utils
S4Vectors, GenomeInfoDb, Biobase (>= 2.33.2), IRanges,
beanplot, RColorBrewer, lattice, nor1mix, siggenes, limma,
preprocessCore, illuminaio (>= 0.23.2), DelayedMatrixStats (>=
1.3.4), mclust, genefilter, nlme, reshape, MASS, quadprog,
data.table, GEOquery, stats, grDevices, graphics, utils,
DelayedArray (>= 0.15.16), HDF5Array, BiocParallel
BiocGenerics, S4Vectors, IRanges, GenomicRanges, data.table,
ggplot2, Biobase, stats, bsseq, methods
utils, methods, graphics, KernSmooth, stats
graph,ROntoTools, ggplot2, org.Hs.eg.db, AnnotationDbi,
Rgraphviz
methods, stats, utils, RCurl, httr, stringr, Hmisc, energy,
entropy, gplots, glmnet, impute, limma,
pcalg,TCGAbiolinks,dplyr,SummarizedExperiment, ctc,
InvariantCausalPrediction, Category, GOstats, org.Hs.eg.db
DBI, RSQLite, stringr, sqldf, plyr, methods
WGCNA, flashClust, dynamicTreeCut, GFA, igraph, linkcomm, MCL,
fabia, NMF, biclust, iBBiG, BicARE, isa2, s4vd, BiBitR, rqubic,
Biobase, PMA, stats, dbscan, subspace, mclust, SOMbrero,
ppclust, Rcpp, utils, SummarizedExperiment, GSEABase,
org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE,
MatrixCorrelation, energy
corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler,
ReactomePA, DOSE, survival, grDevices, graphics, stats,
linkcomm, utils, Rcpp, org.Hs.eg.db, foreach, doParallel
purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap,
reshape2, corrplot, grDevices, graphics, stats, utils,
data.table, R.utils, viridis
AnnotationDbi, BiasedUrn, Biobase, BiocGenerics,
GenomicRanges, GO.db, IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICv2manifest, IRanges, limma,
methods, methylumi, minfi, org.Hs.eg.db, ruv, S4Vectors,
statmod, stringr, SummarizedExperiment
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
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, ggrepel, BiocParallel, utils,
gsignal, rgl
gdata, pls, sfsmisc, MASS, rpart, genefilter, fpc, ggvis,
shiny, gbm, RColorBrewer, hwriter, threejs (>= 0.2.2), mlbench,
stats4, tools, grDevices, graphics, stats, magrittr,
SummarizedExperiment
AnnotationDbi, gplots, graphics, stats, utils
GenomicRanges, locfit, BSgenome, Biostrings, shiny, ggplot2,
RColorBrewer, graphics, grDevices, parallel, S4Vectors, methods
Maaslin2, metafor, fpc, igraph, ggplot2, dplyr, tidyr,
stringr, cowplot, utils, stats, grDevices
cluster, graph, Rgraphviz, flexclust, lattice, naturalsort,
snowfall, stats4, tsne, methods, graphics, stats, utils,
Linnorm, data.table, Rcpp, RcppEigen, matrixStats, grDevices,
e1071, ggplot2, wesanderson
S4Vectors, MASS (>= 1.0.0), limma, viridis, edgeR, graphics,
methods, grDevices, reshape2, NMI, zoo, ClusterR, splines,
matrixStats
grDevices, graphics, stats, utils, WGCNA, dynamicTreeCut,
igraph, cluster, AMOUNTAIN, RColorBrewer
methods, BiocGenerics, GenomicRanges, S4Vectors, IRanges,
XVector, stringi, stringr, crayon, grDevices
rhdf5, dplyr, tidyr, reshape2, pheatmap, ggplot2, methods,
RColorBrewer, cowplot, ggrepel, reticulate, HDF5Array,
grDevices, stats, magrittr, forcats, utils, corrplot,
DelayedArray, Rtsne, uwot, basilisk, stringi
stats, utils, RCy3, stringr, graphics, grDevices, RUnit,
BiocParallel, igraph
methods, graphite, genefilter, BiocGenerics, gplots, GSEABase,
Biobase, parallel, corpcor, svd, cluster, grDevices, graphics,
stats, utils
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
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, GenomeInfoDb, S4Vectors
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
MultiAssayExperiment, methods, survminer, graph, graphite,
AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap,
survival, RColorBrewer, SuperExactTest, reshape, NbClust,
S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap,
FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase,
ggplotify, qpgraph, org.Hs.eg.db, Matrix
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
GenomeInfoDb, graphics, harmonicmeanp, IRanges, matrixStats,
methods, parallel, patchwork, rlang, S4Vectors, stats,
universalmotif,
httr, curl, GenomicRanges, dplyr, ggplot2, reshape2, scales,
gtools, tidyr, data.table, jsonlite, rlist, GenomeInfoDb,
methods, biomaRt, stats, IRanges
data.table (>= 1.14.2), SummarizedExperiment (>= 1.30.2),
BiocParallel (>= 1.28.3), fitdistrplus (>= 1.1), igraph (>=
1.4.3), BiocSingular (>= 1.10.0), S4Vectors (>= 0.32.3),
SingleCellExperiment (>= 1.16.0), bluster (>= 1.4.0), fgsea (>=
1.20.0), scran (>= 1.22.1), ComplexHeatmap (>= 2.16.0), grid,
stats
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
ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges,
MsCoreUtils, methods, stats
ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges,
rawrr (>= 1.13.1), utils, BiocParallel
BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3),
DBI, MsCoreUtils, IRanges, data.table, progress, stringi,
BiocGenerics
methods, S4Vectors, IRanges, Spectra, SummarizedExperiment,
QFeatures, DBI, BiocGenerics
methods, ProtGenerics (>= 1.23.5), MsCoreUtils,
SummarizedExperiment, stats
BSgenome, easyRNASeq, edgeR, GenomicAlignments,
GenomicFeatures, GenomeInfoDb, ggbio, ggplot2, IRanges,
parallel, plyr, Rsamtools, R.utils, stats,
SummarizedExperiment, S4Vectors, utils
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
MsCoreUtils, PSMatch, BiocParallel, IRanges (>= 2.13.28),
plyr, vsn, grid, stats4, affy, impute, pcaMethods, MALDIquant
(>= 1.16), mzID (>= 1.5.2), digest, lattice, ggplot2, scales,
MASS, Rcpp
MSnbase (>= 1.12.1), mzID (>= 1.3.5), R.cache, foreach,
doParallel, parallel, methods, iterators, data.table, Biobase,
ProtGenerics, reshape2, dplyr, mzR, BiocStyle, msmsTests,
ggplot2, RUnit, BiocGenerics, Biostrings, purrr, rlang,
stringr, tibble, AnnotationHub, AnnotationDbi, xtable
QFeatures, SummarizedExperiment, magrittr, rlang, dplyr,
purrr, stats, tidyr, stringr, ggplot2, ggseqlogo, heatmaply,
readr, rstatix, tibble, ggpubr
SummarizedExperiment, S4Vectors, pcaMethods (>= 1.24.0), crmn,
preprocessCore, dplyr (>= 0.7), tidyr, tibble (>= 1.2),
magrittr, rlang, stats, stringr, methods, missForest, sva, VIM,
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
stats, methods, lme4, purrr, BiocParallel, Matrix, MASS,
limma, SummarizedExperiment, MultiAssayExperiment, codetools
MSstatsConvert, data.table, checkmate, MASS, htmltools, limma,
lme4, preprocessCore, survival, utils, Rcpp, ggplot2, ggrepel,
gplots, plotly, marray, stats, grDevices, graphics, methods,
statmod, parallel
data.table, log4r, methods, checkmate, utils, stringi
dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp,
checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse,
scales, stats
minpack.lm, ggplot2, utils, stats, grDevices
dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid
shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2,plotly,
data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM,
MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid,
utils, stats, htmltools, methods, tidyr, grDevices,
graphics,mockery
limma, lme4, lmerTest, methods, data.table, stats, utils,
ggplot2, grDevices, graphics, MSstats, MSstatsConvert,
checkmate, plotly, htmltools
methods, stats, MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, DelayedArray
graphics, grDevices, stats, methods, fields
Biobase, BiocBaseUtils, BiocGenerics, DelayedArray,
GenomicRanges, IRanges, methods, S4Vectors, tidyr, utils
Matrix, ggplot2, MultiAssayExperiment, ropls, graphics,
methods, plotrix, grDevices, pcaMethods
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
stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, S4Vectors, grid, dplyr, tidyr, matrixStats, stats,
fitdistrplus, viridis, ggplot2, circlize, mashr, grDevices
stringr, readr, WGCNA, dplyr, reshape2, data.table, patchwork,
scales, igraph, flashClust, ggplot2, dcanr, cowplot, ggrepel,
methods, SummarizedExperiment
stats, utils, methods, igraph, Matrix, BiocGenerics,
BiocParallel, IRanges, S4Vectors, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, BiocNeighbors,
BiocSingular, ScaledMatrix, beachmat, scuttle, metapod, scran,
batchelor, uwot
glm2, ppcor, qvalue, car, boot, grid, ggplot2, gridExtra,
igraph, SummarizedExperiment, KEGGgraph, RCurl, KEGGREST,
ComplexHeatmap, stats, utils
methods, utils, stats, httr (>= 0.3), jsonlite (>= 0.9.7),
Hmisc, sqldf, plyr, S4Vectors
XML, plyr, parallel, doParallel, foreach, iterators,
ProtGenerics
Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.17.3),
ncdf4
cpp11 (>= 0.2.5), readr, cli, S4Vectors, SummarizedExperiment,
BiocSingular, bsseq, forcats, assertthat, AnnotationDbi, Rcpp,
dplyr, dbscan, e1071, fs, GenomicRanges, Biostrings, ggrastr,
glue, graphics, IRanges, limma (>= 3.44.0), patchwork, purrr,
rlang, R.utils, Rsamtools, scales (>= 1.2.0), stats, stringr,
tibble, tidyr, utils, withr
BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes,
grDevices, IRanges, methods, pheatmap, RColorBrewer, stats,
utils
httr, xml2, utils, methods, grDevices, ggplot2, IRanges,
GenomicRanges, S4Vectors
SingleCellExperiment, SummarizedExperiment, SeuratObject, ks,
Matrix, stats, methods, ggrastr
e1071, nnet, randomForest, naturalsort, graphics, stats,
utils, matrixStats, epiNEM
Rcpp, RcppParallel, parallel, grDevices, graphics, stats,
utils, dynamicTreeCut, WGCNA, impute, colorspace, methods,
BiocStyle, R.utils
glasso, mvtnorm, GeneNet, huge, CompQuadForm, ggm, mclust,
parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2, grDevices, graphics, stats, utils
stats, Matrix, dplyr, doParallel, foreach, parallel,
sparseMVN, ggplot2, gridExtra, pROC
ggplot2, graph, igraph, parallel, plyr, qvalue, RColorBrewer
entropy, SummarizedExperiment, SingleCellExperiment, Matrix,
cluster, data.table, stats, methods, DelayedArray, HDF5Array
(>= 1.15.13)
RCy3, viridisLite, STRINGdb, Biobase, GOstats, AnnotationDbi,
matrixStats, GO.db, org.Hs.eg.db, Matrix, gplots, nnet,
data.table, vegan, stats, utils, reshape, reshape2, penalized,
parallel, doParallel, foreach, ggplot2, ggdendro, grid, MASS,
assertthat, tidyr, methods, dplyr, graphics
methods, SingleCellExperiment, parallel, irlba, Matrix,
DelayedArray, BiocSingular, SharedObject, stats
Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro,
grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate,
methods, plotly (>= 4.9.4), reshape2, 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
vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods,
utils, stats, SummarizedExperiment, matrixStats, ggforce
dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr,
stats, methods
Biobase, methods, BiocGenerics, graphics, stats
stats, IRanges, S4Vectors, graphics, methods
Biobase, BiocGenerics, Biostrings, GenomeInfoDb,
GenomicRanges, IRanges, Rsamtools, S4Vectors, ShortRead, dplyr,
ggplot2, magrittr, parallel, stats, utils, grDevices
stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang,
S4Vectors, scales, InteractionSet, ggplot2, grDevices,
plyranges, data.table, progress, ggridges
multtest (>= 1.7.3), graphics, grDevices, stats, interp
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
utils, ape, Biostrings, GenomicRanges, IRanges, methods,
topGO, jsonlite
compositions, DT, grDevices, knitr, jsonlite, matrixStats,
rmarkdown, shiny, stats, vegan, zCompositions
stats, utils, grDevices, graphics, methods, rexposome, limma,
sva, ggplot2, ggrepel, PMA, omicade4, gridExtra, MultiDataSet,
SmartSVA, isva, parallel, SummarizedExperiment, stringr
methods, matrixStats, graphics, stats, SummarizedExperiment,
MultiAssayExperiment, RaggedExperiment
survminer, survival, fastmatch, reshape2, stringr, beeswarm,
grDevices, DT, shiny, shinythemes, shinyWidgets, plotly,
networkD3, httr, matrixStats, RColorBrewer, Biobase, fgsea,
openxlsx, psych, shinybusy, ggseqlogo, htmlwidgets, graphics,
grid, stats, utils, methods, shinyjs, curl, flatxml, ggplot2,
S4Vectors, SummarizedExperiment, RSQLite, Matrix,
shinycssloaders, ROCR, drc
dplyr, ggplot2, forcats, tibble, gridExtra, magrittr, readr,
tidyselect, grid, stats, stringr
shiny, MSnbase, PSMatch, SummarizedExperiment,
MultiAssayExperiment, shinyBS, shinyjs, shinyjqui, DT,
RColorBrewer, gplots, highcharter, visNetwork, tibble,
grDevices, stats, utils, htmlwidgets, vioplot, graphics,
FactoMineR, dendextend, dplyr, factoextra, tidyr
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
Biobase, S4Vectors, methods, stats, utils, BiocFileCache,
shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT,
igraph, AnnotationHub, SummarizedExperiment, reticulate,
R.utils, httr, basilisk
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
MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist,
summarytools, graphics, stats, utils
fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt,
Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl
limma, stats, reshape, ggplot2, grDevices, RColorBrewer,
pheatmap, knitr, methods, devtools, parallelDist,
transport, parallel, Rfast, robustbase, dbscan, randomForest,
foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse
RSQLite, S4Vectors, GenomeInfoDb, IRanges, GenomicRanges,
GenomicFeatures, AnnotationDbi, rlang, methods, tools, utils,
BiocFileCache, DBI, dbplyr, tibble
methods, utils, stats, DBI, BiocManager, Biobase, graph, RBGL,
S4Vectors, IRanges, GenomicRanges (>= 1.31.13), txdbmaker
dplyr, methods, stats, utils, Matrix, jsonlite, homologene,
gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr,
patchwork, DelayedArray, grr, repmis, ggtree, tools
AnnotationHub, basilisk, BiocParallel, colorspace, cowplot,
DelayedArray, dplyr, ExperimentHub, ggplot2, ggpubr, ggrepel,
ggsci, grDevices, grid, HDF5Array, keras, methods, orthosData,
parallel, plyr, reticulate, rlang, S4Vectors, stats,
tensorflow, tidyr
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
SummarizedExperiment, S4Vectors, stats, methods, abind,
BiocParallel
SummarizedExperiment, KEGGREST, igraph, data.table, methods,
stats, magrittr, CompQuadForm, tibble
matrixStats, igraph, ggplot2, grid, reshape, plyr, RUnit,
hexbin
GenomicRanges, Rsamtools, IRanges, S4Vectors, GenomeInfoDb,
grDevices
clusterProfiler, dplyr, forcats, GSEABase, igraph, limma,
metap, org.Hs.eg.db, parallel, preprocessCore, RColorBrewer,
rlang, tibble, withr, utils
graphics, grDevices, MASS, methods, pvclust, stats, utils,
RedeR
stats, data.table, depmixS4, Seurat, SingleCellExperiment,
AnnotationHub, magrittr, GenomicRanges, BiocStyle
circlize, clusterProfiler, ComplexHeatmap, dplyr, fgsea,
ggforce, ggplot2, ggpubr, ggraph, ggrepel, grid, igraph, purrr,
sigora, stringr, tibble, tidygraph, tidyr, vegan, visNetwork
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, BiocSingular, BiocParallel,
Rcpp, dqrng
data.table, MultiAssayExperiment, ConsensusClusterPlus,
igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro,
CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics,
survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel,
rlang, piano, scales, survcomp, genefu, ggplot2, switchBox,
reportROC, pROC, verification, utils
circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2,
grDevices, grid, gridExtra, methods, plyr, stats, utils
ROTS, limma, affy, genefilter, preprocessCore,
aroma.affymetrix, aroma.core
assertthat, circular, conicfit, doParallel, foreach, genlasso
(>= 1.4), graphics, methods, parallel, scater,
SingleCellExperiment, SummarizedExperiment, stats, utils
graphics, stats, methods, ggplot2, utils, grDevices, stringr,
plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl,
shinyWidgets, htmlwidgets, DT, gridExtra, data.table, plotly,
colourpicker, shinytoastr, scales, shinycssloaders
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
utils, methods, grDevices, graphics, circlize, httr, dplyr,
attempt, lubridate, survival, survminer, ggplot2,
GenomicRanges, SummarizedExperiment, S4Vectors, yaml, parallel,
future, future.apply
data.table, rhdf5client(>= 1.25.1), httr, stringr, stats,
utils, Biobase, methods
BiocGenerics, Biobase, S4Vectors, SummarizedExperiment,
MultiAssayExperiment, BiocParallel, ggplot2, RColorBrewer,
magicaxis, parallel, caTools, methods, downloader, stats,
utils, graphics, grDevices, reshape2, jsonlite, data.table,
checkmate, boot, coop
igraph, Matrix, foreach, doParallel, dplyr, stats, utils,
parallel
Biobase, biodb, biodbChebi, data.table, futile.logger,
ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets,
igraph, limma, methods, MultiAssayExperiment, MultiDataSet,
PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble,
tidyr, utils, VennDiagram
Rcpp (>= 0.12.8), SummarizedExperiment, methods, stats, dplyr,
tibble, ggplot2, tidyr
survival, limma, gplots, Category, AnnotationDbi, hopach,
biomaRt, GSEABase, genefilter, xtable, annotate, mgcv,
hgu133a.db, ellipse
SmoothWin, methods, car, nlme, nortest, MASS, msgps, logistf,
knitr, tools, pingr, ggplot2, reshape, corrplot, graph, lme4,
graphics, grDevices, utils, stats
ape, phangorn, tidyr, ggplot2, ggtree, methods
BiocFileCache, BiocGenerics, methods, GenomicRanges, IRanges,
S4Vectors, edgeR, cli, utils
plyr, stats, graphics, matrixStats, methods
ruv, e1071, dendextend, limma, pcaMethods, stats,
RColorBrewer, circlize, dplyr, igraph, pheatmap,
preprocessCore, tidyr, rlang, graphics, grDevices, utils,
SummarizedExperiment, methods, S4Vectors, BiocGenerics,
ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext,
stringi
ape, bioDist, BiocStyle, Biostrings, colourpicker, data.table,
dplyr, DT, energy, ExperimentHub, extrafont, fastcluster,
ggplot2, gridExtra, pbapply, plotly, RColorBrewer, RCurl,
Rfast, scattermore, shiny, shinyBS, shinycssloaders,
shinyFiles, shinyjs, stringr, tsne, umap, xml2, zoo, yaml
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, 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,
GenomeInfoDb, parallel, stats, utils, rmarkdown
dplyr, utils, stats, GenomicRanges, BiocGenerics, methods
cluster, umap, tsne, kernlab, vegan, dbscan, igraph, scales,
Hmisc, patchwork, grDevices, stats, methods,
SummarizedExperiment
utils, Biobase (>= 2.5.5), MASS, methods
curl, data.table, dplyr, GenomeInfoDb, GenomicRanges, glue,
grDevices, grid, ggplotify, IRanges, methods, plyranges, purrr,
Rcpp, RColorBrewer, rhdf5, rlang, stats, strawr, tools, utils,
withr
mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr,
lmerTest, performance, grid, stats, pheatmap, vegan, Biobase,
BiocStyle, TreeSummarizedExperiment
InteractionSet, GenomeInfoDb, BiocGenerics, GenomicRanges,
plyranges, IRanges, S4Vectors, rlang, dplyr, tibble,
tidyselect, methods, utils
dplyr, purrr, rlang, SummarizedExperiment, tidyr, tidyselect,
vctrs, tibble, pillar, cli, glue, S7, S4Vectors, utils, methods
stats, impute, pcaMethods, missForest, ggplot2, methods,
SummarizedExperiment, S4Vectors, matrixStats, grDevices,
reshape2, utils
ggplot2, gridExtra, mclust, diptest, rlist, shiny, DT,
LaplacesDemon, purrr, shinyjs, readr, grDevices, stats, utils
Rcpp (>= 0.11.1), parallel, stats (>= 4.3.0), graphics,
grDevices, utils, Biobase, BiocGenerics, Matrix, GenomeInfoDb,
IRanges, Biostrings, BSgenome (>= 1.32.0)
methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics
stats, utils, grDevices, mvtnorm, sn, dplyr, flowPeaks,
ggplot2, tidyverse, cowplot, mlrMBO, DiceKriging, smoof,
ParamHelpers, lhs, rgenoud, BiocManager
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
parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges,
Biobase, GenomeInfoDb, S4Vectors
S4Vectors, IRanges, GenomicRanges, randomForest, ModelMetrics,
e1071, PRROC, pROC, caret, utils, cluster, dbscan, doSNOW,
foreach, pbapply, stats, parallel, gtools, rCGH
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
stats, utils, methods, BiocGenerics, SummarizedExperiment,
S4Vectors, extraDistr
Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra,
decoupleR, reshape2
methods, cluster, stats, limma, NMF, ROCR, ggalluvial,
RColorBrewer, dplyr, fgsea, reshape2, viridis, scales, Matrix,
MatrixModels, msigdbr, ggplot2, cowplot, ggrepel, umap, tsne
stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling,
class, kernlab, lattice, nnet, randomForest, proxy, FNN,
hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales,
MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools,
plyr, ggplot2, biomaRt, utils, grDevices, graphics
shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics,
utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker,
shinyhelper, shinyWidgets, shinyjs, colorspace, stats,
grDevices, grid, BiocGenerics, shinydashboard
dplyr, magrittr, data.table, RColorBrewer, ggplot2, S4Vectors,
ComplexHeatmap, stringr, NormalyzerDE, tibble, limma, MASS,
edgeR, matrixStats, preprocessCore, stats, gtools, methods,
ROTS, ComplexUpset, tidyr, purrr, circlize, gprofiler2,
plotROC, MSnbase, UpSetR, dendsort, vsn, Biobase, reshape2,
POMA, ggtext, scales, DEqMS
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.35.1), DAPARdata (>= 1.30.0), rhandsontable,
data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets,
webshot, shinythemes, later, shinycssloaders, future, promises,
shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase,
DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown,
rclipboard, sass, shinyTree, shinyWidgets
gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats,
graphics
utils, stats, igraph, methods, Matrix, BiocParallel,
BiocGenerics, ProtGenerics (>= 1.27.1), QFeatures, MsCoreUtils
Biobase, bit64, chron, data.table, doParallel, DT, enviPat,
foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra,
Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5,
rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats,
utils
magrittr, ggplot2, dplyr, seqTools, zlibbioc, data.table,
reshape2, grDevices, graphics, stats, utils, Rcpp, rlang,
RSeqAn
Biobase, methods, knitr, tools, xtable, pander, S4Vectors
graphics, methods, stats, utils, Biobase (>= 2.18.0), CGHbase
(>= 1.18.0), CGHcall (>= 2.18.0), DNAcopy (>= 1.32.0),
GenomicRanges (>= 1.20), IRanges (>= 2.2), matrixStats (>=
0.60.0), R.utils (>= 2.9.0), Rsamtools (>= 1.20), future.apply
(>= 1.8.1)
methods, stats, utils, S4Vectors, IRanges,
SummarizedExperiment, BiocGenerics, ProtGenerics (>= 1.35.1),
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, GenomeInfoDb, GenomicRanges, GenomicFeatures, mvtnorm,
qtl, Rgraphviz
assertthat, BiocGenerics, Biostrings, dplyr (>= 1.0.0),
ggdendro, ggplot2, graphics, grDevices, IRanges, limma,
magrittr, preprocessCore, purrr, RColorBrewer, readr, rlang,
scales, stats, stringr, tibble, tidyr, tidyselect, utils
SummarizedExperiment, utils, sva, stats, methods, graphics,
Hmisc
dplyr, sva, stats, ggplot2, rlang, methods
methods, rlang, checkmate, dplyr, collapse, vroom, tidyr,
tibble, utils, stats, ashr, S4Vectors, BiocGenerics
Biobase, limSolve, MASS, methods, preprocessCore, stats,
SummarizedExperiment, ggplot2, tidyr, rlang, utils
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
SummarizedExperiment, BiocGenerics, data.table, S4Vectors,
Biobase, parallel, BiocParallel, RColorBrewer, caTools,
magicaxis, methods, reshape2, scales, grDevices, graphics,
stats, utils, assertthat, matrixStats, downloader
BiocBaseUtils, BiocGenerics, GenomeInfoDb, IRanges, Matrix,
MatrixGenerics, methods, S4Vectors, stats,
SummarizedExperiment, utils
parallel, doParallel, foreach, doRNG, methods, data.table,
matrixStats, GenomicRanges, IRanges, BiocGenerics, EnvStats,
ExtDist, S4Vectors, gamlss, gamlss.dist
graphics, stats, utils, digest, glmnet, KernSmooth, grDevices,
GenomicAlignments, Rsamtools, parallel, biomaRt, Biostrings,
BiocGenerics
methods, graphics, utils, stats, Rdpack (>= 0.7)
jsonlite, httr, stringr, R.utils, utils, paws.storage, methods
dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools,
BiocManager, BiocParallel, rawrr (>= 1.15.5), rlang, reshape2,
scales, shiny (>= 1.5), stats, utils
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,GenomeInfoDb,GenomicRanges,AnnotationDbi,
parallel,IRanges,grDevices,aCGH
AUCell (>= 1.1.6), BiocGenerics, data.table, graphics,
GenomeInfoDb, GenomicRanges, arrow (>= 2.0.0), dplyr, tibble,
GSEABase, methods, R.utils, stats, SummarizedExperiment,
S4Vectors, utils, zoo
RColorBrewer, alabama, edgeR, reshape2, tseries, stats, VGAM,
ggplot2 (>= 2.2.1.9000), nleqslv, phyloseq, tensor, MASS,
grDevices, graphics, methods
Biostrings, GOSemSim, curl, doParallel, foreach, httr2,
jsonlite, methods, rlang, stats, utils
RcppAnnoy, igraph, NbClust, Rtsne, ggplot2(>= 3.4.0), methods,
pracma, umap, grDevices, graphics, stats, Rcpp (>= 0.11.0),
MatrixGenerics, SingleCellExperiment
utils, stats, BiocParallel, batchtools, DiagrammeR, shiny,
R.utils, codetools, basilisk
rappdirs, methods, utils, git2r, httr, S4Vectors
httr, methods, RJSONIO, XML, utils, BiocGenerics, stats,
graph, fs, uuid, stringi, glue, RCurl, base64url, base64enc,
IRkernel, IRdisplay, RColorBrewer, gplots
methods, httpuv (>= 1.5.0), BiocGenerics, base64enc, utils
graphics, grDevices, methods, stats, MASS, rgl
Biobase, BiocSingular, dplyr, ggplot2, gplots, httr, igraph,
jsonlite, methods, progress, RColorBrewer,
SummarizedExperiment, tidyr
AnnotationDbi, DOSE (>= 3.5.1), enrichplot, ggplot2 (>=
3.3.5), ggraph, reactome.db, igraph, graphite, gson,
yulab.utils (>= 0.1.5)
utils, methods, knitr (>= 1.32), rmarkdown, CodeDepends,
dir.expiry, filelock, BiocStyle
dplyr, ggplot2, magrittr, tidyr, SummarizedExperiment
phyloseq, ks, reshape2, ggplot2, stats, methods, graphics,
grDevices, matrixStats, Matrix
minfi, HDF5Array, rhdf5, S4Vectors, utils, methods, RCurl,
R.utils, BiocFileCache, basilisk, reticulate,
DelayedMatrixStats
AnnotationDbi, graphics, IRanges (>= 1.13.5), stats, utils
WGCNA, ica, moments, clusterProfiler, msigdbr, RColorBrewer,
car, lme4, lmerTest, pheatmap, biomaRt, stats, grDevices,
BiocParallel, ggplot2, patchwork, BiocGenerics, S4Vectors
stats, RColorBrewer, Rtsne, umap, ggplot2, ggrepel, reshape2,
methods, scales, cluster, grid, grDevices
glmnet, SummarizedExperiment, S4Vectors, limma, edgeR, stats,
pbapply, utils, methods
Biostrings, BSgenome, BSgenome.Hsapiens.1000genomes.hs37d5,
data.table, GenomeInfoDb, GenomicRanges, glmnet, ggplot2,
gridExtra, IRanges, lsa, MutationalPatterns, nnls, parallel,
reshape2, S4Vectors, RhpcBLASctl
Rcwl, RcwlPipelines, BiocFileCache, S4Vectors, stats, tools,
utils, methods, jsonlite, yaml, basilisk
methods, utils, stats, lsr, FactoMineR, stringr, circlize,
corrplot, ggplot2, ggridges, reshape2, pryr, S4Vectors,
imputeLCMD, scatterplot3d, glmnet, gridExtra, grid, Hmisc,
gplots, gtools, scales, lme4, grDevices, graphics, ggrepel,
mice
httr, stringi, rsvg, magick, data.table, Biostrings, utils,
rvest, xml2, IRanges, S4Vectors, jsonlite
utils, GenomeInfoDb, data.table, IRanges, GenomicRanges,
parallel, Rsamtools
Biostrings, GenomicRanges, methods, graphics, seqLogo
GenomeInfoDb, GenomicFeatures, GenomicRanges, ggplot2,
graphics, IRanges, methods, regioneR, S4Vectors, stats,
TxDb.Hsapiens.UCSC.hg19.knownGene
graphics, rjson, GetoptLong (>= 0.0.9), RCurl, utils, stats,
GlobalOptions, shiny, DT, GenomicFeatures, digest, GO.db,
progress, circlize, AnnotationDbi,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, RColorBrewer,
S4Vectors, GenomeInfoDb, foreach, doParallel, Rcpp
txdbmaker, SGSeq, GenomicRanges, methods, utils
dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors,
tidyr, tools, yaml
Rsamtools, IRanges, S4Vectors, baySeq, GenomeInfoDb, seqLogo
plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools,
utils, RSQLite
graphics, methods, stats, utils, grid, gridExtra, reshape2,
gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL,
linkcomm, dynamicTreeCut, gsubfn, hash, png, sqldf, igraph,
BgeeDB, knitr, RITANdata, GenomicFeatures, ensembldb,
AnnotationFilter, EnsDb.Hsapiens.v86
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
Rcpp (>= 0.12.5), consensusSeekeR, BiocGenerics, GenomeInfoDb,
S4Vectors (>= 0.23.10), BiocParallel, stats, graphics, methods,
grDevices
Biobase (>= 2.5.5), e1071, graphics, grDevices, kernlab,
methods, pamr, stats, utils
assertthat, Biobase, ChemmineR, data.table, digest, dplyr,
enviPat, glue, httr, httr2, logger, methods, MSnbase, mzR,
purrr, R.utils, rcdk, readJDX, readr, rjson, S4Vectors, tibble,
tidyselect, webchem, XML, yaml
ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats,
SummarizedExperiment, methods
stats, grDevices, grid, ggplot2, gplots, utils, TMB, nloptr,
scales
GenomicRanges, IRanges, BiocGenerics, GenomeInfoDb,
bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot
methods, S4Vectors, IRanges, BiocGenerics, GenomicRanges, Gviz
methods, BiocGenerics, S4Vectors, IRanges, GenomicRanges,
stats, ranger
methods, S4Vectors, BiocGenerics, IRanges, GenomicRanges, Gviz
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr,
magrittr, rlang, edgeR, foreach, mice
biomaRt,edgeR,heatmap3,matlab,KEGGREST,methods,grDevices,
graphics, stats, Rcpp (>=
0.11.2),recount,ggpubr,SummarizedExperiment,tidyr,dplyr,tidyselect,utils
affy, boot, impute, splines, graphics, qvalue, reshape2
parallel, grDevices, graphics, utils, stats, methods, grid,
RColorBrewer, gplots, ggplot2, limma, Biobase
stats, methods, ROTS, matrixStats, foreach, parallel,
doParallel, doRNG, rngtools, SummarizedExperiment, nlme,
qvalue, grDevices, graphics, utils
httr2, jsonlite, utils, Biobase, BiocGenerics (>= 0.23.1)
Biobase, ggplot2, graphics, grDevices, methods, plotly, stats,
MultiAssayExperiment, MultiDataSet, SummarizedExperiment, utils
Rcpp, stats, Biobase, methods, BiocParallel, lme4
Biostrings, bslib, DT, ggplot2, IRanges, mathjaxr, methods,
patchwork, reshape2, S4Vectors, shiny, shinycssloaders,
shinyFeedback
BiocFileCache, jsonlite, xml2, RCurl, curl, utils
GOSemSim, AnnotationDbi, GO.db, pheatmap, ggplot2, ggrepel,
treemap, tm, wordcloud, shiny, grDevices, grid, stats, methods,
umap
utils, BiocGenerics (>= 0.25.1), S4Vectors (>= 0.17.25),
IRanges (>= 2.13.12), XVector (>= 0.19.7), bitops,
BiocParallel, stats
methods, stats, igraph, stringr, grDevices, Biobase,
S4Vectors, SummarizedExperiment, BiocGenerics
XML, RCurl, assertthat, stringi, rvest, data.table, xml2,
dplyr, purrr, survival, survminer, ggplot2, ggthemes, viridis,
knitr, scales, rmarkdown, htmltools
BiocGenerics, data.table, DelayedArray, GenomicRanges,
GenomeInfoDb, httr, methods, RaggedExperiment, RCurl, RJSONIO,
rvest, S4Vectors, stats, stringr, SummarizedExperiment,
TCGAutils, utils
RedeR, minet, viper, mixtools, snow, stats, limma, data.table,
IRanges, igraph, S4Vectors, SummarizedExperiment, car, pwr,
pheatmap, grDevices, graphics, utils
survival, RColorBrewer, grDevices, graphics, stats, utils,
scales, data.table, egg, ggplot2, pheatmap, dunn.test
Biobase, methods, ggplot2, pROC, fdrtool, splines, utils,
tibble
shiny (>= 0.9), rTRM, MotifDb, org.Hs.eg.db, org.Mm.eg.db
corrplot, MASS, stats, lattice, grDevices, gridExtra,
snowfall, psych, BiocParallel, grid, bladderbatch, reshape2,
graphics
GENLIB, gRain, snpStats, kinship2, methods, stats, utils,
R.utils
httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr,
readr, stringr, purrr, lubridate
methods, stats, utils, Matrix, RcppParallel, CompQuadForm,
survey
tidyverse, utils, reshape2, DescTools, metap, multtest,
plyranges, data.table, scales, RColorBrewer, grid, gtable,
gridExtra, GenomicFeatures, stats, ggplot2, plotly, IRanges
rJava, Biostrings, IRanges, utils, stats, cluster, binom
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, GenomeInfoDb, 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
reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree,
patchwork, proxy, methods, stats, base, utils, dplyr
SingleCellExperiment, SummarizedExperiment, Matrix, methods,
utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel,
iterators, foreach, Seurat
S4Vectors, limma, ggraph, igraph, methods, cluster,
minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix,
ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo
instantiate (>= 0.2.3), callr, fs, stats, SeuratObject,
SingleCellExperiment, parallel, dplyr, tidyr, purrr, magrittr,
rlang, tibble, boot, lifecycle, stats, tidyselect, utils,
ggplot2, ggrepel, patchwork, forcats, readr, scales, stringr,
glue, withr, digest
ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales,
RColorBrewer, corrplot, stats, grDevices, graphics, utils,
MASS, matrixStats, methods
fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm,
SingleCellExperiment, SummarizedExperiment, grDevices,
graphics, stats, S4Vectors, scran
Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0),EBSeq,
BiocParallel, mclust, SingleCellExperiment, cluster, Oscope,
SummarizedExperiment, stats, methods
Rcpp (>= 0.10.4), RcppArmadillo (>= 0.5.400.2.0), mgcv, Rook,
rjson, MASS, Cairo, RColorBrewer, edgeR, quantreg, methods,
nnet, RMTstat, extRemes, pcaMethods, BiocParallel, parallel
dplyr, tibble, stats, methods, mgcv, gamlss, gamlss.dist,
SummarizedExperiment, SingleCellExperiment, mclust, mvtnorm,
parallel, pbmcapply, rvinecopulib, umap, ggplot2, irlba,
viridis, BiocParallel, matrixStats, Matrix, sparseMVN, coop
SingleCellExperiment, methods, isotree, ggplot2, ggridges,
SummarizedExperiment, ranger, transport, speedglm, cramer,
rlang, bluster, patchwork
aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree,
grDevices, magrittr, purrr, rlang, scales, scater, Seurat,
SingleCellExperiment, stats, stringr, tibble, tidyr
Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment,
xgboost, methods, stats, dplyr, pROC
matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph,
Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils,
methods, survival
DelayedArray, DelayedMatrixStats, EnsDb.Hsapiens.v79,
EnsDb.Mmusculus.v79, GSVA, ape, glue, dplyr, ensembldb, gtools,
msigdbr, proxyC, reshape2, spatstat.explore, spatstat.geom,
tidyr, AUCell, BiocParallel, rmarkdown, methods, stats, cli,
SingleCellSignalR, MatrixGenerics, Seurat, DT
hexbin, stats, methods, cluster, dplyr, entropy, ggforce,
grid, rlang, concaveman
S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix,
SummarizedExperiment, IRanges, methods, stats, BiocParallel,
reshape, ggplot2, igraph, grDevices, ggforce, graphics
SpatialExperiment, SummarizedExperiment, spatstat.geom,
spatstat.explore, sf, lwgeom, ggplot2, stats, pheatmap, plotly,
shiny, igraph, janitor, knitr, methods, utils, rlang, isoband,
S4Vectors, grDevices
dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr,
ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra,
tibble, scales, rlang, flowCore, methods, basilisk, reticulate,
here, utils, basilisk.utils
Biobase, SingleCellExperiment, SummarizedExperiment,
BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy,
utils, googleVis, ggplot2, methods, stats, e1071, randomForest,
Rcpp (>= 0.12.12)
BiocParallel, BiocSingular, BiocNeighbors, cluster,
DelayedArray, DelayedMatrixStats, distr, igraph, M3Drop (>=
1.9.4), proxyC, ruv, cvTools, scater, batchelor, scran,
methods, S4Vectors (>= 0.23.19), SingleCellExperiment (>=
1.7.3), SummarizedExperiment
methods, Rcpp (>= 1.0.0), RcppParallel (>= 5.0.1), rstan (>=
2.21.3), rstantools (>= 2.1.0), VGAM, data.table, MASS,
logitnorm, ggplot2, matrixStats, assertthat, viridis, coda,
BiocStyle, cowplot, stats, SummarizedExperiment,
SingleCellExperiment, Matrix, dplyr, S4Vectors
knitr, rmarkdown, bsseq, AnnotationHub, GenomicRanges,
reshape2, stats, utils, BSgenome, DelayedArray (>= 0.5.15),
annotatr, SummarizedExperiment (>= 1.5.6), GenomeInfoDb,
Biostrings, DT, HDF5Array (>= 1.7.5)
data.table, Rcpp, magrittr, plyr, stringr, utils, stats,
methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr,
parallel, grDevices
foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats,
phytools, KernelKnn, gplots, zeallot, crayon, assertthat,
igraph, methods, grDevices, graphics, stats, utils, markdown,
SummarizedExperiment, BiocParallel
SingleCellExperiment, SummarizedExperiment, stats, methods,
graphics, grDevices, parallel, quantreg, cluster, moments,
data.table, BiocParallel, S4Vectors, ggplot2, forcats,
BiocGenerics
graphics, stats, utils, aroma.light, BiocParallel, class,
cluster, compositions, diptest, edgeR, fpc, gplots, grDevices,
hexbin, limma, matrixStats, mixtools, RColorBrewer, boot,
rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment,
DelayedMatrixStats, sparseMatrixStats
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
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 (>= 2.21.6), DelayedArray,
BiocNeighbors (>= 1.99.0), igraph, 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)
assertthat, cubature, dplyr, evmix, ggalluvial, ggdendro,
ggraph, grDevices, igraph, iNEXT, methods, plyr, quantreg,
Rcpp, reshape2, rjson, rlang, S4Vectors, SeuratObject,
SingleCellExperiment, stats, stringr, stringdist,
SummarizedExperiment, tidygraph, truncdist, utils, VGAM, hash,
purrr, lifecycle
DelayedArray, glmpca (>= 0.2.0), Matrix, SingleCellExperiment,
SummarizedExperiment, BiocSingular
Matrix, stats, methods, pscl, VGAM, dgof, BiocParallel, MASS,
emdbook, magrittr, utils
methods, RSQLite, igraph, S4Vectors, plotly, reactome.db,
AnnotationDbi, SummarizedExperiment, SingleCellExperiment,
nnTensor (>= 1.1.5), ccTensor (>= 1.0.2), rTensor (>= 1.4.8),
abind, plotrix, heatmaply, tagcloud, rmarkdown, BiocStyle,
knitr, AnnotationHub, MeSHDbi (>= 1.29.2), grDevices, graphics,
stats, utils, outliers, Category, meshr (>= 1.99.1), GOstats,
ReactomePA, DOSE, crayon, checkmate, BiocManager, visNetwork,
schex, ggplot2
GSEABase, Biobase, SingleCellExperiment, BiocStyle, plotly,
tagcloud, rmarkdown, Rcpp, grDevices, graphics, utils, knitr,
S4Vectors, SummarizedExperiment, RColorBrewer, nnTensor,
methods, scales, msigdbr, schex, tibble, ggplot2, igraph
BiocParallel, Rtsne, grDevices, graphics, stats
data.table, S4Vectors, digest, Matrix, Rtsne, httr, igraph,
clustree, scran, sys, epivizrData, epivizrServer, ggraph,
scater, Seurat, SingleCellExperiment, ggplot2, stats, utils
methods, utils, stats, Matrix, Rcpp, BiocGenerics, S4Vectors,
BiocParallel, GenomicRanges, SummarizedExperiment, S4Arrays,
MatrixGenerics, SparseArray, DelayedArray, beachmat
S4Vectors, seriation, circlize, methods, randomcoloR, stats,
grid, grDevices, matrixStats
ChIPseeker, GenomicRanges, SummarizedExperiment, IRanges,
S4Vectors, bamsignals, ComplexHeatmap, graphics, stats, utils,
methods, chromhmmData
Rsamtools, IRanges, GenomeInfoDb, graphics, grDevices, utils,
abind
nnet, WGCNA, GSA, biomaRt, GenomicRanges, seq2pathway.data
utils, graphics, cvTools (>= 0.3.2), MASS, Matrix, methods,
stats, cluster, matrixStats, fpc, cli, prettyunits, reshape2
(>= 1.4.3), reticulate (>= 1.22), BiocParallel, Biostrings,
grDevices, ggplot2 (>= 3.1.1), ggseqlogo (>= 0.1)
BiocParallel, Biostrings, BSgenome, ChIPseeker, cli,
clusterProfiler, cowplot, factoextra, GenomeInfoDb, ggplot2,
ggimage, graphics, grDevices, gridExtra, heatmaps, magick,
methods, RColorBrewer, scales, seqArchR, seqPattern, stats,
utils
methods, parallel, IRanges, GenomicRanges, GenomeInfoDb,
Biostrings, S4Vectors
ggplot2, grid, igraph, utils, yulab.utils
Biostrings, GenomicRanges, IRanges, KernSmooth, plotrix
e1071, GenomicRanges, gdsfmt, ggplot2, GGally, IRanges,
methods, plotly, RColorBrewer, reshape2, rmarkdown, S4Vectors,
stats, utils
grDevices, graphics, stats, methods, Biobase, BiocGenerics,
gdsfmt, GenomicRanges, IRanges, S4Vectors, GWASExactHW,
logistf, Matrix, data.table,
graphics, BiocParallel, utils, methods, stringr, readr,
tibble, MASS, wheatmap (>= 0.2.0), GenomicRanges, IRanges,
grid, preprocessCore, S4Vectors, ggplot2, BiocFileCache,
GenomeInfoDb, stats, SummarizedExperiment, dplyr, reshape2
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, data.table
ggplot2, expm, caret, plyr, dplyr, GO.db, annotate,
SummarizedExperiment, genefilter, GOstats, RColorBrewer,
xtable, Rgraphviz, reshape2, openxlsx, ggridges, DescTools,
org.Hs.eg.db, methods, grDevices, stats, RSpectra, graph
htmltools, jsonlite, rlang, shiny, shiny.react, fs, digest,
rjson
Biobase, BiocGenerics, graphics, grDevices, htmltools,
MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats,
utils
Biobase, S4Vectors (>= 0.17.25), IRanges (>= 2.13.12),
GenomeInfoDb (>= 1.15.2), GenomicRanges (>= 1.31.8), pwalign,
hwriter, methods, lattice, latticeExtra,
beanplot, glmnet, graphics, grDevices, grid, gridBase,
gridExtra, LiblineaR, matrixStats, methods, pROC, PRROC,
RColorBrewer, scales, stats, stringr, utils, infotheo,
progress, corrplot, lmerTest, mlr3learners, mlr3tuning,
paradox, lgr
biocViews, nlme, e1071, openxlsx, pheatmap, RColorBrewer,
Matrix, SparseM, graphics, stats, utils, SummarizedExperiment,
BiocParallel, methods
stats4, grDevices, graphics, stats, scrime (>= 1.2.5)
AnnotationDbi, ggplot2, data.table, ExperimentHub, HDF5Array,
magrittr, RSQLite, dplyr, fgsea, scales, methods, qvalue,
stats, utils, reshape2, visNetwork, BiocParallel, fastmatch,
reactome.db, Matrix, clusterProfiler, readr, DOSE, rhdf5,
GSEABase, DelayedArray, BiocGenerics, tibble
AnnotationDbi, BiocGenerics, ComplexHeatmap, consensusOV,
cowplot, DGEobj.utils, dplyr, ensembldb, ggplot2, ggridges,
GSVA, IRanges, magrittr, matrixStats, maxstat, methods,
openair, org.Hs.eg.db, patchwork, RColorBrewer,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, SpatialExperiment, stats,
scales, SummarizedExperiment, survival, survminer, viridis
mzR, ggplot2, grid, reshape2, grDevices, stats, utils
basilisk, BiocParallel, data.table, dplyr, ggplot2, tools,
Matrix (>= 1.3.3), methods, phyloseq, proxyC, RColorBrewer,
RCurl, reticulate, sparseMatrixStats, SummarizedExperiment,
tidyr
dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges,
Rsamtools, parallel, graphics, stats, utils, methods
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions,
igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize,
ComplexHeatmap, grDevices, stats, utils, shiny
BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats,
Matrix, stats, SummarizedExperiment, actuar, rlang, S4Vectors,
methods, scales, scuttle
BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors,
grDevices, SummarizedExperiment, methods, cytomapper
simona, ComplexHeatmap (>= 2.7.4), grid, circlize, GetoptLong,
digest, tm, GO.db, AnnotationDbi, slam, methods, clue,
grDevices, stats, utils, cluster (>= 1.14.2), colorspace,
GlobalOptions (>= 0.1.0)
Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
statmod
SummarizedExperiment, BiocParallel, DelayedArray, methods,
utils, Matrix, S4Vectors, stats
methods, utils, stats, S4Vectors, BiocGenerics, GenomicRanges,
DelayedArray
BiocManager, circlize, limma, igraph, gplots, grDevices,
edgeR, data.table, pheatmap, stats, Rtsne, graphics, stringr,
foreach, multtest, scran, utils,
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>=
2.23.5)
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
RColorBrewer, Rcpp, ape, aplot, ggplot2, ggrepel, ggtree,
graphics, grDevices, gridExtra, methods, parallel, seqinr,
stats, tidytree, utils
basilisk, Biobase, DelayedArray, dplyr, ggplot2, methods,
reticulate, rlang, scales, stats
minfi, S4Vectors (>= 0.19.1), RColorBrewer
graphics, grDevices, igraph, matrixStats, methods, S4Vectors,
SingleCellExperiment, SummarizedExperiment
magrittr (>= 1.5), dplyr, stats, tidyr, utils, Rcpp (>= 1.0.0)
dplyr, ggplot2, graphics, Matrix, mclust, methods, mixtools,
sparseMatrixStats, stats, SummarizedExperiment, tidyr, utils
scales, plyr, Hmisc, AnnotationDbi, org.Hs.eg.db, ggplot2,
reactome.db, KEGGREST, BioNet, goseq, methods, IRanges, igraph,
Biobase,tools, S4Vectors, geneLenDataBase, grDevices, graphics,
stats, utils
SpatialExperiment, SummarizedExperiment, sparseMatrixStats,
spdep, methods, utils
R6, httr, rlang, purrr, jsonlite, assertthat, data.table,
Matrix, magrittr, methods, stringr, stats, IRanges,
GenomicRanges, SummarizedExperiment
basilisk, reticulate, irlba, stats, assertthat
graphics, grDevices, stats, utils, BiocGenerics, zlibbioc
terra, sf, smoothr, spatstat.explore, spatstat.geom,
SpatialExperiment, dplyr, ggplot2, patchwork,
SummarizedExperiment, stats, rlang, parallel
matrixStats, matrixTests, rstatix, spatstat.explore,
spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix,
qvalue, stats, utils, methods
Seurat, SingleCellExperiment, SummarizedExperiment, dplyr,
methods, ggplot2, scater (>= 1.13), scran, igraph, shiny, jpeg,
magrittr, utils, S4Vectors, DropletUtils, jsonlite, png
edgeR, ggplot2, Matrix, matrixStats, methods, rlang, scran,
SeuratObject, SingleCellExperiment, SpatialExperiment, stats,
SummarizedExperiment, S4Vectors, utils
babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet,
checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>=
1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>=
2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix,
methods, plotly (>= 4.9.0), stats, utils, viridis
utils, stats, matrixStats, IRanges, XVector
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
methods, glmnet, huge, stats, graphics, utils
nnlasso, nnls, parallel, data.table, Biostrings,
GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2,
gridExtra, reshape2, RhpcBLASctl
ggplot2, methods, stats, dplyr, spatstat.geom,
spatstat.random, SpatialExperiment, SummarizedExperiment, RANN
reticulate, basilisk (>= 1.9.10), checkmate, stats,
SpatialExperiment, methods, SummarizedExperiment, Matrix,
ggplot2, ggrepel, scales, gridExtra
grDevices, stats, utils, graphics, SeuratObject, Biobase,
GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
rjson, grDevices, magick, utils, S4Vectors,
SummarizedExperiment, BiocGenerics, BiocFileCache
data.table, dplyr, edgeR, genefilter, ggplot2, grImport, grid,
gridExtra, igraph, methods, Matrix, rsvg, shiny, grDevices,
graphics, ggplotify, parallel, reshape2, stats,
SummarizedExperiment, SingleCellExperiment, shinydashboard,
S4Vectors, spsComps (>= 0.3.3.0), tibble, utils, xml2
S4Vectors, Biobase, base64enc, EBImage, ggplot2, XML,
scattermore, dplyr, pbapply, data.table, readxl, magick,
grDevices, stringr, plotrix, GeomxTools, BiocFileCache, stats,
utils, methods, ggtext, tools, RBioFormats
limma, edgeR, SingleCellExperiment, Seurat, ggplot2, methods,
stats, grDevices, graphics
ProtGenerics (>= 1.39.2), methods, IRanges, MsCoreUtils (>=
1.7.5), graphics, grDevices, stats, tools, utils, fs,
BiocGenerics, MetaboCoreUtils
dplyr, PRIMME, cluster, Matrix, parallel, BiocParallel,
magrittr, HiCcompare, GenomicRanges, utils
Spectra (>= 1.5.6), MsCoreUtils, methods
apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3),
gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN
(>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>=
1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom,
dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp,
SummarizedExperiment, rlang
ggplot2, concaveman, BiocParallel, spatstat.explore,
spatstat.geom, lmerTest, S4Vectors, methods, pheatmap, rlang,
grDevices, stats, data.table, dplyr, tidyr, scam,
SingleCellExperiment, SpatialExperiment, SummarizedExperiment,
ggforce, ClassifyR, tibble, magrittr, cli, survival, ggthemes,
ggh4x, coxme, ggnewscale, lifecycle, simpleSeg
stats, scales, bamlss, methods, tools, IRanges, Biostrings,
GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome,
S4Vectors, graphics, ggplot2, utils
dplyr, tibble, tidyselect, stats, ggplot2, tidyr,
spatstat.univar, S4Vectors, parallel
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon,
edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods,
rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils,
withr
methods, utils, graphics, igraph, BiocGenerics, S4Vectors (>=
0.17.5), BiocParallel, IRanges (>= 2.21.2), GenomeInfoDb,
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, GenomeInfoDb, utils, plyr,stringr, methods,
BSgenome.Mmusculus.UCSC.mm9, googleVis
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse,
caret, dplyr, biomaRt, randomForest, ggridges, cvms,
ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr,
stringr, tidyr
SpatialExperiment, BRISC, nnSVG, BiocParallel, Matrix,
methods, SummarizedExperiment, stats, utils, scuttle
stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment,
SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap,
rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang
ggplot2, NMF, Matrix, matrixStats, nnls, SingleCellExperiment,
sparseMatrixStats, stats
SpatialExperiment, SummarizedExperiment, BiocNeighbors,
SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco,
grDevices, BiocParallel
stats, methods, SingleCellExperiment, fitdistrplus, graphics,
edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
stats, utils, methods, BiocGenerics, RSQLite, duckdb, DBI
xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble,
ggplot2, shiny, plotly, data.table, caret, stats, graphics,
utils, keys
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils, graphics
dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble,
ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment,
edgeR, methods, ggforce, pheatmap, utils, stringr, gtools,
tidyr
igraph, slam, BiocNeighbors, Matrix, MASS, abind,
SummarizedExperiment, methods, MatrixGenerics, BiocGenerics,
BiocSingular, BiocParallel
dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment,
SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2,
tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics,
grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
BiocParallel, spatstat.geom, concaveman, data.table,
spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble,
stringr, tidyselect, ggplot2, methods, stats,
SummarizedExperiment, S4Vectors, plotly, purrr, ranger,
magrittr, limma, SpatialExperiment, cluster, treekoR
graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2,
pheatmap, grDevices, Seurat, SpatialExperiment,
SummarizedExperiment
dplyr, magrittr, GenomeInfoDb, GenomicAlignments,
GenomicRanges, IRanges, Rsamtools, S4Vectors, grid,
BiocGenerics, ggplot2, reshape2, stats, gridExtra,
TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown
methods, graph, RBGL, parallel, BiocGenerics
png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots,
hash, plotrix
methods,ontologyIndex, datasets, graphics, stats, utils,
knitr, SummarizedExperiment, S4Vectors, rols
methods, BiocGenerics, XVector, stringr, stringi, crayon,
grDevices
ggplot2, ggthemes, grid, gridExtra, methods, scales, sp, stats
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), GenomeInfoDb (>=
1.13.1), S4Arrays (>= 1.1.1), DelayedArray (>= 0.31.12)
dplyr, nloptr, magrittr, methods, tibble, tidyselect,
BEDASSLE, scales, visNetwork, randomcoloR
assertthat, caret, dplyr, tidyr, rsample, methods, rlang,
utils, Biostrings, stats, SummarizedExperiment
ipred, SuppDists, KernSmooth, survivalROC, bootstrap, grid,
rmeta, stats, graphics
matrixStats, stats, graphics, utils, limma, edgeR
data.table, reshape2, ggplot2, stats, grDevices, graphics,
utils, biomaRt, methods
SummarizedExperiment, dplyr, ggplot2, methods, stats
RColorBrewer, lattice, qvalue, multtest, utils, tools,
Biobase, Biostrings, cleaver (>= 1.3.3), readr (>= 0.2),
rmarkdown (>= 1.0)
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
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
dplyr, PRIMME, cluster, Matrix, magrittr, HiCcompare, ggplot2,
tidyr, ggpubr, RColorBrewer, reshape2, cowplot
ape (>= 5.0), phangorn (>= 2.5), utils, methods
methods, GenomicAlignments, GenomicRanges, IRanges,
BiocGenerics, S4Vectors (>= 0.20.1), GenomeInfoDb, BSgenome,
GenomicFeatures, Biostrings, dplyr, tidyr, BiocParallel
BiocGenerics, GenomicRanges, IRanges, matrixStats, methods,
stats, graphics, shiny
ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
AnnotationDbi, BiocGenerics, BiocBaseUtils, GenomeInfoDb,
GenomicFeatures, GenomicRanges, GenomicDataCommons, IRanges,
methods, MultiAssayExperiment, RaggedExperiment (>= 1.5.7),
rvest, S4Vectors, stats, stringr, SummarizedExperiment, utils,
xml2
edgeR, BiocGenerics, reshape2, GenomicRanges, IRanges,
SummarizedExperiment, GenomicAlignments, Rsamtools, e1071,
cluster, ggplot2, grid, grDevices, stats, utils, methods,
locfit
GenomicRanges, rTensor, readr, methods, MOFAdata, tximport,
tximportData, graphics, stats, utils, shiny
methods, ontoProc (>= 0.99.7), SummarizedExperiment,
AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils,
BiocFileCache
AnVIL, BiocFileCache, dplyr, GenomicRanges, methods,
RaggedExperiment, readr, S4Vectors, stats, tidyr, TCGAutils,
utils
arules, fields, GenomicRanges, graphics, stringr, methods,
stats, gplots
GenomicRanges, IRanges, biomaRt, GenomicFeatures, grDevices,
dplyr, stats, utils, R.utils, methods, org.Hs.eg.db
methods, dplyr, magrittr, miniUI, shiny, Rsamtools, GSEABase,
rjson, BiocFileCache, DT, httr, readxl, AnnotationDbi,
org.Hs.eg.db, utils, GenomicFiles, SummarizedExperiment
Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang,
stats, stringr, tibble, tidyr
tidySummarizedExperiment, tidySingleCellExperiment,
tidyseurat, tidybulk, plyranges, nullranges, purrr, rlang,
stringr, cli, utils
dplyr, tidyr, ttservice (>= 0.4.0), SummarizedExperiment,
tibble, ggplot2, magrittr, rlang, purrr, pkgconfig, lifecycle,
methods, utils, S4Vectors, tidyselect, ellipsis, vctrs, pillar,
stringr, cli, fansi, Matrix, stats
ttservice, SummarizedExperiment, SingleCellExperiment,
BiocGenerics, Matrix, S4Vectors, methods, utils, pkgconfig,
tibble, dplyr, tidyr, ggplot2, plotly, rlang, purrr, stringr,
vctrs, tidyselect, pillar, cli, fansi, lifecycle, magick,
tidygate (>= 1.0.13), shiny
dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang,
purrr, lifecycle, methods, utils, S4Vectors, tidyselect,
ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig
doParallel, dplyr, flowCore, foreach, ggplot2, ggraph, glmnet,
methods, parallel, purrr, readr, recipes, rlang, stringr,
survival, tidygraph, tidyr, tidyselect, yardstick, Rcpp,
tibble, stats, utils, RcppHNSW
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
grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2),
MSnbase (>= 2.3.10), PSMatch (>= 1.6.0), ggplot2 (>= 2.2.1),
mzR (>= 2.27.5)
SummarizedExperiment, BiocGenerics, S4Vectors, Biobase,
BiocParallel, ggplot2, tibble, dplyr, caTools, downloader,
magrittr, methods, reshape2, tidyr, data.table, assertthat,
scales, graphics, grDevices, parallel, stats, utils, limma,
jsonlite
biobroom, broom, data.table, doParallel, foreach,
futile.logger, ggplot2, grDevices, gridExtra, grid, knitr,
limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr,
purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines,
stats, stringr, tibble, utils, VennDiagram, VGAM
ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl,
parallel, MASS, BiocParallel, limma
stats, BiocParallel, MatrixGenerics, methods,
SingleCellExperiment, SummarizedExperiment, SpatialExperiment
IRanges, GenomicRanges, XVector, Rsamtools, XML, tractor.base,
stringr, RColorBrewer, methods
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
glmGamPoi, DelayedArray, Matrix, MatrixGenerics,
SummarizedExperiment, HDF5Array, methods, utils, Rcpp
BiocGenerics (>= 0.26.0), Biostrings (>= 2.48.0), dplyr (>=
0.7.6), GenomicRanges (>= 1.32.6), ggplot2 (>= 3.0.0),
grDevices, gridExtra (>= 2.3), methods, parallel, Rcpp (>=
1.0.4.8), scales (>= 1.0.0), stats, TFMPvalue (>= 0.0.8), utils
RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
ggplot2, viridis, mgcv, SingleCellExperiment, slingshot,
princurve, Biobase, methods, RColorBrewer,
SummarizedExperiment, grDevices, graphics, rgl
TreeSummarizedExperiment (>= 1.99.0), edgeR, methods,
SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr,
ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree,
stats, utils, rlang
ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble,
tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)
stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2,
hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt,
edgeR, lme4, multcomp
methods, BiocGenerics, utils, ape, rlang, dplyr,
SummarizedExperiment, BiocParallel, IRanges, treeio
stats, utils, graphics, grDevices, segmented, gplots,
parallel, magrittr, BiocParallel, DT, S4Vectors,
SummarizedExperiment, methods, shiny, shinyFiles
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
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
Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn,
grDevices, graphics, stats, utils
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
SummarizedExperiment, tximport, jsonlite, S4Vectors, IRanges,
GenomicRanges, AnnotationDbi, GenomicFeatures, txdbmaker,
ensembldb, BiocFileCache, AnnotationHub, Biostrings, tibble,
GenomeInfoDb, tools, utils, methods, Matrix
methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel,
BiocNeighbors, SingleCellExperiment, SummarizedExperiment
methods, stats, httr, jsonlite, S4Vectors
AnnotationHub, AnnotationDbi, BiocGenerics, Biostrings,
BSgenome, data.table (>= 1.9.4), DT, GenomicFeatures,
GenomeInfoDb, GenomeInfoDbData, GenomicAlignments,
GenomicRanges, ggplot2, ggrepel, gsubfn, mirbase.db, moments,
Organism.dplyr, plotgardener, R.utils, S4Vectors, shiny,
shinydashboard, shinyFiles, shinyjs, yaml
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
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
methods, stats, IRanges, shiny, shinycssloaders, shinyFiles,
ggplot2
MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0),
iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2,
remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack, rlang, lme4
(>= 1.1.33), grDevices, graphics, Biobase, methods, utils,
stats
IRanges, GenomicRanges, S4Vectors, parallel, matrixStats,
GenomicAlignments, GenomeInfoDb, Rsamtools, cluster, stats,
graphics, methods
BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix,
methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
stats, SummarizedExperiment, utils
methods, stats, Matrix, BiocGenerics, reticulate, S4Vectors,
DelayedArray, basilisk, zellkonverter, scuttle,
SingleCellExperiment, BiocParallel, BiocSingular
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
utils, grDevices, stats, methods, dplyr, purrr, tibble,
magrittr, ggplot2, UpSetR, VennDiagram, grid, futile.logger
utils, data.tree, ape, parallel, Rfast, stats
mixtools, stats, parallel, e1071, KernSmooth
data.table, AnnotationDbi, AnnotationForge, biomaRt,
dendextend, DiagrammeR, DT, dynamicTreeCut, fgsea, GOSemSim,
ggplot2, GO.db, grDevices, heatmaply, htmlwidgets, igraph,
methods, plotly, processx, topGO, RColorBrewer, R.utils,
scales, stats, UpSetR, utils
BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite,
methods, S4Vectors, SingleCellExperiment, SpatialExperiment,
SummarizedExperiment
igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm,
ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb,
ggrepel, textstem, tidygraph, stats, scales, ggraph
cowplot, magrittr, GenomeInfoDb, GenomicAlignments,
RColorBrewer, zoo, Rsamtools, S4Vectors, parallel, reshape2,
methods, graphics, stats
matrixStats, limma, parallel, shiny, qvalue, grDevices, stats,
MultiAssayExperiment, graphics
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
utils, methods, cli, Biobase, SummarizedExperiment, config,
golem, shiny, DT, ggplot2, dplyr, rlang, stringr,
shinydashboard, shinyWidgets, shinycustomloader, RColorBrewer,
logging
dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>=
2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr
limma, matrixStats, locfit, stats, graphics
SummarizedExperiment, SingleCellExperiment, Rfast, singscore,
AnnotationHub, ontologyIndex, tibble, dplyr, BiocParallel,
Matrix, minpack.lm, pracma, methods, readr, magrittr, progress,
quadprog
MSnbase (>= 2.29.3), mzR (>= 2.25.3), methods, Biobase,
BiocGenerics, ProtGenerics (>= 1.37.1), lattice,
MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges,
SummarizedExperiment, MsCoreUtils (>= 1.15.5), MsFeatures,
MsExperiment (>= 1.5.4), Spectra (>= 1.15.7), progress,
RColorBrewer, MetaboCoreUtils (>= 1.11.2)
BiocGenerics, genefilter, graphics, grDevices, gtools,
methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta,
siggenes
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
utils, Biostrings, pwalign, BSgenome, data.table,
GenomicRanges, IRanges, methods, Rcpp, stringi, S4Vectors,
future.apply, stringr, formattable, stats
methods, utils, tools, BiocGenerics, S4Vectors, IRanges
IRanges, stats, S4Vectors, EBImage, Matrix, mzR, data.table,
grDevices, limma
biomaRt, downloader, edgeR, gplots, graphics, limma,
matrixStats, preprocessCore, readr, RColorBrewer, stats,
quantro
basilisk, cli, DelayedArray, Matrix, methods, reticulate,
S4Vectors, SingleCellExperiment (>= 1.11.6),
SummarizedExperiment, utils
variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0),
GSEABase (>= 1.54.0), msigdbr (>= 7.5.1), Rfast, ggplot2,
tidyr, reshape2, progress, utils, Rdpack, stats
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
flowWorkspace
Rcpp, beachmat, Rhdf5lib, BH, dqrng, scuttle
cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rhtslib (>= 3.3.1), S4Vectors, IRanges, XVector, Biostrings
Rcpp, RcppArmadillo, RcppParallel (>= 5.0.0)
S4Vectors, IRanges, XVector, Biostrings, Rhtslib
MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db
knitr, RUnit, BiocGenerics, TENxPBMCData, CHETAH, stringr,
LoomExperiment
R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles
tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf
affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl,
rmarkdown
BiocStyle, magick, knitr, rmarkdown, testthat, BiocGenerics,
DESeq2, magrittr, dplyr, ggplot2, cowplot, ggtext,
RColorBrewer, pheatmap, viridis
BiocStyle, knitr, AnnotationHub (>= 2.7.13), rmarkdown,
methods, CompoundDb (>= 1.1.4)
knitr, rmarkdown, roxygen2 (>= 6.0.0), testthat (>= 3.0.0),
gplots, tidyr
BiocStyle, rmarkdown, knitr, testthat, digest, Matrix,
alabaster.matrix
BiocStyle, rmarkdown, knitr, testthat, jsonlite
BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation,
rtracklayer, Biostrings
testthat, knitr, SummarizedExperiment, BiocParallel,
BiocStyle, rmarkdown
testthat, knitr, BiocStyle, chihaya, BiocSingular,
ResidualMatrix
testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick,
png, digest
testthat, BiocStyle, knitr, rmarkdown, purrr, ggpattern,
ggplot2, cowplot, tidyverse, magick
knitr, BiocStyle, testthat (>= 3.0.0), BiocManager
BiocManager, BiocGenerics, GenomicRanges, GenomeInfoDb,
AnnotationHub, ExperimentHub, ensembldb, httr, tidyr, r3dmol,
bio3d, shiny, shiny.gosling, ggdist, gghalves, colorspace,
knitr, rmarkdown, testthat (>= 3.0.0)
ASICS, BiocStyle, ChemoSpec, cowplot, curl, DT (>= 0.5),
GGally (>= 1.4.0), ggrepel (>= 0.8.0), gridExtra, knitr,
NMRphasing, plotly (>= 4.7.1), progressr, SummarizedExperiment,
S4Vectors, testthat (>= 2.0.0), writexl (>= 1.0), zip (>=
2.0.4)
plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db,
hgu133acdf, Rgraphviz, RColorBrewer
mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment,
SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr,
magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr,
tidyverse
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
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, GenomicRanges, GenomeInfoDb, VariantAnnotation,
Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge,
rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR, Biostrings,
CompoundDb, keras, ensembldb, SummarizedExperiment,
ExperimentHub, gdsfmt, rmarkdown, HubPub
parallel, knitr, rmarkdown, testthat, withr, readr,
BiocStyle, devtools, AnVILAz, AnVILGCP, lifecycle
BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest
AnVIL, AnVILAz, AnVILGCP, BiocStyle, knitr, rmarkdown,
testthat (>= 3.0.0), tinytest
AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr
DESeq2, airway, knitr, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, scRNAseq, scater, scran,
sparseMatrixStats, testthat
MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata,
hgu133atagcdf
BiocStyle, ComplexHeatmap, factoextra, FactoMineR, gProfileR,
knitr, PerformanceAnalytics, org.Mm.eg.db, rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, ASICSdata
testthat, BiocStyle, lintr, knitr, rmarkdown
ggplot2, TENxPBMCData, dplyr, Rtsne, Seurat, AnnotationDbi,
BiocGenerics, stringr, org.Hs.eg.db, knitr, rmarkdown, testthat
(>= 3.0.0)
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,
hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS,
patchwork, mixOmics, mpm, nlme, OlinkAnalyze, org.Hs.eg.db,
org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl,
RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS,
rtracklayer, statmod, testthat, UniProt.ws, writexl, XML
airway, ggplot2, testthat, EDASeq, knitr, BiocStyle,
RefManageR, sessioninfo, rmarkdown
RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, roxygen2
AnnotationDbi, Biostrings, rmarkdown, BiocFileCache, ggplot2,
ComplexHeatmap, circlize, ggbio, gridExtra, knitr, testthat,
BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, ExperimentHub (>= 1.15.3),
DESeq2, NanoporeRNASeq, purrr, apeglm, utils, DEXSeq
testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
testthat, interp, fields, pheatmap, viridis, rmarkdown,
spelling
knitr, rmarkdown, methods, testthat, BiocStyle
BiocStyle, knitr, magick, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, testthat, scRNAseq, magick
knitr, rmarkdown, BiocStyle, testthat, callr
reticulate, knitr, rmarkdown, BiocStyle, testthat, basilisk
testthat, BiocStyle, knitr, rmarkdown, scran, scater,
bluster, scRNAseq
knitr, rmarkdown, BiocStyle, devtools, testthat
testthat, BiocStyle, knitr, rmarkdown, rcmdcheck,
BiocParallel, HDF5Array, beachmat.hdf5
testthat, BiocStyle, knitr, rmarkdown, rhdf5, Matrix
testthat, BiocStyle, knitr, rmarkdown, Matrix
lumi, vsn, affy, hwriter, beadarrayExampleData,
illuminaHumanv3.db, gridExtra, BiocStyle,
TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
testthat, BiocStyle, knitr, rmarkdown, pander, seewave
testthat (>= 3.0.0), BiocStyle, covr, codetools, knitr,
rmarkdown, dplyr, ggplot2, spelling
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
BiocStyle, knitr, rmarkdown, formatR, rrBLUP, testthat (>=
3.0.0)
knitr, BiocStyle, testthat, rmarkdown, markdown
BiocGenerics, RUnit, BiocStyle, minfiData, parallel,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter
BiocStyle, RCurl, biomaRt, knitr, knitcitations,
knitrBootstrap, testthat, ggplot2, rmarkdown
tools, tkWidgets, ALL, RUnit, golubEsets, BiocStyle, knitr,
limma
limma, DESeq2, airway, ggplot2, plyr, GenomicRanges,
testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase,
rmarkdown, SummarizedExperiment
BiocStyle, prettydoc, rmarkdown, knitr, testthat (>= 0.10.0)
BiocStyle, knitr, testthat (>= 3.0.0), rmarkdown
BiocStyle, devtools, gert, jsonlite, rmarkdown, tinytest,
usethis
knitr, testthat, rjsoncons, igraph, BiocStyle
testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Biobase, S4Vectors, IRanges, S4Arrays, SparseArray,
DelayedArray, HDF5Array, GenomicRanges, pwalign, Rsamtools,
AnnotationDbi, affy, affyPLM, DESeq2, flowClust, MSnbase,
annotate, RUnit
BiocManager, BiocStyle, knitr, rmarkdown, sessioninfo,
shinytest2
BiocParallel, testthat, BiocStyle, knitr, rmarkdown
airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1),
GOSemSim, Hmisc, knitr (>= 1.35), org.Hs.eg.db, reactome.db,
rmarkdown, spelling, targetscan.Hs.eg.db, testthat (>= 3.0.0),
WGCNA
BiocGenerics, tools, foreach, BBmisc, doParallel,
GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,
knitr, batchtools, data.table
BiocStyle, knitr, rmarkdown, testthat, tm, lubridate,
networkD3, visNetwork, clipr, blastula, kableExtra, DiagrammeR,
SummarizedExperiment
BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0)
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
testthat, HDF5Array, BiocStyle, rmarkdown, knitr
BiocStyle, covr, devtools, knitr, pkgdown, RefManageR,
rmarkdown, sessioninfo, testthat, utils
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, xml2
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, covr, lgr
roxygen2, BiocStyle, testthat (>= 2.0.0), devtools, knitr,
rmarkdown, covr, lgr
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr, covr
BiocStyle, knitr, mockery, rmarkdown, testthat, httptest2
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
BioMark, BiocGenerics, BiocStyle, golubEsets, hu6800.db,
knitr, omicade4, rmarkdown, testthat
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)
xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db,
lumi, knitr
RUnit, devtools, BiocGenerics, knitr, rmarkdown
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans,
kohonen, apcluster, DirichletMultinomial, vegan, fastcluster
BiocStyle, knitr, rmarkdown, RUnit,
BSgenome.Hsapiens.UCSC.hg19
knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
rmarkdown, markdown, BiocStyle, knitr, testthat (>= 3.0.0),
utils, testthat
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, annotatr,
tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
testthat, BiocStyle, knitr, rmarkdown, devtools
testthat (>= 3.0.0), IRanges, knitr, rmarkdown, BiocStyle,
rtracklayer
testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix,
doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38,
batchtools
BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>=
3.0.0)
knitr, markdown, rmarkdown, STexampleData, testthat (>=
3.0.0), codetools, Matrix, lattice, cluster, survival, MASS,
nlme
testthat, RUnit, doParallel, 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)
testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle,
rmarkdown, covr, sessioninfo
testthat (>= 3.1), knitr, rmarkdown, BiocStyle
RefManageR, BiocStyle, covr, knitr, testthat (>= 3.0.0),
sessioninfo
BiocStyle, diffcyt, flowWorkspace, ggcyto, knitr, openCyto,
rmarkdown, testthat, uwot
EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6),
hgu95av2.db, KEGGREST, karyoploteR, geneplotter, limma,
lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db
knitr, GO.db, KEGGREST, estrogen, org.Hs.eg.db, hgu95av2.db,
limma, affy, genefilter, rmarkdown
fossil, interp, knitr, BiocStyle, tictoc
BiocStyle, jsonlite, knitr, survival, survminer, rmarkdown,
testthat
knitr, arules, concaveman, ReactomePA, bnviewer, rmarkdown,
withr, BiocStyle, testthat (>= 3.0.0)
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, sessioninfo, scRNAseq, scater,
mclust, testthat (>= 3.0.0), splatter
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
knitr, BiocStyle, BiocGenerics, testthat, RUnit
knitr, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle
limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
BiocStyle, testthat (>= 3.0.0), knitr, rmarkdown
BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation
BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr,
destiny, ggrepel
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics,
BiocManager, kableExtra, rgl
BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics,
hgu133plus2CellScore, knitr, testthat (>= 3.0.0)
AnnotationDbi, destiny, RUnit, scater, scran, knitr,
org.Mm.eg.db, rmarkdown
zellkonverter, SingleCellExperiment, HDF5Array, tidyr,
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery
BiocStyle, knitr, rmarkdown, testthat, ggplot2
knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater,
scMerge, fgsea, escape, pheatmap
scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14),
devtools (>= 2.3.0), BiocStyle, testthat
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
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
argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat,
Rsamtools, GenomicInteractions, GenomicRanges, IRanges,
AnnotationHub
BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix,
BiocStyle, testthat, rmarkdown, knitr
testthat, roxygen2, devtools, knitr, lintr
BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene,
BSgenome.Mmusculus.UCSC.mm9, BiocStyle, knitr
AnnotationDbi (>= 1.38.2), knitr, markdown, rmarkdown,
rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr
BiocStyle, knitr, rmarkdown, testthat, webshot
knitr, rmarkdown, DT, mclust, scater, ExPosition, BiocStyle,
pkgdown
limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot,
BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools,
gtable, scales, e1071, rmarkdown, IRanges, robustbase, glmnet,
class, randomForestSRC, MatrixModels, xgboost, data.tree,
ggnewscale
BiocStyle, rmarkdown, knitr, RUnit, BiocGenerics (>= 0.1.0)
RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS,
BiocStyle
BiocParallel, knitr, rmarkdown, testthat, CAMERA
RUnit, knitr, BiocGenerics, rmarkdown, BiocStyle, roxygen2
BiocStyle, knitr, testthat, MAST, Rtsne, scran, igraph,
rmarkdown
knitr, rmarkdown, kableExtra, scRNAseq, BiocStyle
yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
AnnotationHub, knitr, jsonlite, readr, rmarkdown,
org.Hs.eg.db, prettydoc, BiocManager, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel,
BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr,
data.table, R.utils
BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
minet, Rgraphviz, RUnit, BiocGenerics, igraph
AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked,
BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment,
TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData,
ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown,
statmod
knitr, parallel, testthat, BiocStyle, rmarkdown,
AnnotationHub, LOLA
testthat, knitr, rmarkdown, BiocStyle, SeuratObject,
BiocFileCache
testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle,
rmarkdown, covr
BiocStyle, knitr, markdown, testthat (>= 3.0.0)
genefilter, mvtnorm, testthat (>= 0.3), samr, pamr, kohonen,
NMF, WGCNA, Rtsne, umap, clusterProfiler, ReactomePA, DOSE,
AnnotationDbi, gplots, hu6800.db, BiocManager, data.tree,
dendextend, Polychrome, rmarkdown, simplifyEnrichment, cowplot,
flexclust, randomForest, e1071
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), statmod
BiocStyle, corrplot, knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
flowWorkspace (>= 3.33.1), flowCore, ncdfFlow, shiny,
testthat, devtools, flowWorkspaceData, ggplot2, progress
BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq,
TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree,
tidytree, statmod, covr, sva, tcltk
BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr,
rtracklayer
testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,
fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,
grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),
gridGraphics, gplots, rmarkdown, Cairo, magick
knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19),
MsBackendMgf
BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans,
patchwork, rmarkdown, scater, SFEData,
SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0)
knitr, testthat, rmarkdown, covr, viridis, ggplot2,
RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats
BiocStyle, ggplot2, knitr, rmarkdown, magick
knitr, BiocStyle, rmarkdown, testthat, Seurat
BiocStyle, knitr, rmarkdown, tidyr, ggplot2, gridExtra,
magick, Cairo, limma
pander, markdown, BiocStyle, rmarkdown, knitr, formatR,
testthat
ade4, BiocStyle, CellBench, DuoClustering2018, knitr,
rmarkdown, scater, testthat
testthat, knitr, rmarkdown, piano, ggplot2
testthat (>= 3.2.0), proto, spelling, knitr, data.table,
gsubfn, R.utils, tidyverse, rmarkdown, htmlwidgets, MASS,
Rtsne, plotly, BiocStyle, cowplot, qpdf, GEOquery, sf, torch
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
BiocStyle, msigdbr, depmap, pool, RSQLite, mygene, testthat
(>= 3.0.0), knitr, rmarkdown
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
testthat
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, testthat
BiocStyle, knitr, rmarkdown, shinyFeedback, testthat (>=
3.0.0), BSgenome.Hsapiens.UCSC.hg38
BiocStyle, GenomicFeatures, knitr, rmarkdown, readxl,
rtracklayer, sangerseqR, testthat, VariantAnnotation
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr,
rmarkdown, rtracklayer, testthat, utils
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
testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown,
SummarizedExperiment, SingleCellExperiment
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0),
InteractiveComplexHeatmap
testthat, knitr, covr, rmarkdown, spelling, biomaRt, remotes
BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown,
testthat
zellkonverter, rmarkdown, knitr, testthat, basilisk, arrow,
reticulate, spelling, forcats, ggplot2,
tidySingleCellExperiment, rprojroot
magrittr, dplyr, purrr, knitr, stringr, rmarkdown, tidyr
ncdfFlow, testthat, rmarkdown, knitr, edgeR, limma, glmnet,
BiocStyle, flowStats
gridExtra, knitr, RColorBrewer, testthat, uwot
BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat,
shinytest
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, HDCytoData
testthat, flowWorkspaceData , knitr, rmarkdown, parallel
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, reshape2, dplyr, CytoPipelineGUI
testthat (>= 3.0.0), vdiffr, diffviewer, knitr, rmarkdown,
BiocStyle, patchwork
BiocStyle, knitr, rmarkdown, markdown, testthat
XML, grImport, grImport2, BiocStyle, knitr, rmarkdown,
testthat
BiocStyle, biomaRt, biovizBase,
BSgenome.Dmelanogaster.UCSC.dm6, knitr, limma, org.Dm.eg.db,
rmarkdown, testthat (>= 3.0.0),
TxDb.Dmelanogaster.UCSC.dm6.ensGene
testthat, BiocStyle, AnnotationDbi, clusterProfiler, graph,
diptest, cluster, vioplot, visNetwork, vsn, igraph, FactoMineR,
factoextra, dendextend, parallel, doParallel, Mfuzz, apcluster,
forcats, readxl, openxlsx, multcomp, purrr, tibble, knitr,
norm, scales, tidyverse, cp4p, imp4p (>= 1.1),lme4, dplyr,
limma, preprocessCore, stringr, tidyr, impute, gplots,
grDevices, reshape2, graphics, stats, methods, ggplot2,
RColorBrewer, Matrix, org.Sc.sgd.db
ALDEx2, ANCOMBC, apeglm, ashr, Biobase, corncob, covr,
DESeq2, devtools, furrr, future, knitr, lefser, limma,
Maaslin2, metagenomeSeq, microbiome, rmarkdown, roxygen2,
roxyglobals, roxytest, rstatix, SummarizedExperiment,
TreeSummarizedExperiment, testthat (>= 3.0.0)
EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa,
SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle,
edgeR
testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse,
rmarkdown, BiocStyle
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl
BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick,
knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat
(>= 3.0.0)
BiocParallel, HDF5Array (>= 1.17.12), genefilter,
SummarizedExperiment, airway, lobstr, DelayedMatrixStats,
knitr, rmarkdown, BiocStyle, RUnit
testthat, knitr, rmarkdown, BiocStyle, SeqArray, GDSArray
testthat, knitr, rmarkdown, BiocStyle, microbenchmark,
profmem, HDF5Array, matrixStats (>= 1.0.0)
testthat, knitr, BiocStyle, rmarkdown, Matrix
markdown, rmarkdown, BiocStyle, knitr, testthat, magrittr,
dplyr, reticulate
BiocStyle, cowplot, DropletUtils, knitr, reshape2, rmarkdown,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, ggplot2, uwot, testthat
uwot, testthat, knitr, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, rmarkdown, dplyr, tidyr, tibble,
ggplot2, missForest, pheatmap, RColorBrewer, ggrepel,
BiocStyle, ggbeeswarm
rmarkdown, tensorflow, BiocStyle, RUnit, knitr, BiocGenerics
sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19),
RefManageR, rmarkdown (>= 0.3.3), testthat, covr
biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData
(>= 0.99.0), sessioninfo, knitr (>= 1.6), BiocStyle (>=
2.5.19), org.Hs.eg.db, RefManageR, rmarkdown (>= 0.3.3),
testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, covr
knitr, rmarkdown, igraph, testthat, FNN, tidyverse,
gridExtra, cowplot, conflicted, viridis, rgl, scRNAseq,
org.Mm.eg.db, scran, repr
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
knitr, RUnit, BiocGenerics,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylationEPICv2anno.20a1.hg38,
FlowSorted.Blood.EPIC, tissueTreg, DMRcatedata, EPICv2manifest
knitr, rmarkdown, testthat, sessioninfo, BiocStyle
AnnotationHub, knitr, rmarkdown, testthat,
BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19,
caret
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
BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub,
RUnit, muscData, scater, scuttle
PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid,
BiocStyle, knitr, testthat
testthat, knitr, BiocStyle, rmarkdown, jsonlite,
DropletTestFiles
RUnit, BiocStyle, knitr, rmarkdown, ggplot2, reshape2, DT,
EnsDb.Hsapiens.v86
BiocStyle, knitr, rmarkdown, tidyverse, testthat (>= 3.0.0)
limma, convert, GEOquery, dyebiasexamples, methods
knitr, rmarkdown, testthat (>= 3.0.0), Seurat, BiocManager,
devtools, BiocStyle
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, readr, rhdf5, splines, knitr, AnnotationDbi,
Biobase, BiocStyle, SummarizedExperiment, org.Hs.eg.db, Matrix,
SeuratObject
knitr, tximportData, testthat (>= 3.0.0)
knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie,
Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38,
ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker,
rtracklayer
SummarizedExperiment, testthat, Biobase, survminer,
affycoretools, knitr, plotROC, limma, rmarkdown
minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, org.Hs.eg.db, testthat (>= 3.0.0),
BiocStyle
testthat (>= 0.3), knitr, markdown, rmarkdown, genefilter,
RColorBrewer
ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools,
airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr,
rmarkdown, statmod
clusterProfiler, dplyr, europepmc, ggarchery, ggupset, glue,
knitr, rmarkdown, org.Hs.eg.db, prettydoc, tibble, tidyr,
ggforce, ggHoriPlot, AnnotationDbi, ggplotify, ggridges,
grDevices, gridExtra, ggstar, scales, ggtreeExtra, tidydr
BiocStyle, knitr, rmarkdown, ggplot2, testthat, magick
GenomeInfoDb, SummarizedExperiment, VariantAnnotation, RUnit,
knitr, rmarkdown, ggplot2
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr,
org.Hs.eg.db, regioneR, Seurat, survival, survminer,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
multiMiR, miRBaseConverter
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo
epiregulon, knitr, rmarkdown, parallel, BiocStyle, testthat
(>= 3.0.0), EnrichmentBrowser, msigdbr, dorothea, scMultiome,
S4Vectors, scuttle, vdiffr, ggrastr, ggrepel
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown,
EnrichedHeatmap, biomaRt, rtracklayer, covr, vdiffr, magick
BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat
(>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, httptest,
AnnotationHub, ensembldb, ggplot2, EpiTxDb.Hs.hg38,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Scerevisiae.UCSC.sacCer3,
TxDb.Hsapiens.UCSC.hg38.knownGene
testthat, roxygen2, knitr, Biobase, SummarizedExperiment,
antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle,
minfi, rmarkdown
testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors,
IRanges, SummarizedExperiment, antiProfilesData,
hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny,
minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr,
AnnotationHub
testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus,
TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown,
BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer,
utils, RMySQL, DBI, matrixStats
testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9),
Mus.musculus, Biobase, BiocStyle
Seurat, hexbin, scran, knitr, rmarkdown, markdown, BiocStyle,
RColorBrewer, rlang, spelling, testthat (>= 3.0.0), vdiffr
STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle,
ggpubr, scran, scater, scuttle, Seurat, hexbin
ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, dplyr,
kableExtra
rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat
(>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2,
MAST, DelayedMatrixStats, ggdendro, scales, patchwork
knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments
GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub
BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran,
scater, scds, TENxPBMCData, airway
testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle
BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, BiocManager
BiocFileCache, BiocStyle, graphics, knitr, memuse, rmarkdown,
spelling, testthat (>= 3.0.0)
rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0),
BiocStyle
biomaRt, tidyr, testthat, knitr, rmarkdown, devtools, covr
shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown,
testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi,
GOSemSim
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
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
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
knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment,
SummarizedExperiment, airway
knitr, BiocStyle, rmarkdown, BiocManager,
BSgenome.Hsapiens.UCSC.hg19, DT, rtracklayer, testthat (>=
3.0.0), RBGL
BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene
pathview, gageData, org.Hs.eg.db, hgu133a.db, GSEABase,
Rsamtools, GenomicAlignments,
TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq2, edgeR, limma
testthat, knitr, rmarkdown, KEGGREST, AnnotationDbi,
org.Mm.eg.db, reactome.db, fgsea, readr, BiocStyle, R.utils
BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Mmusculus.UCSC.mm10
knitr, ggplot2, testthat, BEDMatrix, genio
edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db,
BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
affydata, tools, splines, hgu95av2cdf, hgu95av2probe
BiocStyle, knitr, rmarkdown, RUnit,
TxDb.Hsapiens.UCSC.hg38.knownGene, gDNAinRNAseqData
BiocStyle, BumpyMatrix, futile.logger, gDRstyle (>= 1.1.5),
gDRtestData (>= 1.1.10), kableExtra, knitr, markdown, purrr,
rmarkdown, SummarizedExperiment, testthat, yaml
BiocStyle, gDRstyle (>= 1.1.5), gDRimport (>= 1.1.9),
gDRtestData (>= 1.1.10), IRanges, knitr, pkgbuild, qs,
testthat, yaml
BiocStyle, gDRtestData (>= 1.3.3), gDRstyle (>= 1.3.3),
knitr, purrr, qs, testthat
BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.1.5),
gDRtestData (>= 1.1.10), IRanges, knitr, lintr, purrr, qs,
rcmdcheck, rmarkdown, scales, testthat, tools, yaml
testthat, knitr, markdown, rmarkdown, BiocStyle, BiocManager
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, htmltools,
pcaExplorer, AnnotationDbi, macrophage, topGO, biomaRt,
ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db
knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown
testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2,
ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap,
viridis, poolr, kableExtra, listviewer, shiny
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
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods, BiocStyle
spelling, rmarkdown, BiocStyle, testthat (>= 3.0.0), knitr
R.utils, data.table, GenomicRanges, Rsamtools,
GenomicAlignments, GenomicFeatures, BSgenome,
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
RUnit, BiocStyle, knitr, rmarkdown, rtracklayer, testthat,
TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db
Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>=
2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>=
1.13.53), GenomicAlignments, rtracklayer, BSgenome,
GenomicFeatures, txdbmaker, Gviz, VariantAnnotation,
AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph,
RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGGREST,
hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
TxDb.Athaliana.BioMart.plantsmart22,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr,
rmarkdown, BiocStyle
RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation,
gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader,
data.table, DT, magrittr, shinydashboard,
BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38,
MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v4.0.GRCh38,
SNPlocs.Hsapiens.dbSNP144.GRCh37,
TxDb.Hsapiens.UCSC.hg38.knownGene
knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis,
BiocStyle, testthat, forcats, stats, wordcloud, circlize,
EnrichmentBrowser, clusterProfiler, msigdbr, cluster,
RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr,
utils
testthat, knitr, BiocStyle, rmarkdown, covr,
GenomicAlignments, Biostrings
VAExprs, stringdist, knitr, testthat, rmarkdown
BiocCheck, roxygen2, knitr, rmarkdown, testthat
knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud
RUnit, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
manipulateWidget, shiny, BiocStyle, knitr, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph,
Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork
knitr, rmarkdown, BiocGenerics, testthat, covr, markdown
knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr,
clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq,
testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery,
BiocGenerics
devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat
(>= 3.0.0)
airway, knitr, DESeq2, recount3, rmarkdown, stringr, testthat
(>= 3.0.0)
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, BiocStyle, rmarkdown,
readxl, ggnewscale, kableExtra, gggenes, testthat (>= 3.0.0)
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
BiocStyle, rmarkdown, knitr, STexampleData, BumpyMatrix,
scater, scran, uwot, testthat, patchwork
emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,
prettydoc, rmarkdown, testthat, tibble, glue
aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust,
rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils
treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc,
markdown, testthat (>= 3.0.0), pillar
knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0)
roxygen2, knitr, rmarkdown, testthat, BiocStyle
testthat (>= 2.1.0), zoo, DESeq2, edgeR, limma, MASS,
statmod, ggplot2, bench, BiocParallel, knitr, rmarkdown,
BiocStyle, TENxPBMCData, muscData, scran, dplyr
BiocStyle, curatedTCGAData, knitr, magrittr, reshape2, pROC,
rmarkdown, survival, testthat, VennDiagram, withr
GO.db, golubEsets, hu6800.db, vsn, Rgraphviz
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
Homo.sapiens, BiocStyle, knitr, markdown, rmarkdown, testthat
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, rappdirs, readr, rmarkdown, testthat,
tidyr, tidyselect, ROCR
BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db,
org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db,
org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db,
org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db
hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter,
RColorBrewer, xtable, SparseM, GSEABase, geneplotter,
org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr
knitr, rmarkdown, RUnit, BiocManager, BiocGenerics,
BiocStyle, devtools
SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle,
knitr
checkmate, a4Preproc, ALL, BiocStyle, codetools,
hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db,
parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat,
topologyGSA (>= 1.4.0)
MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate,
org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR,
BiocStyle
hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools,
testthat, BiocStyle, knitr, RUnit
BiocStyle, GSE62944, knitr, rappdirs, rmarkdown
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm
knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp,
Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP,
iC10TrainingData, pamr, testthat
BiocGenerics, RUnit, BiocStyle, knitr, rmarkdown, limma,
RColorBrewer, org.Hs.eg.db, genefilter, edgeR, GSVAdata, shiny,
shinydashboard, ggplot2, data.table, plotly, future, promises,
shinybusy, shinyjs
testthat (>= 1.0.0), knitr, RColorBrewer, markdown,
rmarkdown, ComplexHeatmap (>= 1.99.0), Cairo, png, jpeg, tiff
knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, TxDb.Hsapiens.UCSC.hg19.knownGene,
org.Hs.eg.db, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, formatR, rrBLUP
ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
VariantAnnotation, parallel, BiocStyle, knitr
knitr, rmarkdown, testthat, BiocStyle, digest, jsonvalidate,
DBI, RSQLite, S4Vectors, methods
BiocParallel, ExperimentHub, TENxBrainData, HDF5Array,
testthat, knitr, rmarkdown, BiocStyle
knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics, rmarkdown
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
LoomExperiment, SummarizedExperiment, SingleCellExperiment,
S4Vectors, methods, testthat (>= 3.0.0), knitr, rmarkdown,
BiocStyle
BiocParallel, GenomicRanges, SummarizedExperiment (>=
1.15.1), h5vcData, ExperimentHub, TENxBrainData, zellkonverter,
GenomicFeatures, SingleCellExperiment, DelayedMatrixStats,
genefilter, RSpectra, RUnit, knitr, rmarkdown, BiocStyle
RColorBrewer, pheatmap, MASS, patchwork, testthat
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray,
knitr, markdown, rmarkdown, Rsamtools
knitr, rmarkdown, testthat, BiocStyle, BiocManager, rhdf5
HiContacts, HiContactsData, BiocFileCache, rtracklayer,
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
HiContactsData, rtracklayer, GenomicFeatures, Biostrings,
BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra,
patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
HiContacts, HiContactsData, AnnotationHub, BiocFileCache,
BiocStyle, testthat, knitr, rmarkdown
knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.99.0),
markdown, RColorBrewer, RCurl, GetoptLong, rmarkdown
knitr, annotate, gwascat, testthat, rmarkdown
knitr, rmarkdown, markdown, devtools, BiocStyle
org.Hs.eg.db, GO.db, AnnotationDbi, knitr, BiocStyle,
testthat, rmarkdown, dplyr, DT
rmarkdown, colorspace, e1071, kernlab, ranger,
SummarizedExperiment, Biostrings, randomForest, gprofiler2,
gridExtra, ggthemes, BiocStyle, BiocGenerics, RUnit, tools,
knitr
AnnotationHubData, ExperimentHubData, testthat, knitr,
rmarkdown, BiocStyle,
knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot,
DescTools, RColorBrewer
knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, ggrepel, patchwork
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
CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown,
testthat
BiocStyle, ggplot2, knitr, markdown, rmarkdown, scRepertoire,
spelling, testthat, viridis
BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
knitr, org.Hs.eg.db, org.Mm.eg.db,
IlluminaHumanMethylation450kanno.ilmn12.hg19, AnnotationDbi,
sesameData, TCGAbiolinks (>= 2.29.4)
knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0),
SummarizedExperiment
BiocGenerics,BiocManager, BiocStyle,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.UCSC.hg19,
EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, knitr, markdown,
rmarkdown, rtracklayer, RUnit, grDevices,
TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Mmusculus.UCSC.mm10.knownGene
knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges,
data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap,
cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3,
GOexpress, SingleCellExperiment, scater, gplots, pheatmap,
airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve
(>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks
RUnit, hgu95av2.db, knitr, GenomicRanges,
SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer,
metagenomeSeq, gplots, vegan, Biobase
testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite,
processx, attempt, BiocStyle, httr
gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat
BiocStyle, knitr, rmarkdown, gridExtra, testthat,
minionSummaryData
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown,
roxygen2, vegan, withr, extraDistr, ggalluvial, scales,
gridExtra, R.utils, RefManageR, flexdashboard, circlize,
plotly, gtools, eulerr, openxlsx, jsonlite, pheatmap,
BiocParallel, progressr, future, doFuture, foreach, psych,
data.table, Rcapture
testthat, covr, BiocStyle, knitr, rmarkdown, scRNAseq,
TENxPBMCData, scater, DelayedArray, HDF5Array, RColorBrewer,
viridis, htmltools, GenomicRanges
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, MGnifyR, 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, png, limma, grid, DT, randomForest, digest, testthat,
rmarkdown, BiocStyle, magick, statmod, codetools
RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db,
SPIA
RUnit, BiocGenerics, BiocStyle, knitr, markdown
testthat (>= 3.0.0), SummarizedExperiment, rmarkdown, knitr,
sesame, gprofiler2, ggrastr
BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice,
msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat,
mzR
BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats,
VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75,
Rsamtools, GenomicFiles (>= 1.13.6)
knitr, rmarkdown, curatedMetagenomicData, BiocStyle,
phyloseq, pkgdown, covr, withr
testthat (>= 3.0.0), tidyverse, uwot, dplyr, edgeR, knitr,
rmarkdown, BiocStyle
BiasedUrn, ellipse, gplots, knitr, locfit, MASS, splines,
affy, AnnotationDbi, Biobase, BiocStyle, GO.db, illuminaio,
org.Hs.eg.db, vsn
BiocStyle, pander, rmarkdown, car, gridExtra, knitr, testthat
(>= 3.0.0)
BiocStyle, ggplot2, magick, testthat (>= 3.0.0), knitr,
rmarkdown, caret, ROTS
MASS (>= 7.3.0), knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, markdown, gplots, RColorBrewer,
moments, testthat, matrixStats
knitr, rmarkdown, igraph, reshape2, limma,
knitr, rmarkdown, BiocStyle, ggrepel, plotly, spelling,
testthat
SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>=
3.0.0)
parallel, testthat, knitr, BiocStyle, rmarkdown
testthat, BiocStyle, knitr, rmarkdown, reticulate
LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2,
testthat
beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
nnls, knitr, testthat, rmarkdown, BiocStyle, GenomicRanges,
limma, ExperimentHub, AnnotationHub, DelayedMatrixStats,
BisqueRNA, DelayedArray
ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat,
Biobase
knitr, testthat (>= 2.1.0), rmarkdown, markdown
knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra
knitr, BiocStyle, optparse, testthat (>= 2.1.0), rmarkdown,
markdown
testthat, knitr, rmarkdown, BiocStyle, MACSdata
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors, curl
BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo,
testthat (>= 3.0.0)
knitr, testthat (>= 3.0.0), dplyr, rmarkdown, ExperimentHub,
marinerData
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
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, BisqueRNA, clusterProfiler,
ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra,
jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle,
singscore, splatter, testthat (>= 3.0.0), UpSetR
Matrix, sparseMatrixStats, SparseArray, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0)
knitr, markdown, BiocStyle, testthat (>= 3.0.0)
beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData,
scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
Biobase, BiocGenerics, BiocStyle, FlowSorted.Blood.450k,
knitr, leukemiasEset, minfi, minfiData, rmarkdown, RUnit
testthat, knitr, rmarkdown, fgsea, BiocManager
testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData,
BiocStyle, rmarkdown, brgedata
knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0)
covr, knitr, BiocStyle, sessioninfo, rmarkdown, rtracklayer,
derfinder, GenomeInfoDb, tools, RefManageR, testthat
cowplot, BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Dmelanogaster.UCSC.dm6, forcats, testthat (>= 2.1.0),
knitr, MotifDb, pheatmap, PMCMRplus, plyranges (>= 1.9.1),
rmarkdown, covr
shiny, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 (>=
1.4.0), org.Hs.eg.db, clusterProfiler,
TxDb.Hsapiens.UCSC.hg19.knownGene
knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>=
2.22.0), BiocStyle
BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra,
knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0)
testthat, knitr, msdata, BiocStyle, rmarkdown, plotly, shiny,
shinyjs, DT, microbenchmark, mzR
BiocStyle, testthat, knitr, rmarkdown, robustbase
BiocStyle, covr, knitr, HDF5Array, httptest, rmarkdown,
structToolbox, testthat, pmp, grid, png
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
annotate, BiocGenerics, biomformat, knitr, gss, testthat (>=
0.8), vegan, interactiveDisplay, IHW
knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2),
UpSetR
BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr
(>= 1.48), testthat (>= 3.2.1.1)
BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC,
RUnit
rmarkdown, knitr, testthat (>= 2.1.0), BiocGenerics,
BiocStyle, tidyr, ggplot2
BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
BiocStyle, doParallel, testthat, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, devtools, R.utils
BiocStyle, bsseqData, knitr, rmarkdown, testthat (>= 2.1.0),
covr
lumi, lattice, limma, xtable, SQN, MASS, matrixStats,
parallel, rtracklayer, Biostrings, TCGAMethylation450k,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr
covr, httptest, knitr, rmarkdown, testthat (>= 3.0.0),
rgoslin, DT, RSQLite, CompoundDb, BiocStyle, BiocFileCache,
msPurity, ChemmineOB, rsvg, metabolomicsWorkbenchR, KEGGREST,
plyr, magick, structToolbox, RVenn, ggVennDiagram, patchwork,
XML, GO.db, tidytext, tidyr, tidyselect, ComplexUpset,
jsonlite, openxlsx
biomformat, broom, ggplot2, knitr, rmarkdown, testthat, xml2,
BiocStyle, miaViz, vegan, scater, phyloseq, magick
ade4, BiocStyle, biomformat, dada2, knitr, miaViz,
microbiomeDataSets, NMF, patchwork, phyloseq, reldist, rhdf5,
rmarkdown, stringr, testthat, topicdoc, topicmodels, yaml
ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2,
igraph, network, reshape2, sna, vegan, rmarkdown, knitr,
BiocStyle, testthat, mia, miaViz, colourvalues, philentropy
BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, knitr,
patchwork, rmarkdown, testthat, vegan
BiocGenerics, BiocStyle, Cairo, knitr, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), prettydoc
rmarkdown, prettydoc, testthat, knitr, nlme, phangorn,
DECIPHER, randomForest, jsonlite, biomformat, scales, yaml,
withr, S4Vectors, purrr, seqmagick, glue, ggupset,
ggVennDiagram, gghalves, ggalluvial (>= 0.11.1), forcats,
phyloseq, aplot, ggnewscale, ggside, ggh4x, hopach, parallel,
shadowtext, DirichletMultinomial, ggpp, BiocManager
BiocStyle, gghighlight, knitr, rmarkdown, methods,
RefManageR, sessioninfo, SingleCellExperiment,
SummarizedExperiment, testthat (>= 3.0.0)
testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle
testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown,
uwot, scuttle, BiocStyle, MouseGastrulationData,
MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq,
graphics, sparseMatrixStats
biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
breastCancerVDX, future, future.apply
IlluminaHumanMethylation450kmanifest (>= 0.2.0),
IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1),
minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>=
1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools
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, knitr, rmarkdown, R.cache, SPONGE
BiocStyle, edgeR, knitr, minfiData, rmarkdown,
tweeDEseqCountData, DMRcate, ExperimentHub
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
BiocStyle, knitr, rmarkdown, testthat, microbenchmark, magick
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
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 (>= 1.0.0), timecoursedata, knitr, rmarkdown,
markdown, covr, BiocStyle
testthat, knitr, rmarkdown, dplyr, shinycssloaders, shiny,
shinyFiles, shinydashboard, shinyjs
BiocStyle, knitr, rmarkdown, testthat, usethis
knitr, testthat, Seurat, SeuratObject, ggpubr, foreach,
psych, MultiAssayExperiment, SummarizedExperiment,
SingleCellExperiment, ggrastr, mvtnorm, GGally, rmarkdown,
data.table, tidyverse, BiocStyle, Matrix, markdown
BiocStyle, knitr, rmarkdown, testthat, viper
destiny, Hmisc, knitr, Seurat, scater, testthat
BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2,
png, edgeR
knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat
(>= 3.0.0)
RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq,
rmarkdown, kableExtra, testthat (>= 3.0.0)
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
knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc
AnnotationHub, BiocStyle, BSgenome.Hsapiens.UCSC.hg19,
extraChIPs, ggdendro, knitr, MotifDb, rmarkdown, rtracklayer,
testthat (>= 3.0.0), VGAM
rmarkdown, knitr, svglite, bookdown(>= 0.34), testthat (>=
3.0.0)
Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
rmarkdown, knitr, devtools, testthat, ggplot2, BiocStyle
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, rmarkdown
testthat, rmarkdown, mzR, knitr, BiocStyle
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown
BiocStyle (>= 2.5), ExperimentHub, MsBackendMgf, knitr,
lattice, mzR, protViz (>= 0.7), rmarkdown, tartare (>= 1.5),
testthat
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
RSQLite, msdata, rmarkdown, microbenchmark, mzR
testthat, knitr, BiocStyle, rmarkdown, roxygen2, imputeLCMD,
impute, norm, pcaMethods, vsn, Matrix, preprocessCore,
missForest
ExperimentHubData, DT, BiocStyle, knitr, rmarkdown, testthat
(>= 3.0.0), Spectra, mzR, PSMatch, QFeatures (>= 1.13.3)
testthat, knitr (>= 1.1.0), roxygen2, BiocStyle (>= 2.5.19),
rmarkdown, rpx, mzR, msdata, MsBackendSql (>= 1.3.2), RSQLite
testthat, roxygen2, BiocStyle, pheatmap, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, ComplexHeatmap, imputeLCMD
BiocStyle, doFuture, future, knitr, rmarkdown, roxygen2,
tinytest
testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>=
1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.43.3), magick,
msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub,
BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots,
XML, shiny, magrittr, SummarizedExperiment, Spectra
knitr, testthat (>= 3.0.0), downloadthis, DT, rmarkdown,
BiocStyle, imputeLCMD
BiocStyle, knitr, rmarkdown, testthat (>= 1.0.2)
MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
msPurityData, CAMERA, RPostgres, RMySQL
multcomp, gridExtra, knitr, BiocStyle, RefManageR,
sessioninfo, rmarkdown, testthat, tidyverse, plotly, msdata,
MSnbase, matrixStats, MsCoreUtils, covr
BiocStyle, knitr, rmarkdown, tinytest, covr, markdown,
mockery
BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
knitr, rmarkdown, tinytest, covr, mockery, testthat (>=
3.0.0)
rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0),
shinytest2,
HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr,
SingleCellMultiModal, CiteFuse, scater
BiocStyle, HDF5Array, knitr, maftools, R.rsp,
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)
BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2)
testthat, BiocStyle, knitr, covr, rmarkdown
BiocStyle, doParallel, ExperimentHub, knitr, markdown,
rmarkdown, testthat (>= 3.0.0), vegan
testthat, knitr, BiocStyle, rmarkdown, scater, bluster,
DropletUtils, scRNAseq
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, rmarkdown
BiocStyle, DSS, Mus.musculus (>= 1.3.1), Homo.sapiens (>=
1.3.1), org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm39.refGene, knitr, rmarkdown,
rtracklayer, testthat (>= 3.0.0), covr
biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf
grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly,
rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
knitr, BiocStyle, rmarkdown, RUnit, BiocGenerics
testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran,
DropletUtils, igraph, BiocFileCache, Seurat
knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db,
org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr,
markdown
knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI,
pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
testthat (>= 2.1.0), knitr, rmarkdown, pkgdown
testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp,
BiocStyle, knitr
BiocStyle, Cairo, DT, knitr, pander, readr, testthat,
truncnorm
BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth,
knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>=
4.0.0), spatstat.explore, stringr, survival, tidyverse,
testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, STexampleData,
WeberDivechaLCdata, scran, ggplot2, testthat
knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
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, nullrangesData, excluderanges,
ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38,
patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt,
DiagrammeR, tidySummarizedExperiment
BiocStyle, knitr, rmarkdown, snpStats, brgedata
BiocStyle, knitr, rmarkdown, testthat, GEOquery,
VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges,
FDb.InfiniumMethylation.hg19, snpStats
knitr, rmarkdown, BiocStyle, magick, testthat
RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis,
desc, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, testthat, Matrix, graph
testthat (>= 3.1.4), jsonlite, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown,
bookdown, pander
knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle,
SingleCellExperiment, celldex, rmarkdown, AnnotationDbi, magick
flowWorkspaceData, knitr, rmarkdown, markdown, testthat,
utils, tools, parallel, ggcyto, CytoML, flowStats(>= 4.5.2),
MASS
knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2,
gridExtra, knitr, Matrix, rmarkdown, scales, testthat
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat,
knitr, rmarkdown, magick, BiocStyle, ggplot2
Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19,
AnnotationHub, FDb.UCSC.tRNAs, mirbase.db, rtracklayer,
biomaRt, RUnit, RMariaDB, BiocStyle, knitr
rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown,
testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape,
phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat
(>= 3.0.0)
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
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle, rmarkdown
rmarkdown, knitr, IRanges, testthat (>= 3.0.0)
AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite,
knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0),
vdiffr
gage, org.Mm.eg.db, org.EcK12.eg.db, RUnit, BiocGenerics
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, beachmat, RMTstat, ggalt, DESeq2,
airway, org.Hs.eg.db, magrittr, rmarkdown
testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr,
HDF5Array
testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander,
BiocStyle
diffviewer, testthat (>= 3.0.0), vdiffr, rmarkdown,
BiocStyle, knitr, withr, qpdf, shinytest2, covr, devtools,
R.devices, usethis, magick
statmod, BiocStyle, knitr, rmarkdown, tidyr
knitr, markdown, rmarkdown, BiocStyle, PepsNMRData
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, rhdf5,
GEOquery
pander, rmarkdown, knitr, knitcitations, crayon, testthat,
markdown, BiocStyle, R.utils
BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4,
rmarkdown, testthat
knitr, rmarkdown, forcats, testthat, BiocStyle,
SingleCellExperiment
testthat, knitr, ecodist, rmarkdown, BiocStyle, phyloseq,
SummarizedExperiment, TreeSummarizedExperiment, glmnet, dplyr,
mia
BiocStyle, testthat, knitr, rmarkdown, covr, dplyr, readr,
withr
testthat, knitr, rgl, sna, ClueR, directPA, rmarkdown,
org.Rn.eg.db, org.Mm.eg.db, reactome.db, annotate, BiocStyle,
stringr, calibrate
yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM,
gtools, biomaRt, snowfall, AnnotationDbi, knitr, rmarkdown,
BiocStyle
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
ggplot2, testthat, tidyr, scales, minfi, EpiDISH, knitr,
rmarkdown
BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>=
3.0.0)
knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf,
BiocStyle, biocViews, testthat (>= 3.0.0)
AnnotationDbi, AnnotationHub, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, ComplexHeatmap, GenomicFeatures,
ggplot2, InteractionSet, knitr, org.Hs.eg.db, rtracklayer,
plotgardenerData, pdftools, png, rmarkdown, scales, showtext,
testthat (>= 3.0.0), TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, htmltools, BiocStyle, rmarkdown, testthat
tidyverse, BSgenome.Mmusculus.UCSC.mm10, Biostrings,
BiocParallel, scales, HiContactsData, rtracklayer, BiocStyle,
covr, knitr, rmarkdown, sessioninfo, testthat (>= 3.0.0),
RefManageR
devtools, knitr, rmarkdown, testthat, airway, IRanges, here
testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra,
magick
BSgenome.Hsapiens.UCSC.hg38.masked,
TxDb.Hsapiens.UCSC.hg38.knownGene,
BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24),
VariantAnnotation, SummarizedExperiment, knitr
knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, rmarkdown, ddPCRclust
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
testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr,
tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown,
BiocStyle
airway, biomaRt, BiocFileCache, broom, Seurat,
SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl,
pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools,
knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject
testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2,
xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr,
akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13),
nipals, reshape, magick
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat
(>= 3.0.0)
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT
msdata, rpx, mzID, mzR, Spectra, SummarizedExperiment,
BiocStyle, rmarkdown, knitr, factoextra, testthat
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData,
ropls
MotifDb, BSgenome, BSgenome.Dmelanogaster.UCSC.dm3,
PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel,
PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background,
BiocStyle, knitr
affy, MSnbase, ggplot2, lattice, mzR, BiocStyle, rmarkdown,
markdown
SingleCellExperiment, MsDataHub (>= 1.3.3), Matrix,
HDF5Array, msdata, ggplot2, gplots, dplyr, limma, DT, shiny,
shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn,
preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute,
norm, ComplexHeatmap
Rtsne, missForest, vsn, pcaMethods, pls, MsFeatures, impute,
imputeLCMD, nlme, testthat (>= 3.0.0), BiocStyle, knitr,
rmarkdown
RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db,
rlecuyer, snow, Category, GOstats
patchwork, knitr, qPLEXdata, rmarkdown, statmod, testthat,
UniProt.ws, vdiffr
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR,
rmarkdown, sessioninfo, testthat (>= 3.0.0)
testthat, BiocStyle, knitr, rmarkdown, covr
AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery,
knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat,
tibble
rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle
QUBICdata, qgraph, fields, knitr, rmarkdown
rmarkdown, BiocStyle, knitr, pander, markdown
BiocStyle, knitr, rmarkdown, testthat, MultiAssayExperiment
RUnit, knitr, rmarkdown, ggplot2, gridExtra, annotatr, LOLA,
org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene
knitr, rmarkdown, pander, BiocStyle,
BSgenome.Ecoli.NCBI.20080805
knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle,
testthat (>= 2.1.0), limma, sva
markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>=
3.0.0)
BiocStyle, covr, knitr, tinytest, mockery
BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat
BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7),
rmarkdown, tartare (>= 1.5), testthat
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph
testthat, parallel, BiocStyle, knitr, rmarkdown
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW,
parallel, rmarkdown
Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach,
gplots, rtracklayer, igraph, knitr,
RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat,
visNetwork
testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse,
tinytex
BiocStyle, testthat, knitr, rmarkdown, base64enc, graph
BiocStyle, knitr, rmarkdown, igraph, grDevices
knitr, rmarkdown, RUnit, testthat (>= 3.0.0)
devtools, knitr, ReactomeGSA.data, rmarkdown, scater, scran,
scRNAseq, scuttle, Seurat (>= 3.0), SingleCellExperiment,
testthat
BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db,
prettydoc, testthat
testthat, igraph, XML, BiocManager, RCurl, bookdown,
rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows
knitr, rmarkdown, testthat (>= 2.1.0), here
minfiData, minfiDataEPIC, knitr, testthat, ggplot2,
gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma,
ExperimentHub, AnnotationHub
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
rmarkdown, BiocStyle, GenomeInfoDb, knitr, testthat (>=
3.0.0)
testthat, BiocStyle, knitr, rmarkdown, BiocSingular
BiocStyle, knitr, rmarkdown, testthat, DescTools, ggplot2,
corrplot, cowplot, grid, colorspace, png, reshape2, pals, RCurl
mclust, flexmix, testthat, BiocStyle, knitr, formatR,
rmarkdown
R4RNA, treeio, knitr, BiocStyle, rmarkdown, BiocGenerics,
RUnit
testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra,
BiocManager, stringr, stringi, ggplot2, tibble, lipidr
RUnit, BiocStyle, BiocGenerics, xtable, sna
testthat (>= 0.3), knitr, rmarkdown, BiocManager,
org.Mm.eg.db, msigdbr, KEGGREST, reactome.db
bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr,
ggplot2, mockery, BiocParallel
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7)
BiocStyle, knitr, rmarkdown, tinytest, mockery
knitr, rmarkdown, BiocManager, BiocStyle, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, knitr, rmarkdown, nucleoSim, RUnit
BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown,
RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1)
readxl, knitr, rmarkdown, reshape2, pander, testthat
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
Biostrings, RNAmodR.Data
BiocStyle, knitr, rmarkdown, testthat, RNAmodR.Data,
RNAmodR.AlkAnilineSeq, GenomicFeatures, Rsamtools, rtracklayer,
keras
BiocStyle, knitr, rmarkdown, testthat, rtracklayer,
RNAmodR.Data
BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr,
testthat (>= 3.0.0)
Category, GOstats, Gviz,
IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19,
RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach,
doParallel, ggbio, isva, mclust, mgcv, minfi, nlme,
org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog,
rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue,
argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19,
scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin,
RUnit, MethylSeekR, sesame
BiocStyle, knitr, rmarkdown, GSEABenchmarkeR,
EnrichmentBrowser, preprocessCore, DESeq2
GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat,
lubridate, DT, rmarkdown,
BiocGenerics, BiocStyle, knitr, multtest, omicade4, phenomis,
rmarkdown, testthat
knitr, rmarkdown, testthat, RUnit, BiocGenerics
BiocStyle, covr, kableExtra, knitr, rmarkdown, styler,
testthat (>= 3.0.0)
Biostrings, BiocStyle, testthat, knitr, tibble, rmarkdown
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0),
shinydashboard, DT, plotly, heatmaply, magrittr, utils,
clusterProfiler, DOSE, slam, org.Ag.eg.db, org.At.tair.db,
org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db,
org.Dr.eg.db, org.EcK12.eg.db, org.EcSakai.eg.db, org.Gg.eg.db,
org.Hs.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Pt.eg.db,
org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db
GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle, knitr
testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
e1071, parallel, doParallel
BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer, pwalign
Rtsne, ape, Seurat, knitr, rmarkdown, tictoc, BiocStyle,
testthat (>= 3.0.0)
devtools, testthat, pander, Biobase, GenomicRanges, IRanges,
S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations,
RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation,
RTCGA.CNV, magrittr, tidyr
BiocStyle, Homo.sapiens, knitr, readr, rmarkdown
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics
Fletcher2013b, knitr, rmarkdown, BiocStyle, RUnit,
BiocGenerics
knitr, BiocStyle, TPP, testthat, rmarkdown
RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt,
Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db,
org.Mm.eg.db, ggplot2, BiocStyle, knitr, rmarkdown
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, testthat,
knitr, rmarkdown, BiocStyle
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle,
knitr
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
parallel, markdown, rmarkdown, crayon, SNPRelate, RUnit,
knitr, ggmanh, BiocGenerics
BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db,
markdown, rmarkdown, RUnit
knitr, kableExtra, testthat,
TxDb.Hsapiens.UCSC.hg38.knownGene, Homo.sapiens,
TxDb.Mmusculus.UCSC.mm10.knownGene, Mus.musculus,
GenomicAlignments
knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub,
ensembldb, edgeR, DEXSeq, stageR, DelayedArray
knitr, rmarkdown, mclust, scater, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, BiocSingular,
DelayedMatrixStats
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
testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle,
rmarkdown
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown,
knitr, loo, prettydoc, tidyseurat, tidySingleCellExperiment,
bayesplot, posterior
PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra,
rmarkdown
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
mvnfast, igraph, knitr, rmarkdown, testthat (>= 3.0.0),
RefManageR, sessioninfo, BiocStyle
AUCell, BiocStyle, knitr, Matrix, rmarkdown, scran, scRNAseq,
SingleR, celldex, scuttle, scater, dplyr, testthat (>= 3.0.0)
AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
scuttle, SeuratObject, testthat, vdiffr
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
knitr, S4Vectors, survival, survminer, BiocStyle, ClassifyR,
org.Hs.eg.db, clusterProfiler
ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr,
TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph,
scran, tibble, scuttle
knitr, markdown, rmarkdown, scater, scattermore, scales,
matrixStats, deldir
BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0)
BiocStyle, covr, HDF5Array, knitr, Matrix, rmarkdown, scales,
proxy, testthat, badger
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38,
TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase,
BiocGenerics, ggplot2, ggthemes
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM,
R.utils
knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0)
BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2,
rmarkdown, scran, scRNAseq, shiny, testthat, 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
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
testthat, knitr, rmarkdown, BiocStyle, MatrixGenerics,
sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment,
SingleCellExperiment, scRNAseq
testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown,
testthat
BiocManager, BiocStyle, circlize, knitr, rmarkdown, scales,
scater, Seurat, spelling, testthat (>= 3.0.0), vdiffr
BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array,
knitr, markdown, rmarkdown, TENxPBMCData, testthat
testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens,
AnnotationHub
knitr, BiocStyle, testthat, SC3, scRNAseq, rmarkdown, msd16s,
metagenomeSeq, epivizrStandalone, GenomeInfoDb
BiocStyle, knitr, scRNAseq, rmarkdown, testthat,
sparseMatrixStats, DelayedMatrixStats, scran
testthat, knitr, rmarkdown,
TxDb.Hsapiens.UCSC.hg18.knownGene, Gviz
knitr, rmarkdown, testthat, BiocStyle, ggplot2, dplyr, tidyr
cowplot, hopach (>= 2.42.0), BiocStyle, knitr (>= 1.22),
rmarkdown (>= 1.12), testthat (>= 3.0.2), covr, vdiffr (>=
0.3.0)
BSgenome.Dmelanogaster.UCSC.dm6, BiocStyle, CAGEr (>= 2.0.2),
covr, knitr (>= 1.22), org.Dm.eg.db, pdftools, rmarkdown (>=
1.12), slickR, TxDb.Dmelanogaster.UCSC.dm6.ensGene, xfun
Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate,
digest, crayon, knitr, markdown, rmarkdown, Rsamtools,
VariantAnnotation
emojifont, knitr, rmarkdown, prettydoc, tibble
testthat (>= 3.0.0), edgeR, BiocStyle, knitr, rmarkdown
BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics,
BiocStyle
scales, BiocManager, knitr, DNAcopy, e1071, randomForest,
RPMM, rmarkdown, testthat, tidyr, BiocStyle, ggrepel,
grDevices, KernSmooth, pals
knitr, rmarkdown, BiocManager, devtools, BiocStyle
testthat, parallel, knitr, rmarkdown, BiocStyle
config, covr, knitr, lintr, mockery (>= 0.4.3), rcmdcheck,
rmarkdown, sessioninfo, spelling, testthat (>= 3.0.0),
GenomicRanges, VariantAnnotation, StructuralVariantAnnotation,
biovizBase, ggbio
shinyMethylData, minfiData, BiocStyle, knitr, testthat
BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi,
knitr
BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0),
TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle
testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx
knitr, testthat, rmarkdown, BiocStyle, signatureSearchData,
DT
BiocStyle, edgeR, grid, kableExtra, knitr, limma, testthat
(>= 3.0.0)
curl, knitr, matrixStats, rmarkdown, Seurat (>= 5.0.0),
SeuratObject (>= 5.0.0), testthat (>= 3.0.0)
RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments,
rtracklayer, rmarkdown, BiocStyle
BiocGenerics, BiocStyle, testthat, knitr, igraph
knitr, testthat, BiocManager, GO.db, org.Hs.eg.db, proxyC,
AnnotationDbi, Matrix, DiagrammeR, ragg, png,
InteractiveComplexHeatmap, UniProtKeywords, simplifyEnrichment,
AnnotationHub, jsonlite
ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>=
3.0.0)
BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
knitr, ggplot2, cowplot, mclust, apcluster, MCL, dbscan,
igraph, gridExtra, dynamicTreeCut, testthat, gridGraphics,
flexclust, BiocManager, InteractiveComplexHeatmap (>= 0.99.11),
shiny, shinydashboard, cola, hu6800.db, rmarkdown, genefilter,
gridtext, fpc
BiocStyle, knitr, biomaRt, stringr, monocle
scaeData, knitr, rmarkdown, BiocStyle, scran, scater,
scuttle, ggplot2, patchwork, org.Hs.eg.db, AnnotationDbi,
DropletUtils, testthat (>= 3.0.0)
testthat, BiocStyle, knitr, rmarkdown, Matrix, scRNAseq (>=
2.9.1), Rtsne
testthat, knitr, rmarkdown, BiocStyle, BiocGenerics,
SingleCellExperiment, scuttle, scrapper, scRNAseq, ggplot2,
pheatmap, grDevices, gridExtra, viridis, celldex
pkgdown, BiocStyle, hexbin, knitr, rmarkdown, testthat, covr
BiocStyle, devtools, knitr, magick, rmarkdown, testthat
rmarkdown, knitr, testthat (>= 3.0.0), TENxPBMCData, scuttle,
scran, scater, SingleR, celldex, cowplot, SummarizedExperiment,
beachmat.hdf5, BiocStyle, BiocManager, SingleCellExperiment
BiocGenerics, BiocStyle, clusterExperiment,
DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl,
rmarkdown, testthat, uwot, covr
BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater,
splatter, testthat (>= 3.0.0), tidytext, UpSetR
BiocStyle, knitr, STexampleData, scuttle, scran, scater,
ggspavis, testthat
BiocManager, bit64, covr, knitcitations, knitr (>= 1.6),
devtools, BiocStyle (>= 2.5.19), rmarkdown (>= 0.9.5), testthat
(>= 2.1.0)
knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0)
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
knitr, rmarkdown, ggspavis, BiocStyle, imcdatasets,
ggfortify, tidyr, testthat (>= 3.0.0)
data.table, devtools, dplyr, ggplot2, hrbrthemes, knitr,
RColorBrewer, cowplot, readbitmap, rjson, rmarkdown, BiocStyle,
testthat (>= 3.0.0), viridis, CoGAPS
testthat (>= 3.0.0), knitr, rmarkdown, prettydoc, pkgdown,
covr, BiocStyle, Seurat, patchwork, ggforce, ggnewscale
AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle,
DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin,
magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr,
PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown,
SummarizedExperiment, statmod, stringr, testthat, webshot
HDF5Array, ExperimentHub, testthat, knitr, rmarkdown,
BiocStyle
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>=
5.0.0)
BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5,
BiocStyle, testthat, knitr,
RefManageR, BiocStyle, knitr, testthat (>= 3.0.0),
sessioninfo, rmarkdown, markdown
testthat, knitr, rmarkdown, qpdf, Seurat
knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix,
DropletUtils
AnnotationDbi, av, BiocParallel, BiocFileCache, BiocGenerics,
BiocStyle, BiocSingular, Biobase, cachem, DESeq2, dendextend,
DT, dynamicTreeCut, flashClust, gplots, ggdendro, HDF5Array,
htmltools, htmlwidgets, kableExtra, knitr, limma, magick,
memoise, ExpressionAtlas, GEOquery, org.Hs.eg.db, org.Mm.eg.db,
org.At.tair.db, org.Dr.eg.db, org.Dm.eg.db, pROC, plotly,
rmarkdown, rols, rappdirs, RUnit, Rtsne, rhdf5, scater,
scuttle, scran, shinyWidgets, shinyjs, shinyBS, sortable,
Seurat, sparkline, spsUtil, uwot, UpSetR, visNetwork, WGCNA,
xlsx, yaml
knitr, 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), msdata (>= 0.19.3), roxygen2,
BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0),
rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick
BiocCheck, BiocManager, BiocStyle, knitr, rmarkdown,
microbenchmark, testthat, covr
testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr,
S4Vectors, BiocStyle, mzR
BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown,
testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap,
elsa
SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown,
imcRtools, testthat (>= 3.0.0)
covr, testthat, rmarkdown, markdown, knitr, devtools,
BSgenome.Mmusculus.UCSC.mm10.masked,
BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle,
hexbin
BASiCS (>= 1.7.10), BiocManager, BiocSingular, BiocStyle,
Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2
(>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick,
mfa, phenopath, preprocessCore, progress, pscl, rmarkdown,
scales, scater (>= 1.15.16), scDD, scran, SparseDC, spelling,
testthat, VariantAnnotation, zinbwave
testthat, knitr, rmarkdown, ggplot2, tidyr
igraph, Gviz, txdbmaker, TxDb.Hsapiens.UCSC.hg19.knownGene,
RNAseqData.HNRNPC.bam.chr14, RUnit
knitr, DelayedMatrixStats, rmarkdown, BiocStyle, ggplot2,
ggpubr, MASS, scales, scRNAseq, testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, assertthat, HD2013SGI, dplyr,
ggplot2
testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra,
digest, doParallel, bigmemory, GSVA
testthat (>= 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, BiocStyle, rmarkdown, tinytest, doFuture
BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools,
knitr, pander, patchwork, rmarkdown, spelling, testthat (>=
3.0.0), tidyverse
scran, scater, knitr, UpSetR, gridExtra,
SingleCellMultiModal, BiocStyle, magrittr, testthat (>= 3.0.0),
purrr, sparseMatrixStats
knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma,
DEXSeq, testthat
knitr, ExperimentHub, rmarkdown, scater, uwot, ggpubr,
ggrepel, cluster, testthat (>= 3.0.0)
RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>=
1.3), roxygen2, doSNOW
BiocStyle, knitr, testthat (>= 3.0.0), ClassifyR, spicyR,
ggsurvfit, lisaClust, survival
RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz
testthat, rstudioapi, rmarkdown, covr, BiocStyle, openxlsx,
ggplot2, magick
testthat, knitr, rmarkdown, tRNAscanImport, BiocStyle
agricolae, BiocFileCache, BiocStyle, car, covr, cowplot,
e1071, emmeans, ggdendro, knitr, magick, nlme, openxlsx, pls,
pmp, reshape2, ropls, rmarkdown, Rtsne, testthat, rappdirs
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
devtools, MutationalPatterns, RUnit, BiocManager,
BiocGenerics, BiocStyle, knitr, rmarkdown
jsonlite, rhdf5, HDF5Array (>= 1.7.5), annotate,
AnnotationDbi, GenomicFeatures, SparseArray,
SingleCellExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene,
hgu95av2.db, airway (>= 1.15.1), BiocStyle, knitr, rmarkdown,
RUnit, testthat, digest
rmarkdown, markdown, knitr, testthat (>= 3.0.0)
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
knitr, rmarkdown, ggplot2, testthat, VariantAnnotation
knitr, testthat (>= 3.0.0), gplots, htmltools, BiocParallel
Hmisc, clinfun, xtable, Biobase, BiocManager
pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat
BiocStyle, knitr, rmarkdown, testthat (>= 3.1.6)
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse,
BiocStyle
synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN,
BiocStyle, knitr
BiocStyle, knitr, igraph, markdown, rmarkdown
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
BiocStyle, knitr, rmarkdown, systemPipeRdata,
GenomicAlignments, grid, dplyr, testthat, rjson, annotate,
AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT,
rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools,
GenomicFeatures, txdbmaker, VariantAnnotation (>= 1.25.11)
testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>=
2.2.0), systemPipeRdata (>= 2.0.0), rhandsontable, zip, callr,
pushbar, fs, readr, R.utils, DESeq2, SummarizedExperiment,
glmpca, pheatmap, grid, ape, Rtsne, UpSetR, tidyr, esquisse (>=
1.1.0), cicerone
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
AnnotationHub, BiocStyle, curatedTCGAData, ComplexHeatmap,
devtools, dplyr, httr,
IlluminaHumanMethylation450kanno.ilmn12.hg19, impute, knitr,
magrittr, mirbase.db, org.Hs.eg.db, RColorBrewer, readr,
rmarkdown, RTCGAToolbox (>= 2.17.4), rtracklayer, R.utils,
testthat, TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene
org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle
AnVILBase, knitr, rmarkdown, BiocStyle, withr, testthat (>=
3.0.0)
knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2,
DESeq2, BiocGenerics, ggrepel, rcompanion,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
knitr, data.table, testthat, AnnotationFilter, Biobase,
GenomicFeatures, GenomicRanges, Gviz, IRanges, S4Vectors,
EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db,
GenomeInfoDb, UpSetR, ggplot2, png, gwascat, MotifDb,
motifStack, RColorBrewer, rmarkdown
BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown,
sessioninfo, testthat (>= 3.0.0)
tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr (>=
1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6)
rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>=
3.0.0)
BiocStyle, testthat, knitr, markdown, rmarkdown,
SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph,
GGally, uwot, celldex, dittoSeq, plotly
BiocStyle, testthat, knitr, markdown, scater, igraph,
cowplot, DropletUtils, tidySummarizedExperiment
BiocStyle, testthat, knitr, markdown, rmarkdown, plotly
ConsensusClusterPlus, Biobase, broom, covr, diffcyt, emdist,
FlowSOM, forcats, ggrepel, HDCytoData, knitr, markdown,
philentropy, rmarkdown, Rtsne, statmod, SummarizedExperiment,
testthat (>= 3.0.0), lmerTest, lme4, ggridges, spelling,
scattermore, preprocessCore, SingleCellExperiment, Seurat,
SeuratObject, embed, rsample, BiocGenerics
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
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData,
ggbeeswarm, ggsci, survminer, tidyverse
limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat,
reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr,
rmarkdown, BiocStyle
topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat,
BiocStyle, xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest,
Rgraphviz, globaltest
rmarkdown, testthat, BiocStyle, knitr, tinytex, devtools,
PharmacoGx, xtable, markdown
BiocStyle, knitr, nnSVG, rmarkdown, scran, scuttle,
STexampleData, escheR, ggpubr, colorspace, BumpyMatrix,
sessioninfo, testthat (>= 3.0.0)
knitr, rmarkdown, testthat, covr, clusterExperiment,
DelayedMatrixStats
BiocNeighbors, DelayedArray, DelayedMatrixStats,
BiocParallel, testthat, knitr, BiocStyle, rmarkdown
testthat, TENxPBMCData, scran, knitr, rmarkdown, BiocStyle
testthat, roxygen2, knitr, BiocStyle, rmarkdown
scater, dplyr, testthat (>= 3.0.0), covr, S4Vectors,
rmarkdown, knitr
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer
knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle
Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0)
ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap,
sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0),
tibble, tidyr, SingleCellExperiment
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, CircStats,
cowplot, htmltools, Seurat, org.Hs.eg.db, org.Mm.eg.db
BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0)
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer
BiocGenerics, shinycssloaders, tidyverse, BiocManager,
Biostrings, xtable, rlist, motifStack, knitr, rmarkdown,
testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr
knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport
BiocGenerics, knitr, rmarkdown, testthat, httptest,
BiocStyle, rtracklayer
BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways,
magick
knitr, testthat, scuttle, scran, metapod, BiocParallel,
BiocNeighbors, batchelor
fgsea, knitr, testthat, reticulate, rmarkdown
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db,
DESeq2, fishpond, edgeR, limma, devtools
knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), arrow,
limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats,
Matrix, eds
scater, scRNAseq, reshape2, patchwork, ggplot2, BiocStyle,
Seurat(>= 5.0.0), SeuratObject(>= 5.0.0), knitr, rmarkdown
DBI, RMariaDB, GenomeInfoDb, testthat, knitr, rmarkdown,
BiocStyle
BSgenome.Hsapiens.UCSC.hg38, BiocStyle, httpuv, knitr,
org.Hs.eg.db, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene
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
BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
tximport, tximportData, ballgown, DESeq2, RUnit, cowplot,
Rfast, zenith, statmod, BiocGenerics, r2glmm, readr
breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
BiocStyle, testthat, knitr, rmarkdown, pkgdown, scran,
scater, scRNAseq, Rtsne, graphics, grDevices, ggplot2, cowplot,
GGally, patchwork, metR
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager
arrow, BiocStyle, data.table, knitr, readr, rmarkdown,
tinytest
testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore,
knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr
GenomicFeatures, TxDb.Scerevisiae.UCSC.sacCer3.sgdGene,
testthat, covr, knitr, rmarkdown, pkgdown
knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle,
clusterProfiler, httr
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
BiocStyle, knitr, rmarkdown,
IlluminaHumanMethylationEPICmanifest, irlba,
FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore
knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR,
EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi,
ComplexHeatmap, patchwork, testthat (>= 2.1.0)
MSnbase, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR
testthat, knitr, rmarkdown, ggplot2, randomForest, tidyr,
EnhancedVolcano
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown,
MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal,
mgcv
BiocStyle, knitr, rmarkdown, markdown, testthat,
BSgenome.Hsapiens.UCSC.hg38, pander
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
anndata, BiocFileCache, BiocStyle, covr, HDF5Array, knitr,
pkgload, rhdf5 (>= 2.45.1), rmarkdown, scRNAseq, spelling,
testthat, withr
BiocStyle, BiocGenerics, knitr, pander, rmarkdown,
tweeDEseqCountData, edgeR, kableExtra, RUnit
knitr, limma, edgeR, GEOquery, stringr, printr, rmarkdown
knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq,
ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats
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
parallel, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Hs.eg.db, org.Dm.eg.db
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