a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
R (>= 2.10), cluster, survival, multtest
R (>= 2.10), Biobase (>= 2.5.5), methods, BiocGenerics
R (>= 3.6), adductData, ExperimentHub, AnnotationHub
R (>= 2.7.0), tools, methods, utils, Biobase, affy, affydata
R (>= 2.10),methods,Biobase,limma,affy (>=
1.22),preprocessCore,affycoretools
R (>= 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 (>= 2.99.3)
R (>= 2.6.0), tools, methods, utils, parody, Biobase, affy
R (>= 3.3), methods, stats, ggplot2, graphics, BiocParallel,
ellipse
R (>= 4.1), S4Vectors, Biobase, MSnbase, pRoloc
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 (>= 2.8.1), PolynomF, Biostrings, lattice
R (>= 2.6.0), BufferedMatrix (>= 1.3.0), methods
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 (>= 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 (>= 4.2), ggplot2, SingleCellExperiment
BiocParallel, ProtGenerics (>= 1.39.2), R (>= 4.5.0)
methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges,
Biostrings
R (>= 4.1.0), generics, methods, S4Vectors,
MultiAssayExperiment, BiocParallel, survival
R (>= 2.13.1),limma, statmod, rgl, lattice, scatterplot3d,
graphics, grDevices, stats, utils, Biobase, tools, methods
R (>= 3.6.0), SingleCellExperiment, SummarizedExperiment (>=
1.15.4), BiocGenerics
R (>= 3.6), stats, utils, graphics, infotheo, lattice,
latticeExtra, httr, jsonlite
R (>= 3.0.0), methods, BiocParallel, baySeq, graphics, stats,
utils
R (>= 3.0), Biobase, methods, ff, oligoClasses, snow
R (>= 2.10), methods, tools, stats, genefilter
R (>= 2.10), BiocGenerics (>= 0.3.2), methods, Biobase (>=
2.17.8), limma
R (>= 4.0.0), 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 (>= 4.0), EBImage, SingleCellExperiment, methods
R (>= 4.0.0), methods, stats4, Matrix, BiocGenerics (>=
0.53.3), MatrixGenerics (>= 1.1.3), S4Vectors (>= 0.47.6),
IRanges (>= 2.17.3), S4Arrays (>= 1.9.3), SparseArray (>=
1.7.5)
MatrixGenerics (>= 1.15.1), DelayedArray (>= 0.31.7)
SparseArray (>= 1.5.15), DelayedArray (>= 0.31.6)
R (>= 2.15.1), methods, ggplot2, changepoint, wavethresh,
tseries, pvclust, fBasics, grid, reshape, scales
R (>= 4.3.0), variancePartition (>= 1.36.1),
SingleCellExperiment, ggplot2
R (>= 2.10), affy, limma, biomaRt, ArrayExpress, GEOquery,
DrugVsDiseasedata, cMap2data, qvalue
blockmodeling, gplots, testthat, R (>= 3.0.0)
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)
methods, BiocGenerics (>= 0.15.10), AnnotationHub (>= 3.99.3),
BiocFileCache (>= 2.99.3)
utils, BiocGenerics (>= 0.15.10), S4Vectors, AnnotationHubData
(>= 1.21.3)
R (>= 4.0.0), SummarizedExperiment, SingleCellExperiment,
SpatialExperiment, TreeSummarizedExperiment
R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma,
S4Vectors, xml2, RCurl, jsonlite, BiocStyle
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 (>= 4.1), survcomp, biomaRt, iC10, AIMS
R (>= 2.10), methods, Biobase (>= 2.5.5), genefilter
R (>= 2.10), methods, Biobase, BiocGenerics, lattice, annotate
R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods
R (>= 3.6), 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 (>= 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 (>= 4.5.0), Biobase, SummarizedExperiment
R (>= 2.13.1), Homo.sapiens, org.Hs.eg.db, GenomicFeatures,
AnnotationDbi
R (>= 4.5), methods, rhdf5, BiocGenerics, SparseArray
R(>= 4.3), QFeatures, S4Vectors, Spectra
R (>= 2.8.0), stats, graphics, grDevices, Biobase, methods
R (>= 2.11.0), cluster, Biobase, methods
R (>= 2.9.0), Biobase, fdrtool, MASS, survival
R (>= 2.10), methods, Biobase, annotate, plotrix
R (>= 4.0.0), methods, utils, stats, BiocGenerics (>= 0.53.2),
S4Vectors (>= 0.47.6)
R(>= 4.2.0), Matrix, parallel, BiocParallel,
SummarizedExperiment, BiocGenerics, lme4, nnls
R (>= 2.0.0), GLAD, ITALICSData, oligo, affxparser,
pd.mapping50k.xba240
R (>= 3.3.0), methods, stats, utils, graphics
R (>= 2.13.2), methods, graphics, fdrtool
R (>= 4.1), ExperimentHub, AnnotationHub
R (>= 4.1), HDF5Array, RnBeads, snpStats, crlmm
cluster, gplots, diptest, Biobase, R (>= 3.0.2)
SingleCellExperiment (>= 1.2.0), R(>= 3.5)
R (>= 4.4), BiocParallel, Matrix, methods
R (>= 3.3.0), stats, gplots, gtools,graphics,base,
utils,grDevices
R (>= 2.15), grDevices, graphics, methods, stats, utils
R (>= 4.0), Rsolnp, snowfall, deSolve, CNORode
R (>= 4.1.0), BiocParallel, fields, markdown, fdrtool, fgsea,
ggplot2, ggrepel
R (>= 3.1.2), stringr, seqinr, gplots, Biostrings, pwalign
R (>= 4.1.0), methylclockData, devtools, quadprog
R (>= 4.3.0), SummarizedExperiment, stats
R (>= 4.1), MultiAssayExperiment (>= 1.8.3)
R (>= 3.5), methods, ggplot2, grDevices, MultiAssayExperiment
R (>= 3.5), Rcpp, methods, BiocGenerics (>= 0.13.11), Biobase,
annotate, cluster
R (>= 4.0), SummarizedExperiment, topGO, stats
data.table, parallel, utils, stats, R (>= 4.1)
R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment,
limma
R (>= 2.10), methods, BiocGenerics, Biobase
R (>= 3.2.1), GenomicFeatures, txdbmaker
R (>= 2.15.1), BiocStyle, Rgraphviz, rmarkdown, methods,
minet, mclust, reshape2
R (>= 3.3), Biobase, illuminaio, quadprog
R(>= 2.14.0), stats, RColorBrewer, Biobase, methods, ReadqPCR,
qpcR
R (>= 4.5.0), ggplot2, SummarizedExperiment
dplyr, optimalFlowData, rlang (>= 0.4.0)
R (>= 4.1.0), SummarizedExperiment, S4Vectors
R (>= 3.0.0), KEGGdzPathwaysGEO, methods,Biobase
R (>= 3.0.0), methods, Biobase, BiocGenerics,
graph, Rgraphviz, RColorBrewer, cMAP, AnnotationDbi, methods,
stats4
R (>= 3.6.0), Biobase, methods, annotate, Heatplus, BMA,
ggplot2, Hmisc
R (>= 2.6.2), Biobase (>= 2.5.5), LPE, MASS, methods
R (>= 4.1), Biobase, SingleCellExperiment, MAST
biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb,
yeastExpData
R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
methods, annotate
R (>= 3.2.0), oligo (>= 1.32.0),graphics,grDevices, methods,
stats, utils, mclust, oligoClasses
BiocGenerics, S4Vectors, IRanges, Biostrings (>= 2.71.5)
R (>= 3.5.0), methods, BiocGenerics, Biostrings
R (>= 4.1), MultiAssayExperiment (>= 1.33.6)
R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
R (>= 3.2.1), stats, methods, Rmpfr, gmp
BiocGenerics, DelayedArray, R (>= 4.1.0)
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 (>= 4.4.0), SummarizedExperiment, MultiAssayExperiment,
shinyBS, dplyr, ggplot2, htmltools, knitr, coseq
R (>= 2.6.0), methods, utils, graph, grid
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
foreach, doParallel, parallel, Biostrings, methods, utils
R (>= 4.3.0), methods, Matrix, abind, BiocGenerics (>=
0.45.2), S4Vectors (>= 0.47.6), 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 (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
R (>= 4.1), Seurat, SingleCellExperiment, SummarizedExperiment
R (>= 4.0), S4Vectors, SingleCellExperiment,
SingleCellExperiment (>= 1.7.4), ggplot2 (>= 3.2.1)
R (>= 3.4), methods, SummarizedExperiment
R (>= 4.0), SummarizedExperiment, ComplexHeatmap
R (>= 3.1), AnnotationDbi, GO.db, annotate
R (>= 4.0.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
R(>= 4.2.0), Rcpp, SummarizedExperiment, org.Hs.eg.db
R (>= 3.1.1), methylumi, wateRmelon, mixsmsn,
IlluminaHumanMethylation450kmanifest
R (>= 4.0), princurve (>= 2.0.4), stats, TrajectoryUtils
R (>= 4.1.0), methods, SingleCellExperiment
R (>= 2.10.0), mclust (>= 3.3.1), Biobase (>= 1.15.13),
fields, hwriter (>= 1.1), RColorBrewer, methods
R (>= 4.3.0), SummarizedExperiment, CATALYST
R (>= 3.3), 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
SummarizedExperiment, pheatmap, survival, survminer,
clustvarsel, stats, utils
R (>= 3.2), mgcv, genefilter, BiocParallel
R (>= 4.4.0), SingleCellExperiment, ttservice (>= 0.4.0)
R (>= 4.3.0), SpatialExperiment, tidySingleCellExperiment,
ttservice
R (>= 4.3.0), SummarizedExperiment, ttservice (>= 0.5.0)
SparseArray (>= 1.5.20), DelayedArray (>= 0.31.7)
R (>= 2.12.0), data.table, impute, aroma.affymetrix
R (>= 3.6), EpiDISH, limma, nnls, quadprog
R (>= 3.4), Biobase, dplyr, magrittr, tidyr
R (>= 3.6.0), stats, utils, dplyr, methods
R(>= 3.6.0), SingleCellExperiment, S4Vectors (>= 0.23.18),
Biostrings
R (>= 4.4.0), SingleCellExperiment, TrajectoryUtils
R (>= 2.15.2), methods, BiocGenerics, Biobase
R (>= 4.2.0), methods, BiocGenerics (>= 0.51.1), S4Vectors
R (>= 4.3.0), ggplot2, limma (>= 3.62.2), BiocParallel
R (>= 4.2.0), SpatialFeatureExperiment (>= 1.7.3)
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, grDevices, graphics, methods, stats, splines, utils
bit, DNAcopy, tilingArray, waveslim, cluster, aCGH
checkmate, BiocParallel, data.table, DrImpute, kernlab, MASS,
Matrix, methods, rsvd, S4Vectors, SAVER, SingleCellExperiment,
stats, SummarizedExperiment, utils
AnnotationDbi, Biobase (>= 1.5.12), cluster (>= 1.9.1), GO.db
(>= 1.8.1), graphics, grDevices, KEGGREST (>= 1.30.1), multtest
(>= 1.6.0), stats (>= 2.1.0)
affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods,
preprocessCore, stats, utils
affy, limma, GOstats, gcrma, splines, xtable, AnnotationDbi,
ggplot2, gplots, oligoClasses, ReportingTools, hwriter,
lattice, S4Vectors, edgeR, RSQLite, BiocGenerics, DBI, Glimma
affxparser (>= 1.16.0), affy, graphics, Biobase
grDevices, graphics, stats, utils, tcltk, tkrplot, limma,
affy, affyio, affyPLM, gcrma, BiocGenerics, AnnotationDbi,
BiocManager, R2HTML, xtable
stats, methods, S4Vectors, SummarizedExperiment,
SingleCellExperiment, Matrix, tibble, rlang
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, utils, grDevices, S4Vectors, alabaster.sce, rhdf5
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 (>= 1.3.1), rlang, curl,
BiocFileCache, spdl, memoise, BiocBaseUtils, utils, stats,
tools, methods, whisker, ggplot2
callr (>= 3.0.0.9001), Matrix, Rcpp, BiocFileCache, DT,
MultiAssayExperiment, circlize, curatedTCGAData, foreach,
glmnet, httr, limma, matrixStats, readr, reshape2, tibble,
rmarkdown, graphics, grid, parallel, stats, knitr, ggplot2,
gridExtra, utils
S7, stats, methods, igraph, Matrix, forcats, S4Vectors,
SummarizedExperiment, MultiAssayExperiment,
SingleCellExperiment, TreeSummarizedExperiment, rlang, ggplot2,
ggforce, patchwork, ggraph, tidygraph
stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack,
doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest,
multcomp, nloptr, parallel, utils
igraph, Biobase, survival, MASS, stats, RColorBrewer
bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix,
pbapply, S4Vectors, SingleCellExperiment, stats,
SummarizedExperiment, tidyr, withr
cli, lifecycle, Matrix, methods, purrr, R6 (>= 2.4.0),
reticulate (>= 1.41.1), rlang, stats
Biobase, DBI, xtable, graphics, utils, stats, methods,
BiocGenerics (>= 0.13.8), httr
DBI, RSQLite, S4Vectors (>= 0.9.25), stats, KEGGREST
utils, methods, grDevices, RSQLite, BiocManager, BiocVersion,
curl, rappdirs, AnnotationDbi (>= 1.31.19), S4Vectors, httr2,
yaml, dplyr, BiocBaseUtils
AnVILBase, BiocBaseUtils, curl, httr2, jsonlite, methods,
rjsoncons, tibble, utils
httr, httr2, dplyr, jsonlite, methods, tibble
methods, DT, shiny, bigrquery, shinytoastr, DBI, magrittr,
dplyr, lubridate, plotly, ggplot2
AnVILBase, BiocBaseUtils, dplyr, GCPtools (>= 0.99.4), httr,
jsonlite, methods, rlang, stats, tibble, tidyr, utils
AnVIL, AnVILGCP, BiocBaseUtils, BiocManager, httr, jsonlite,
rmarkdown, yaml, readr, whisker, tools, utils, stats
Matrix, RSpectra, ggrepel, ggplot2, viridisLite, plotly,
SeuratObject, SingleCellExperiment, magrittr,
SummarizedExperiment, topGO, methods, stats, utils,
org.Hs.eg.db, org.Mm.eg.db, rlang
oligo, limma, httr, utils, jsonlite, rlang, tools, methods
graphics, grDevices, grid, gridBase, hexbin, limma, marray,
methods, RColorBrewer, stats, utils
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
gplots, graphics, grDevices, msm, Rlab, stats, sva, utils,
ggplot2, yaml
SingleCellExperiment, SummarizedExperiment, S4Vectors, Rcpp
(>= 1.0.7), cluster, utils, plot3D, ComplexHeatmap, circlize,
grid, grDevices, graphics
SummarizedExperiment, spsUtil, lubridate, survival, glmnet,
siggenes, survcomp, scales, ROCR, ggplot2, grDevices, graphics,
utils, Rdpack
BSgenome, BiocFileCache, BiocParallel, Rcpp, data.table,
ggplot2, grDevices, graphics, grid, motifStack, rappdirs,
stats, testthat, utils, lifecycle
Biobase, limma, cluster, GOstats, graphics, stats,
reactome.db, KEGGREST, org.Hs.eg.db, utils, methods
DelayedArray, DelayedMatrixStats, data.table, graphics,
grDevices, GSEABase, Matrix, methods, mixtools, R.utils, stats,
SummarizedExperiment, BiocGenerics, utils
abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster,
codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce,
ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma,
lme4, magrittr, matrixStats, methods, MultiAssayExperiment,
parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors,
scales, stats, stringi, SummarizedExperiment, survival, tidyr,
tidyselect, tools, utils, vsn
dplyr, Peptides, progress, purrr, ranger, rlang, stats,
stringr, tidyr, toOrdinal, utils
Rcpp, doRNG, MASS, data.table, R.utils, doParallel, parallel,
foreach, methods, stats, graphics, ggplot2, DRIMSeq,
BiocParallel
Rcpp (>= 1.0.4.6), pRolocdata, lbfgs, ggplot2, dplyr, plyr,
knitr, methods, BiocParallel, robustbase, BiocStyle,
ggalluvial, ggrepel, tidyr, circlize, graphics, stats, utils,
grDevices, rlang, RColorBrewer, gtools, gridExtra, coda (>=
0.19-4)
aricode, BiocParallel, data.table, dbscan, SpatialExperiment,
SingleCellExperiment, SummarizedExperiment, S4Vectors, stats,
Matrix, MatrixGenerics, mclust, igraph, irlba, leidenAlg (>=
1.1.0), utils, uwot, RcppHungarian, GenomeInfoDb
magrittr, tidyr, dplyr, grid, circlize, ComplexHeatmap,
ggplot2, logistf, limma, stats, igraph, utils, data.table,
S4Vectors, SummarizedExperiment
scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2,
RColorBrewer, scales, SummarizedExperiment
Rcpp (>= 0.12.12), BB, foreach, iterators, doSNOW, Matrix,
parallel, MASS, locfit, fitdistrplus, stats, methods, graphics,
grDevices, SingleCellExperiment, SummarizedExperiment,
BiocParallel, utils
methods, DelayedArray (>= 0.27.2), SparseArray, BiocGenerics,
Matrix, Rcpp
methods, beachmat, HDF5Array, DelayedArray, Rcpp
methods, beachmat, tiledb, TileDBArray, DelayedArray, Rcpp
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
dplyr (>= 1.0), tidyr, ggplot2 (>= 3.4.1), shiny (>= 1.6),
tibble, ComplexHeatmap, bslib, rlang, circlize, stats, grid,
methods, cowplot, Hmisc, sortable, shinyjqui, grDevices,
scales, DT, SummarizedExperiment, S4Vectors, jsonlite, utils
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, pak, cli, glue, gert, gh, gitcreds, httr,
usethis, dplyr, purrr, tibble, methods, rprojroot, stringr,
yaml, tools, utils, rlang, quarto, renv
BiocBaseUtils, BiocFileCache, BiocManager, biocViews, callr,
cli, codetools, graph, httr2, knitr, methods, rvest,
stringdist, tools, utils
DT, shiny, jsonlite, graph, tidyr, visNetwork, dplyr, utils,
methods, BiocBaseUtils
methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl,
httr2
Rgraphviz, geneplotter, graph, BiocGenerics, methods
AnnotationHub, ExperimentHub, DT, htmlwidgets, rclipboard,
S4Vectors, shinyAce, shinybiocloader, shinyjs, shinythemes,
utils
stats, utils, futile.logger, parallel, snow, codetools
BiocFileCache, BiocManager, biocViews, tibble, methods, rlang,
stringr, stats, rvest, dplyr, xml2, readr, httr, httr2,
htmltools, DT, tools, utils, igraph (>= 2.0.0), jsonlite, gh,
RBGL, graph, curl, glue, lubridate, purrr, tidyr, yaml
methods, tibble, utils, rlang, plyr, S4Vectors, BiocIO,
AnnotationDbi, KEGGREST, ontologyIndex, tidyr
BiocGenerics, S4Vectors, Matrix, methods, utils, DelayedArray,
BiocParallel, ScaledMatrix, irlba, rsvd, Rcpp, beachmat (>=
2.25.1)
bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils,
yaml, BiocManager
BiocManager, fs, glue, rlang, styler, usethis (>= 2.0.1)
Biobase, graph (>= 1.9.26), methods, RBGL (>= 1.13.5), tools,
utils, XML, RCurl, RUnit, BiocManager
BiocStyle, bookdown, git2r, httr, knitr, rmarkdown,
rstudioapi, stringr, tools, utils, usethis
R6, RSQLite, Rcpp, XML, chk, fscache (>= 1.0.2), jsonlite,
lgr, lifecycle, methods, openssl, plyr, progress, rappdirs,
sched (>= 1.0.1), sqlq, stats, stringr, tools, withr, yaml
ggplot2, graphics, Rcpp, SummarizedExperiment, animation,
rlang, biocViews, sessioninfo, BiocStyle
AnnotationDbi, BiocFileCache, curl, httr2, progress, stringr,
utils, xml2
stringr, viridis, fgsea, grid, methods, AnnotationDbi, dplyr,
GO.db, org.Hs.eg.db (>= 3.19.1), rSpectral, WGCNA, ggplot2,
ggrepel, minpack.lm, cowplot, data.table, scales, stats, Matrix
WGCNA, dynamicTreeCut, ggdendro, matrixStats, sva,
RColorBrewer, ComplexHeatmap, ggplot2, rlang, ggrepel,
patchwork, reshape2, igraph, ggnetwork, intergraph, NetRep,
stats, grDevices, utils, methods, BiocParallel, minet, GENIE3,
SummarizedExperiment
igraph (>= 1.0.1), AnnotationDbi, Biobase
Biobase, methods, e1071, grDevices, graphics,
MultiAssayExperiment, MultiDataSet, randomForest, ropls, stats,
SummarizedExperiment, utils
methods, utils, grDevices, stats, crayon
stats, methods, dplyr, tibble, ggplot2, ggsci, superheat,
assertthat, drtmle (>= 1.0.4), S4Vectors, BiocGenerics,
BiocParallel, SummarizedExperiment, limma
grid, stats, grDevices, utils, circlize, viridis,
RColorBrewer, ComplexHeatmap, SummarizedExperiment, pasilla
SummarizedExperiment, SingleCellExperiment, ggplot2, viridis,
patchwork, Matrix, scater, methods, rlang, BiocParallel, boot,
dplyr, mgcv, stats, MatrixGenerics, Seurat (>= 4.0.0)
SummarizedExperiment, ExperimentHub, methods, grid, graphics,
stats, grDevices, circlize, testthat, ComplexHeatmap(>=
1.99.8), ggplot2, matrixStats, gtools, reshape2,
preprocessCore, randomcoloR, V8, limma
stats, methods, utils, cluster, Matrix, Rcpp, igraph,
S4Vectors, BiocParallel, BiocNeighbors
CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
methods, Biobase, tidyselect, dplyr, ggplot2, magrittr, rlang,
stringr, withr, edgeR, ComplexHeatmap, impute (>= 1.80.0),
data.table (>= 1.16.0), RColorBrewer (>= 1.1-3), circlize (>=
0.4.16), ggrepel (>= 0.9.6), e1071 (>= 1.7-8),
SummarizedExperiment, utils
dplyr, Rcpp, tibble, stringr, magrittr, purrr, BiocParallel,
crayon, utils, tidyr, grDevices, rlang, BiocFileCache, rappdirs
BiocFileCache, httr2, RCurl, cli, curl, rlang, jsonlite,
matrixStats, methods, doParallel, glmnet, ggalluvial, ggplot2,
gridExtra, grid, Rtsne, ggrepel, foreach, multtest, igraph,
orthogene, stabledist, circlize (>= 0.4.14), ComplexHeatmap (>=
2.0.0), stats, scales, RANN, SpatialExperiment,
SummarizedExperiment, tools
devtools, stringi, gtools, stats, utils, SummarizedExperiment,
Biostrings, IRanges
utils, methods, Matrix, S4Vectors, IRanges
gplots, methods, grDevices, stats, SummarizedExperiment
SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots,
grDevices, methods, stats, utils
doParallel, ggplot2, gplots, graphics, grid, gtable, knnmi,
MASS, methods, misc3d, plyr, ppcor, R.cache, reshape2, stats,
SummarizedExperiment
checkmate, dplyr, ggplot2, magrittr, openxlsx, scales,
SummarizedExperiment, tidyr
ggplot2, dplyr, org.Hs.eg.db, vcfR, clusterProfiler, stringr,
DT, MesKit, maftools, data.table, utils, stats, methods, tidyr
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
Rcpp (>= 1.0.7),RcppArmadillo, SummarizedExperiment, methods,
MCMCpack, fields, wrMisc, concaveman, sp, dplyr, sf, Matrix,
RANN, ggplot2, reshape2, RColorBrewer, S4Vectors, scatterpie,
grDevices,ggcorrplot, stats, nnls, BiocParallel, RcppML, NMF,
spatstat.random, gtools, SingleCellExperiment,
SpatialExperiment
readr, stringr, lpSolve, igraph, dplyr, tibble, tidyr, rjson,
rmarkdown
circlize, ComplexHeatmap, ConsensusClusterPlus, cowplot,
data.table, dplyr, drc, flowCore, FlowSOM, ggplot2, ggrepel,
ggridges, graphics, grDevices, grid, gridExtra, Matrix,
matrixStats, methods, nnls, purrr, RColorBrewer, reshape2,
Rtsne, SummarizedExperiment, S4Vectors, scales, scater, stats
utils, stats, graph, RBGL, GSEABase, genefilter, annotate, DBI
AnnotationDbi, hwriter, GSEABase, Category (>= 2.33.1),
GOstats, annotate, colorspace, graph, RCy3 (>= 1.99.29),
methods, grDevices, utils
Seurat (>= 5.0.1), ggplot2, networkD3, stringr, pracma,
reshape2, rdist, igraph, geometry, Rfast, data.table, abind,
pheatmap, EBImage, S4Vectors, SeuratObject,
SingleCellExperiment, SpatialExperiment, Matrix, methods,
SummarizedExperiment, msigdbr
BiocFileCache, RColorBrewer, cBioPortalData, genefilter,
gplots, grDevices, stats, utils, openxlsx, zip
R6, ggraph, tidygraph, ggplot2, patchwork, cowplot, magrittr,
igraph, rlang, grDevices, coda, graphics, stats, TCGAbiolinks,
BiocParallel
ggplot2, magrittr, graphite, ggraph, igraph, bnlearn (>= 4.7),
patchwork, org.Hs.eg.db, clusterProfiler, utils, enrichplot,
reshape2, ggforce, dplyr, tidyr, stringr, depmap,
ExperimentHub, Rmpfr, graphlayouts, BiocFileCache, ggdist,
purrr, pvclust, stats, rlang
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
assertthat, BiocGenerics, BiocFileCache, BiocParallel, dplyr,
rlang, glue, memoise, purrr (>= 0.3.0), rappdirs, tidyr,
tidyselect, lubridate
Rcpp, RcppArmadillo, stats, utils, Matrix, tictoc, scater,
stringr, irlba, data.table, glue, pbapply, umap, Rtsne,
reticulate, fastmatch, matrixStats, ggplot2, BiocParallel,
SummarizedExperiment, fgsea
AnnotationDbi, e1071, ggplot2, graphics, grDevices, grid,
mvoutlier, org.Hs.eg.db, org.Mm.eg.db, robustbase, stats,
topGO, utils
base, ggplot2, ggforce, ggtree, patchwork, ape, methods, Rcpp
(>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
2.18.1), rstantools (>= 2.4.0), stats, utils, scales
tiff, graphics, stats, utils, reshape2, parallel, doParallel,
grDevices, matrixStats, FME, SpatialTools, sp, vioplot,
FactoMineR, Hmisc
BiocNeighbors, ggplot2, scater, viridis, cowplot,
SummarizedExperiment, SingleCellExperiment, tidyr, magrittr,
dplyr, ggridges, stats, purrr, methods, BiocParallel,
BiocGenerics
BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats,
ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv,
reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
httr, curl, utils, tools, cli, shiny, DT, rjsoncons
methods, scales, dplyr, data.table (>= 1.9.4), WGCNA, grid,
ggplot2, ggpmisc, ggthemes, ggrepel, sna, clusterProfiler,
fgsea, stringr, knitr, rmarkdown, igraph, DT, htmltools,
pracma, intergraph, grDevices, utils, network, matrixStats,
ggdendro, gridExtra, gtable, fastcluster
BiocParallel, broom.mixed, dirmult, dplyr, edgeR,
fitdistrplus, lme4, magrittr, MASS, methods, mice, multcomp,
purrr, rlang, S4Vectors, stats, stringr, SummarizedExperiment,
survival, tibble, tidyr, utils
DelayedMatrixStats, DelayedArray, HDF5Array, S4Vectors,
methods, SingleCellExperiment, SummarizedExperiment, ggplot2,
rlang, grDevices, patchwork, reshape2, BiocParallel, stats,
dplyr, purrr
furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr,
future, stats
Biobase, CGHbase, CGHcall, methods, stats, utils
rjson, graphics, stats, RCurl, DBI, digest, BiocGenerics, Rcpp
(>= 0.11.0), ggplot2,grid,gridExtra,
png,base64enc,DT,rsvg,jsonlite,stringi
shiny, plotly, pheatmap, bioDist, dendextend, cowplot,
corrplot, grDevices, stats, graphics, reshape2, S4Vectors,
SummarizedExperiment
matrixStats, MASS, Hmisc, Delaporte, methods, grDevices,
graphics, stats, utils
Biobase, GEOquery, frma, affy, bigmemory, biganalytics
graphics, stats, utils, methods, survival
methods, S4Vectors, MsCoreUtils (>= 1.7.5), Spectra
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
grid, genefilter, utils, dplyr, tidyr, rlang, ranger, ggplot2
(>= 3.5.0), ggpubr, reshape2, ggupset, broom, dcanr
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
Rcpp (>= 0.12.15), xcms(>= 3.0.0), MSnbase, igraph, coop,
slam, matrixStats, methods
FactoMineR, bigstatsr, clValid, doSNOW, parallel, foreach,
dplyr, fpc, mice, modeest, flock, networkD3, methods,
ComplexHeatmap, cluster, RColorBrewer, circlize, grDevices,
ggplot2, grid, stats, utils, pbapply
methods, NMF, RColorBrewer, ape (>= 5.0), cluster, stats,
limma, locfdr, matrixStats, graphics, parallel, BiocSingular,
kernlab, stringr, S4Vectors, grDevices, DelayedArray (>=
0.7.48), HDF5Array (>= 1.7.10), Matrix, Rcpp, edgeR, scales,
zinbwave, phylobase, pracma, mbkmeans
methods, igraph, ggplot2, scales, BiocParallel, graphics,
stats, utils, Matrix, cowplot, dplyr, reshape2, Seurat,
SeuratObject, SingleCellExperiment, ggdendro
AnnotationDbi, DOSE (>= 3.23.2), dplyr, enrichplot (>= 1.9.3),
GO.db, GOSemSim (>= 2.27.2), gson (>= 0.0.7), httr, igraph,
magrittr, methods, plyr, qvalue, rlang, stats, tidyr, utils,
yulab.utils (>= 0.1.6)
methods, pracma, princurve (>= 2.0.5), scatterplot3d,
RColorBrewer, grDevices, graphics, utils, stats
cowplot, dplyr, entropy, fgsea, ggplot2, Matrix, rlang,
scales, stringr, tibble, tidyr, stats, methods,
SingleCellExperiment, SummarizedExperiment, SeuratObject,
matrixStats, S4Vectors, proxy, httr, utils
blaster, future, future.apply, grDevices, igraph, methods,
Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>=
2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils,
posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales
BiocParallel, BiocNeighbors, bluster (>= 1.16.0), scater,
harmony, SingleCellExperiment, SummarizedExperiment, methods,
Matrix, reshape2
methods, rhdf5, data.table, flowCore, SummarizedExperiment,
matrixStats
DBI, affxparser, oligo, DNAcopy, preprocessCore, lattice
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
ggplot2, nleqslv, phyloseq, tensor, stats, limma, Matrix (>=
1.6.0), BB, reshape2, alabama, cobs, Biobase, vegan, grDevices,
graphics, methods, SummarizedExperiment
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
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, methods, grDevices, Matrix, ggplot2, ggrepel, gghalves,
ggthemes, graphics, parallel, parallelly, tibble, tidyr, dplyr,
BiocSingular, parallelDist, ComplexHeatmap, circlize, grid,
scales, RColorBrewer, utils, rlang, Rfast, stringr, Seurat,
dendextend, zeallot, assertthat, withr, SingleCellExperiment,
proxy, RSpectra
parallel, genefilter, grDevices, stats, graphics
SummarizedExperiment, grDevices, reshape2 , survival ,
survminer , ggplot2 , MTLR , glmnet , rms , preprocessCore ,
Matrix , stats, Hmisc, ggfortify, randomForestSRC, caret,
SurvMetrics, MASS,
methods, corpcor, BiocParallel, ggplot2, plyr
splines, graphics, nor1mix, stats, quantreg
BiocGenerics, BSgenome, crisprBase (>= 0.99.15), Seqinfo,
Rbwa, readr, stats, stringr, utils
BiocGenerics, Biostrings, IRanges, methods, randomForest,
reticulate, stringr, utils, XVector
BiocManager, cli, crisprBase, crisprBowtie, crisprScore,
crisprScoreData, crisprDesign, crisprViz, rlang, tools, utils
methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, utils,
lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1), matrixStats,
VGAM, parallel, graphics, limma, beanplot
Rdpack, viridis, tidytree, variancePartition (>= 1.36.3),
SingleCellExperiment, ggtree, dplyr, stats, MASS, Rfast
WGCNA, glue, RhpcBLASctl, matrixStats, Rcpp
bayesbio, dplyr, ggplot2, henna, kerntools, methods, qs,
reshape2, rlang, Seurat, SeuratObject, SummarizedExperiment,
sgof, spatstat.utils, stats, textshape, wesanderson
RCurl, stringr, S4Vectors, stringdist, ggplot2, igraph, utils,
grid, gridExtra, methods, stats, BiocFileCache
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
CytoGLMM, diffcyt, DT, dplyr, ggplot2, magrittr, methods,
rlang, stats, shiny, shinyFeedback, shinyjs, shinyMatrix,
SummarizedExperiment, tibble, tidyr
stats, methods, BiocParallel, RColorBrewer, cowplot,
doParallel, dplyr, factoextra, flexmix, ggplot2, magrittr,
mbest, pheatmap, 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
BiocGenerics, bluster, destiny, igraph, MASS, Matrix, methods,
miloR, purrr, rlang, S4Vectors, SingleCellExperiment, spam,
stats, SummarizedExperiment, uwot, RANN
igraph, foreach, plyr, stringr, reshape2, methods, Matrix,
graphics, stats, RColorBrewer, circlize, doRNG
MCMCpack, matrixStats, robustbase, aod, e1071
Biobase (>= 1.10.0), RColorBrewer (>= 0.1-3), xtable, lattice,
BiocGenerics
plotrix, clue, parallel, ggplot2, openxlsx, R.utils, flowCore,
flowDensity (>= 1.13.3), SamSPECTRAL, flowPeaks
CompQuadForm, dplyr, ggplot2, KernSmooth, magrittr,
matrixStats, methods, patchwork, parallel, pbapply, reshape2,
rlang, scattermore, stats, statmod, survey, tibble, viridisLite
methods, DBI, S4Vectors, IRanges, XVector
BiocParallel, broom, dplyr, magrittr, Matrix, parallelly,
purrr, rlang, stats, stringr, tibble, tidyr, tidyselect, withr
fgsea, ggplot2, stringr, ggpubr, BiocParallel, pROC, stats,
grDevices, graphics, depmap, readr, dplyr
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,
stats, MASS, Matrix, ggplot2, gridExtra, methods
Rcpp, basilisk, assertthat, reticulate, Rtsne, irlba
IRanges (>= 1.99.27), Matrix, methods, S4Vectors (>= 0.2.2)
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
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
dplyr, tidyr, numbers, purrr, stringr, stats, utils, methods,
Rcpp (>= 0.11.2), BH
BiocParallel, dplyr, gdata, glasso, igraph (>= 2.0.3),
janitor, Matrix, methods, netgsa, stats, stringr, utils,
SummarizedExperiment
scales, ggnewscale, SummarizedExperiment, dplyr, rlang,
ggforce, geomtextpath, ggplot2
biomaRt, ComplexHeatmap, circlize, ggpubr, grDevices, grid,
igraph, Matrix, methods, plyr, stats, utils, magrittr, purrr,
dplyr
sva, impute, digest, mnormt, methods, grDevices, graphics,
stats, SummarizedExperiment, utils
methods, drc, stats, httr, jsonlite, reshape2 , vsn, affy,
limma, stringr, ggplot2, graphics, grDevices, calibrate,
corrgram, gridExtra, DT, shiny, shinydashboard, readxl,
prodlim, matrixStats
AnnotationDbi, BiocParallel, fgsea, ggplot2, GOSemSim (>=
2.31.2), methods, qvalue, reshape2, stats, utils, yulab.utils
(>= 0.1.6)
edgeR, methods, stats, graphics, matrixStats, mclust, lme4,
RUnit, SummarizedExperiment, digest, S4Vectors
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, RSQLite, UniProt.ws, biomaRt,ensembldb,
BiocFileCache,dplyr,rappdirs, AnnotationFilter, S4Vectors
annotate, hgu133a.db, hgu133a2.db, hgu133plus2.db, RUnit,
BiocGenerics, xtable
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, 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, splines, sva, qvalue(>= 1.99.0), MASS
gplots, Biobase, GEOquery, limma, impute, RColorBrewer, zoo,
igraph, plyr, MASS, RCurl, methods
PADOG (>= 1.6.0), GSVA (>= 1.12.0), globaltest (>= 5.18.0),
limma (>= 3.20.9), edgeR (>= 3.6.8), HTMLUtils (>= 0.1.5),
hwriter (>= 1.2.2), gplots (>= 2.14.2), ggplot2 (>= 1.0.0),
safe (>= 3.4.0), stringi (>= 0.5.0), parallel, stats, metap,
grDevices, graphics, utils, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, RColorBrewer, methods, EGSEAdata (>= 1.3.1),
htmlwidgets, plotly, DT
snow, tools, snowfall, RUnit, methods, ChemmineR, RCurl,
digest, BiocGenerics, RcppAnnoy (>= 0.0.9)
emdist, BiocParallel, matrixStats, ggplot2, CDFt,
preprocessCore
survivalROC, glmnet, rms, mboost, Matrix, igraph, methods,
survivalsvm, ggplot2, boot, e1071, survival, BiocFileCache
BiocGenerics, Rgraphviz, hash, S4Vectors, dplyr, ggplot2,
graph, magrittr, methods, pheatmap, graphics, utils, purrr,
tidyr, stats
AnnotationDbi, BiocFileCache, BiocManager, GSEABase, GO.db,
KEGGREST, KEGGgraph, Rgraphviz, S4Vectors, SPIA, edgeR,
graphite, hwriter, limma, methods, pathview, safe
aplot (>= 0.2.1), DOSE (>= 3.31.2), ggfun (>= 0.1.7),
ggnewscale, ggplot2 (>= 3.5.0), ggrepel (>= 0.9.0), ggtangle
(>= 0.0.5), graphics, grid, igraph, methods, plyr, purrr,
RColorBrewer, reshape2, rlang, stats, tidydr, utils,
scatterpie, GOSemSim (>= 2.31.2), magrittr, ggtree, yulab.utils
(>= 0.1.6)
gprofiler2, strex, RCy3, jsonlite, stringr, enrichplot, DOSE,
igraph, reshape2, methods
MASS, e1071, quadprog, parallel, stats, matrixStats, stringr,
locfdr, Matrix
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
BiocParallel, data.table, matrixStats, stats, survival,
igraph, batchtools, qgraph, grDevices, parallel, ggplot2, grid,
bigmemory, graphics, utils
epivizrData (>= 1.5.1), epivizrServer, htmltools, rjson,
methods, BiocGenerics
git2r, epivizrServer, Seqinfo, BiocGenerics, GenomicFeatures,
S4Vectors
edgeR, gplots, grid, gtools, limma, locfit, MASS, plyr,
qvalue, reshape2, ROCR, scales, stringr, knitr
SpatialExperiment (>= 1.6.1), SingleCellExperiment, rlang,
SummarizedExperiment
mpm, hexbin, Rtsne, MLP, grid, Biobase, MASS, stats, utils,
grDevices, methods
corrplot (>= 0.84), grDevices, graphics, reshape2, ggplot2,
ggdendro, plotrix, stats, matrixStats, Rdpack, MASS, class,
prabclus, mclust, kableExtra, dplyr, dendextend (>= 1.16.0)
stats, utils, methods, ewceData (>= 1.7.1), dplyr, ggplot2,
reshape2, limma, stringr, HGNChelper, Matrix, parallel,
SingleCellExperiment, SummarizedExperiment, DelayedArray,
BiocParallel, orthogene (>= 0.99.8), data.table
methods, ExperimentHub, BiocManager, DBI, httr, curl
shiny (>= 1.5.0), shinydashboard, DT, cowplot, utils, dplyr,
magrittr, tidyr, ggplot2, stats, methods, rintrojs, scales,
tibble, MASS, limma, S4Vectors, shinyjs, rlang
methods, graphics, grDevices, stats, utils
BiocParallel, brio, cli, curl (>= 6.0.0), data.table, httr2
(>= 1.0.0), MCMCpack, methods, openEBGM, rlang, rvest, tools,
utils, vroom, xml2
gap (>= 1.1-17), Matrix, BiocGenerics, utils, survey
ape, data.table, dynamicTreeCut, methods, R.utils, rJava,
stats, stringr, utils
tcltk, graphics, grDevices, stats, utils
SingleCellExperiment, methods, stats, utils, irlba, TSCAN,
SC3, matrixStats
pheatmap, MASS, pracma, stats, SummarizedExperiment, methods
openxlsx, tibble, dplyr, data.table, ggplot2, ggthemes,
forcats, RColorBrewer, RCy3, utils, stats
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
Biobase, BiocParallel, parallel, stats, SummarizedExperiment,
survival, utils
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
Biobase, MASS, DBI, affy, methods, oligo, oligoClasses,
preprocessCore, utils, BiocGenerics
Biobase, DBI, methods, preprocessCore, stats, utils
NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db,
dplyr, stringr
pls, matrixStats, minfi, methods,
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb,
grDevices, graphics, stats
psych, FCPS, analogue, coop, pheatmap, ggplotify, fastcluster,
fpc, ggplot2, stringr, ggpubr, proxy, cluster, diptest,
methods, SummarizedExperiment, stats, S4Vectors
AnnotationDbi, BiocGenerics, dplyr, DT, Seqinfo, GenomeInfoDb,
openxlsx, GenomicFeatures, methods, purrr, S4Vectors, shiny,
shinyjs, tidyr, shinythemes
DaMiRseq, MLSeq, stats, methods, SummarizedExperiment
splancs, mvoutlier, methods, stats, diptest, flowCore, flowFP
data.table, igraph, BioNet, plyr, methods, XML, sna,
intergraph, network, ggnetwork, scales, grid, ggplot2, mwcsr,
pryr, htmlwidgets, htmltools, shinyCyJS (>= 1.0.0)
AnVILBase, BiocBaseUtils, dplyr, httr, rlang, tibble, tidyr,
utils
Biobase, limma, RobustRankAggreg, ggplot2,
SummarizedExperiment, grid, rmarkdown, grDevices, graphics,
methods, ComplexHeatmap, stats, utils, parallel
Biobase, affy (>= 1.23.2), affyio (>= 1.13.3), XVector,
Biostrings (>= 2.11.32), splines, BiocManager
BumpyMatrix, BiocParallel, checkmate, futile.logger, gDRutils
(>= 1.7.1), MultiAssayExperiment, purrr, stringr, S4Vectors,
SummarizedExperiment, data.table
assertthat, BumpyMatrix, checkmate, CoreGx, PharmacoGx,
data.table, futile.logger, gDRutils (>= 1.7.1), magrittr,
methods, MultiAssayExperiment, readxl, rio, S4Vectors, stats,
stringi, SummarizedExperiment, tibble, tools, utils, XML, yaml,
openxlsx
BiocCheck, BiocManager, BiocStyle, checkmate, desc, git2r,
lintr (>= 3.0.0), rcmdcheck, remotes, yaml, rjson, pkgbuild,
withr
BiocParallel, BumpyMatrix, checkmate, data.table, digest, drc,
jsonlite, jsonvalidate, methods, MultiAssayExperiment,
S4Vectors, stats, stringr, SummarizedExperiment, qs, utils
Matrix, shiny, shinyWidgets, bs4Dash, rintrojs, utils, DT,
dplyr, shinyBS, STRINGdb, igraph, visNetwork, shinycssloaders,
fontawesome, grDevices, parallel, stats, ggplot2, plotly, expm,
RColorBrewer, scales, readxl, ggdendro, ComplexHeatmap,
BiocNeighbors, tm, wordcloud2, tools, BiocParallel,
BiocFileCache, cluster, methods, circlize, proxyC, simona
tcltk, ggplot2, methods, stats, grDevices, graphics, utils
dplyr, grDevices, ggplot2, magrittr, mixtools, scales,
pbmcapply, parallel, stats, utils
magrittr, glue, memoise, jsonlite, data.table, rlang,
lubridate, utils, stringr, SummarizedExperiment, Biobase,
tibble, tidyr, S4Vectors, httr, rappdirs, bit64, assertthat,
digest, R.utils, kableExtra, base64enc
graphics, grDevices, methods, stats, tcltk, utils, xtable
utils, 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
ComplexHeatmap, ggplot2, methods, S4Vectors, Biobase, ggpubr,
dplyr, plotly, BiocFileCache, grid, flextable, irlba
Matrix, robust, plyr, lme4, Rcpp (>= 1.0.4.6), withr, methods,
graphics, stats, testthat, GeomxTools, NanoStringNCTools
xml2, rvest, stringr, RCurl, doParallel, foreach, plyr
BiocGenerics, rjson, readxl, EnvStats, reshape2, methods,
utils, stats, data.table, lmerTest, dplyr, stringr, grDevices,
graphics, GGally, rlang, ggplot2, SeuratObject
readr (>= 1.3.1), xml2, dplyr, data.table, tidyr, magrittr,
limma, curl, rentrez, R.utils, stringr, SummarizedExperiment,
S4Vectors, rvest, httr2
utils, data.table, plyr, cqn, topconfects, stats,
SummarizedExperiment, methods
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, data.table, dplyr, magick, patchwork,
shadowtext, stringr, tibble, methods, utils, stats, grDevices,
gtable
Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot,
RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA,
grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1)
Rcpp, RcppParallel, cli, dplyr, ggfun (>= 0.1.5), ggplot2,
grDevices, grid, methods, rlang, scattermore, stats, Seurat,
SingleCellExperiment, SummarizedExperiment, tidydr, tidyr,
tibble, utils, RColorBrewer, yulab.utils, scales
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
ggside, grid, ggrepel, RColorBrewer, scales, grDevices,
methods, stats
ape, aplot, dplyr, ggplot2 (>= 4.0.0), grid, magrittr,
methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>=
0.1.6), tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils,
scales, stats, cli, ggiraph (>= 0.9.1)
ggplot2 (>= 4.0.0), utils, rlang, ggnewscale, stats, ggtree,
tidytree (>= 0.3.9), cli, magrittr
interp, ape, dplyr, GGally, ggplot2, grid, ggtree, phytools,
rlang, tibble, tidyr, tidyselect, stats
KEGGREST, UniProt.ws, XML, rentrez, httr, utils, memoise,
cachem, jsonlite, rvest
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), S4Vectors,
DelayedArray, HDF5Array, Matrix, SummarizedExperiment,
SingleCellExperiment, BiocGenerics, methods, stats, utils,
splines, rlang, vctrs
biomaRt, checkmate, dplyr, forcats, futile.logger, ggplot2,
glue, httr, lifecycle, methods, parallel, readr, rlang, glmnet,
Matrix, MultiAssayExperiment, SummarizedExperiment, survminer,
TCGAutils, utils
annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
utils, stats, MASS, mclust, ggplot2, RANN, FNN, BiocParallel,
mvnfast, SingleCellExperiment, rlang, RColorBrewer, pheatmap,
vegan, cluster, boot, permute
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
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 (>= 0.2.1)
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
Matrix, Rcpp, stats, ggplot2, methods, cowplot, matrixStats
AnnotationDbi, graph (>= 1.67.1), httr, rappdirs, stats,
utils, graphics, rlang, lifecycle, purrr, dir.expiry
graphics, grDevices, reshape2, stats, utils
SummarizedExperiment, nloptr, fGarch, methods, BiocParallel,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, BiocParallel,
edgeR, EnrichmentBrowser, ExperimentHub, grDevices, graphics,
KEGGandMetacoreDzPathwaysGEO, KEGGdzPathwaysGEO, methods,
S4Vectors, stats, utils
dplyr, tidytext, dendextend, tibble, ggplot2, ggwordcloud,
stringr, gridExtra, rlang, grDevices, graphics, stats, methods
cluster, doParallel, foreach, matchingR, nsga2R, survival,
proxy, stats, methods,
methods, graphics, stats, utils, genefilter, Biobase,
GSEABase, les (>= 1.1.6)
methods, stats, utils, graphics, BiocGenerics, MatrixGenerics,
S4Vectors, S4Arrays, HDF5Array, SparseArray, DelayedArray,
IRanges, Biobase, SummarizedExperiment, GSEABase, Matrix (>=
1.5-0), parallel, BiocParallel, SingleCellExperiment,
SpatialExperiment, sparseMatrixStats, DelayedMatrixStats,
BiocSingular, cli, memuse
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
Rcpp (>= 0.11.2), graphics, stats, Ckmeans.1d.dp, parallel,
methods, matrixStats
dplyr, tidyr, ggplot2, BiocStyle, knitr, methods, grDevices,
stats, MsCoreUtils
Rcpp (>= 1.0.0), RcppEigen(>= 0.3.2.0), Matrix, RANN, ape,
dendextend, ggplot2, mclust, patchwork, dplyr, grDevices,
methods, stats
ggplot2, graphics, stats, reshape2, gridExtra, Rtsne, umap,
dplyr, rlang, magrittr, irlba, Matrix, SingleCellExperiment,
ggrepel
knitr, rmarkdown, SpatialExperiment, SummarizedExperiment,
circlize, ComplexHeatmap, scico, rlang, utils, ggplot2, grid,
methods, stats, RANN, Rcpp (>= 1.0.9)
graphics, grDevices, stats, utils, BiocGenerics
dplyr, openxlsx, ggplot2, tibble, xml2, stats, utils,
gridExtra
dplyr (>= 1.0.6), httr (>= 1.4.2), readr, tidyr, tibble,
utils, stringr, magrittr, caret, corrplot, ggplot2, pROC,
PRROC, igraph, graphics, stats, purrr, grDevices, protr, MCL
affy, Biobase, gplots, graphics, grDevices, limma, methods,
RColorBrewer, stats, stats4, utils
httr2, dplyr, tidyr, tibble, rjsoncons, utils, stringr,
whisker, purrr, rlang
available, usethis, biocthis, dplyr, aws.s3, fs, BiocManager,
utils
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, utils, rlang
mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI
(>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11),
parallelly , glmnet, stats, utils, SummarizedExperiment,
stringr, S4Vectors, DescTools, MatrixExtra, methods
methods, utils, stats, tools, R.utils, curl, httr, xml2,
rvest, xtable, jsonlite, S4Vectors, IRanges, GenomeInfoDb
methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel
(>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0),
SummarizedExperiment, tidyr
methods, slam, lpsymphony, fdrtool, BiocGenerics
Matrix, parallel, foreach, aricode, LiblineaR, SparseM,
ggplot2, cowplot, RSpectra, umap, Rtsne, fastcluster,
parallelDist, cluster, dendextend, DescTools, plyr, scales,
pheatmap, reshape2, dplyr, doRNG, SingleCellExperiment,
SummarizedExperiment, S4Vectors, methods, stats, doSNOW, utils
DT, dplyr, bslib, bsicons, ggplot2, viridis, tidyr, leaflet,
clipr, rlang
STRINGdb, pwalign, igraph, graphics, utils, seqinr
hash, httr, Matrix, matrixStats, methods, Rcpp, rvest,
SingleCellExperiment, stats, stringr, utils
Biostrings, httr, jsonlite, methods, rvest, tibble, yaml
methods, stats, graphics, grid, lattice, grDevices
ggplot2, httr, jsonlite, patchwork, UniProt.ws
stringr, ontologyIndex, curl, ggplot2, readr, rvest, tidyr,
xml2, maps, rlang
config (>= 0.3.2), golem (>= 0.4.1), shiny (>= 1.7.5),
ComplexHeatmap, DT, RColorBrewer, WGCNA, corrplot, cowplot,
dynamicTreeCut, ggplot2, glassoFast, impute, purrr, stringr,
tidyr, visNetwork, shinyBS, httr, dplyr, stats, iModMixData,
SummarizedExperiment, ExperimentHub (>= 2.99.0)
graphics, grDevices, RColorBrewer, gplots, futile.logger,
stats, utils, methods, ape, phyclust, Matrix, fastcluster,
parallelDist, dplyr, HiddenMarkov, ggplot2, edgeR, coin,
caTools, digest, RANN, igraph, reshape2, rjags, fitdistrplus,
future, foreach, doParallel, Seurat, BiocGenerics,
SummarizedExperiment, SingleCellExperiment, tidyr, parallel,
coda, gridExtra, argparse
stats, grDevices, utils, graphics, pbapply, matlab, png,
raster, grid, uwot, gtools, Biobase, generics, parallel,
methods, xgboost
SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2
grDevices, stats, shiny, grid, GetoptLong, S4Vectors (>=
0.26.1), digest, IRanges, kableExtra (>= 1.3.1), utils,
svglite, htmltools, clisymbols, jsonlite, RColorBrewer,
fontawesome
config, golem, shiny, DT, shinydashboard, shinyFiles,
shinycssloaders, data.table, fs, dplyr, tidyr, circlize,
colourpicker, dendextend, factoextra, ggplot2, plotly, plyr,
shinyFeedback, shinyalert, tibble, umap, visNetwork,
wordcloud2, readxl, htmlwidgets, colorspace, signal, scales,
htmltools, ComplexHeatmap, grDevices, stats, tools, utils,
biomaRt, rlang, fmsb, igraph
igraph (>= 1.0.1), FGNet (>= 3.0.7), knitr (>= 1.12.3), stats,
utils, grDevices, graphics
utils, dplyr, readr, tidyr, purrr, rlang, tibble, stringr, fs,
lubridate, lifecycle, ggplot2, ggrepel, stats, readxl, tools,
grDevices, forcats, glue, shiny, shinyWidgets, datamods, bslib,
vegan, data.table, DT
methods, BiocGenerics, S4Vectors, utils, stats, shiny,
shinydashboard, shinyAce, shinyjs, DT, rintrojs, ggplot2 (>=
3.4.0), 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
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
affxparser, DBI, GLAD, oligo, oligoClasses, stats
graphics, grDevices, stats, survival, utils
shiny, survival, survminer, hwriter, plotly, ggplot2,
S4Vectors, graphics, stats, utils, UpSetR
spatstat.geom, dplyr, glmnet, caret, foreach, stats, magrittr,
doParallel, BiocParallel, methods,
BumpyMatrix,SpatialExperiment
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
curl, igraph, foreach, doParallel, sortable, dplyr, forcats,
data.tree, graphics, grDevices, parallel, RColorBrewer, Rfast,
stats, SummarizedExperiment, utils, purrr, stringi, stringr,
Matrix, tidyr, jsonlite, readr, configr, DT, tools, fs,
data.table, htmltools, htmlwidgets, bsplus, shinyvalidate,
shiny, shinythemes, shinyFiles, shinyjs, shinyBS,
shinydashboard, biomaRt, callr, logr, ggplot2, svglite
data.table, vcfR, tidyr, stats, utils, graphics, grDevices,
ggplot2, gridExtra, survival, survminer, RColorBrewer,
Biostrings
BiocGenerics (>= 0.25.1), Seqinfo, httr, Matrix
stats, gplots, readr, tibble, gplots, methods,
SummarizedExperiment
akima, ggplot2, irr, jsonlite, parallel, plot3D, plyr, RCurl,
ROCR, testthat
stats, utils, irlba, methods, SingleCellExperiment,
SummarizedExperiment, rlang (>= 1.1.0), vctrs (>= 0.6.0),
glmGamPoi (>= 1.12.0), BiocGenerics, S4Vectors, Matrix,
DelayedMatrixStats, HDF5Array, MatrixGenerics, matrixStats,
Rcpp, harmony (>= 1.2.0), limma, BiocNeighbors
Hmisc, stats, energy, grDevices, graphics, utils,
MultiAssayExperiment, ggplot2, ggpubr
grDevices, graphics, stats, utils, methods, statmod
methods, grDevices, graphics, limma, R2HTML, tcltk, tkrplot,
xtable, utils
ggplot2, stringr, plyr, ggrepel, reshape2, grDevices,
graphics, doParallel, parallel, dplyr, tibble, tidyr, ggsci,
tidyverse, methods, stats, SummarizedExperiment, S4Vectors
limma, stringr, qvalue, utils, stats, BiocParallel, S4Vectors,
dplyr
scales, cluster, graphics, ggpubr, gridExtra, vegan, rio,
MultiAssayExperiment, emmeans, reshape2, data.table
Rcpp (>= 0.12.2), RcppArmadillo (>= 0.8.100.1.0), fpc, vegan,
mclust, apcluster, ggplot2, ellipse, limma, utils, statmod,
MASS, igraph, grDevices, graphics, fastcluster, ggdendro, zoo,
stats, amap, Rtsne, gmodels
methods, stats, utils, data.table, S4Vectors, rlang, dplyr,
tidyr, forcats, ggplot2, limma, fgsea, ropls, imputeLCMD,
magrittr
dplyr, ggnewscale, ggplot2, magrittr, methods, rlang,
SummarizedExperiment, MKmisc, matrixTests
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,
stats, utils, SummarizedExperiment, SingleCellExperiment,
BiocBaseUtils, jsonlite
methods, stats, utils, AnnotationDbi, RSQLite, DBI, Biobase
BiocParallel, dplyr, ggplot2, ggrepel, magrittr, stats, utils
data.table, plyr, dplyr, reshape, VennDiagram, ggplot2, ineq,
RColorBrewer, circlize, grid, utils, stats, ggtree, msa,
Biostrings, phangorn, stringdist, UpSetR
ggplot2, Matrix, doSNOW, cluster, parallel, foreach,
doParallel, matrixcalc, Rtsne, corpcor, umap
RColorBrewer, gplots, bbmle, statmod, grDevices, graphics,
stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods,
scater
dplyr, plyr, pbapply, lmerTest, parallel, lme4, optparse,
logging, multcomp, ggplot2, RColorBrewer, patchwork, scales,
rlang, tibble, ggnewscale, survival, methods, BiocGenerics,
SummarizedExperiment, TreeSummarizedExperiment
readxl, graphics, tools, utils, grDevices, ggplot2, ggrepel,
methods, stats, latticeExtra, lattice, rmarkdown, png, grid,
gridExtra, prettydoc, rvest, xml2
utils, reticulate, S4Vectors, methods, basilisk,
ExperimentHub, AnnotationHub
data.table, grDevices, methods, RColorBrewer, Rhtslib,
survival, DNAcopy, pheatmap
doParallel, igraph, bigstatsr, rjson, plyr, data.table,
UpSetR, reshape2, jsonlite, methods, ff, argparse, impute,
RnBeads.hg19, RnBeads.hg38, utils, stats
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
circlize, edgeR, ComplexHeatmap, ggh4x, ggplot2, ggpubr, grid,
gridExtra, pROC, RColorBrewer, reshape2, rstatix, scales,
stats, utils, fgsea, limma, ggrepel, effectsize, msigdbr,
tibble
Rcpp, SummarizedExperiment, utils, methods, ggplot2, dplyr,
magrittr, rlang, S4Vectors
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
BiocParallel, graphics, utils, stats, AnnotationDbi, GO.db,
org.Hs.eg.db, GGally, ggplot2, scales, cluster, WGCNA
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
methods, AnnotationDbi (>= 1.31.19), RSQLite, Biobase
AnnotationDbi, DOSE, enrichplot, GOSemSim (>= 2.31.2),
methods, utils, AnnotationHub, MeSHDbi, yulab.utils (>= 0.1.5)
markdown, rmarkdown, BiocStyle, knitr, methods, stats, utils,
fdrtool, MeSHDbi, Category, S4Vectors, BiocGenerics, RSQLite
methods, data.table, Biostrings, dplyr, tidyr (>= 1.0.0), ape
(>= 5.4.1), ggrepel, pracma, ggridges, AnnotationDbi, IRanges,
circlize, cowplot, mclust, phangorn, ComplexHeatmap (>= 1.9.3),
ggplot2, RColorBrewer, grDevices, stats, utils, S4Vectors
dplyr (>= 1.0), methods, mgcv, caret, S4Vectors, stats, utils,
rlang, graphics, matrixStats, tidyr
BiocGenerics, MsCoreUtils, MetaboCoreUtils, ProtGenerics,
methods, S4Vectors, Spectra (>= 1.17.6), BiocParallel,
SummarizedExperiment, QFeatures, AnnotationHub, graphics,
CompoundDb
utils, MsCoreUtils, BiocParallel, methods, stats
dplyr, ggplot2, KEGGREST, methods, Rcpp (>= 0.12.0),
RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>=
2.4.0), S4Vectors, stringr, SummarizedExperiment, tidyr,
dynamicTreeCut, rlang, ape, ggtree, patchwork
optimx, Formula, plyr, multtest, BiocParallel, ggplot2
KEGGgraph, hpar, igraph, RCurl, KEGGREST, EnsDb.Hsapiens.v75,
stats, graphics, utils, org.Hs.eg.db, biomaRt, AnnotationDbi,
MWASTools, mygene
flowCore (>= 1.4),tidyr (>=
0.7),fastcluster,ggplot2,metafor,cluster,FlowSOM, grDevices,
graphics, stats, utils
stats, RANN, igraph, vegan, edgeR, ecodist, ggplot2, viridis,
ggpubr, ape, cluster, matrixStats
utils, ggplot2, ggrepel, stringr, pheatmap, grDevices, stats,
clusterProfiler, RecordLinkage, RCy3
Biobase, BiocParallel, BiocGenerics, ggplot2, grid, gridBase,
grDevices, graphics, hexbin, matrixStats, minfi (>= 1.22.0),
methods, RColorBrewer, shiny, stats, SummarizedExperiment,
utils
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
shiny, shinyjs, seriation, BiocParallel, seqinr, Biostrings,
pwalign, Rfast, grDevices, graphics, stats, utils, tools,
methods, shinyFiles, data.table, SummarizedExperiment
SummarizedExperiment, deSolve, stats, poweRlaw,
MatrixGenerics, S4Vectors
Biostrings, compositions, dplyr, reshape2, Rtsne, scales,
stats, tibble, tidyr, utils, vegan
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)
TCA, nnls, purrr, TOAST, magrittr, BiocParallel, ggplot2,
ggpubr, ggridges, glue, S4Vectors, dirmult
BiocNeighbors, BiocGenerics, SingleCellExperiment, Matrix (>=
1.3-0), MatrixGenerics, S4Vectors, stats, stringr, methods,
igraph, irlba, utils, cowplot, BiocParallel, BiocSingular,
limma, ggplot2, tibble, matrixStats, ggraph, gtools,
SummarizedExperiment, patchwork, tidyr, dplyr, ggrepel,
ggbeeswarm, RColorBrewer, grDevices, Rcpp, pracma, numDeriv
BiocGenerics, S4Vectors, preprocessCore, grDevices, methods,
grid, gtable, scales, DBI, affy, affyPLM, oligo, oligoClasses
methods, stats, Rcpp, MCL, RSpectra, apcluster, bigmemory,
foreach, ggplot2, parallel, parallelDist, reshape2, plyr,
biganalytics, stringr, Hmisc, utils
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, RColorBrewer,
grid, MCL, fabia, NMF, biclust, iBBiG, BicARE, isa2, methods,
rJava, BiBitR, rqubic, Biobase, PMA, stats, dbscan, mclust,
SOMbrero, ppclust, Rcpp, utils, SummarizedExperiment, GSEABase,
org.Hs.eg.db, clusterProfiler, ReactomePA, DOSE,
MatrixCorrelation, energy
corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler,
ReactomePA, DOSE, survival, grDevices, graphics, stats, utils,
Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel
purrr, MASS, pscl, assertthat, caTools, dplyr, pheatmap,
reshape2, corrplot, grDevices, graphics, stats, utils,
data.table, R.utils, viridis
assertthat, caret, deldir, digest, distances, dplyr (>=
1.1.0), filelock, furrr (>= 0.2.0), ggplot2, methods, purrr,
ranger, readr (>= 2.0.0), ridge, rlang, rlist, R.utils, stats,
stringr, tibble, tidyr, tidyselect (>= 1.2.0), utils, withr
stats, grDevices, graphics, utils, MASS, plyr, reshape2,
parallel, GGally, grid, gridExtra, knitr, rmarkdown, ggplot2,
gplots, beeswarm, echarts4r, kableExtra, dplyr, network
AnnotationDbi, ape, circlize, clusterProfiler, ComplexHeatmap,
ggplot2, ggtree, magrittr, org.Hs.eg.db, ReactomePA, scales
igraph, ellipse, corpcor, RColorBrewer, parallel, dplyr,
tidyr, reshape2, methods, matrixStats, rARPACK, gridExtra,
grDevices, graphics, stats, ggrepel, BiocParallel, utils,
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
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
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
Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust,
isa2, QUBIC, akmbiclust, RColorBrewer
S4Vectors, scales, stats, graphics, statmod
BiocParallel, methods, progress, stats, SummarizedExperiment
Rcpp (>= 0.11.1), BiocGenerics, IRanges (>= 1.20.0),
S4Vectors, tools
BiocParallel, S4Vectors, IRanges, methods, ProtGenerics (>=
1.35.3), MsCoreUtils, DBI, utils
curl, ProtGenerics, BiocFileCache, S4Vectors, methods,
progress
ProtGenerics (>= 1.35.3), BiocParallel, S4Vectors, IRanges,
MsCoreUtils, methods, stats
ProtGenerics (>= 1.35.3), MsCoreUtils, S4Vectors, IRanges,
rawrr (>= 1.17.2), utils, BiocParallel
BiocParallel, S4Vectors, methods, ProtGenerics (>= 1.35.3),
DBI, MsCoreUtils, IRanges, data.table, progress, stringi,
fastmatch, BiocGenerics
methods, S4Vectors, IRanges, Spectra, SummarizedExperiment,
QFeatures, DBI, BiocGenerics
methods, ProtGenerics (>= 1.23.5), MsCoreUtils,
SummarizedExperiment, stats
data.table (>= 1.13.0), doRNG, fmsb, foreach, magrittr,
org.Hs.eg.db, pROC, randomForest, RankProd, stats, utils
MsCoreUtils, PSMatch (>= 1.13.2), BiocParallel, IRanges (>=
2.13.28), plyr, vsn, grid, stats4, affy, impute, pcaMethods,
MALDIquant (>= 1.16), mzID (>= 1.5.2), digest, lattice,
ggplot2, scales, MASS, Rcpp
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, limma, SummarizedExperiment, magrittr, rlang,
dplyr, purrr, stats, tidyr, stringr, ggplot2, ggseqlogo,
heatmaply, readr, rstatix, tibble, ggpubr, imputeLCMD
plyr, dplyr, dbplyr, magrittr, foreach, parallel, doSNOW,
stringr, mzR, reshape2, fastcluster, ggplot2, DBI, RSQLite
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, rlang
arrow, DBI, dplyr, MSstats, MSstatsConvert, readr, sparklyr,
utils
data.table, log4r, methods, checkmate, utils, stringi, Rcpp,
parallel
dplyr, gridExtra, stringr, ggplot2, grDevices, MSstats,
MSstatsConvert, data.table, Biostrings, MSstatsPTM, Rcpp,
checkmate, factoextra, ggpubr, purrr, tibble, tidyr, tidyverse,
scales, stats, plotly, htmltools
minpack.lm, ggplot2, utils, stats, grDevices
dplyr, gridExtra, stringr, stats, ggplot2, stringi, grDevices,
MSstatsTMT, MSstatsConvert, MSstats, data.table, Rcpp,
Biostrings, checkmate, ggrepel, plotly, htmltools
shiny, MSstatsQC, ggExtra, gridExtra, plotly, dplyr, grid
BiocParallel, ggplot2, dplyr, stats, parallel, data.table
shiny, shinyBS, shinyjs, shinybusy, dplyr, ggplot2, plotly,
data.table, Hmisc, MSstats, MSstatsTMT, MSstatsPTM,
MSstatsConvert, gplots, marray, DT, readxl, ggrepel, uuid,
utils, stats, htmltools, methods, tidyr, grDevices, graphics,
mockery, MSstatsBioNet, shinydashboard, arrow, tools
limma, lme4, lmerTest, methods, data.table, stats, utils,
ggplot2, grDevices, graphics, MSstats, MSstatsConvert,
checkmate, plotly, htmltools
methods, stats, MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, DelayedArray, S4Vectors
graphics, grDevices, stats, methods, fields
Matrix, ggplot2, MultiAssayExperiment, ropls, graphics,
methods, plotrix, grDevices, pcaMethods
mclust, ctc, survival, cluster, dendextend, amap, graphics,
grDevices
magrittr, graphite, AnnotationDbi, metaboliteIDmapping, dplyr,
fgsea, metap, rappdirs, rlang, methods
stats, XML, RCurl, purrr (>= 0.2.2), tibble (>= 2.0), methods,
BiocGenerics, AnnotationDbi, dplyr,
methods, S4Vectors, data.table, grid, dplyr, tidyr,
matrixStats, stats, fitdistrplus, viridis, ggplot2, circlize,
mashr, grDevices
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
BiocGenerics, Biostrings, ggbeeswarm, ggiraph, ggthemes,
grDevices, IRanges, methods, pheatmap, RColorBrewer, stats,
utils
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)
methods, SingleCellExperiment, parallel, irlba, Matrix,
DelayedArray, BiocSingular, SharedObject, stats
Biostrings, checkmate, dplyr (>= 1.1.0), forcats, ggdendro,
grDevices (>= 3.6.0), grid, jsonlite, lifecycle, lubridate,
methods, plotly (>= 4.9.4), rlang, rmarkdown, scales, stats,
stringr, tidyr, tidyselect (>= 0.2.3), utils, zoo
ComplexHeatmap, dplyr, fgsea, ggplot2 (>= 3.0.0), graphics,
grid, methods, MultiAssayExperiment, SummarizedExperiment,
pracma, rlang, RSpectra, scales, stats
graphics, grDevices, marray, methods, nnet, stats
SpatialExperiment, SingleCellExperiment, SummarizedExperiment,
BRISC, BiocParallel, Matrix, matrixStats, stats, methods
limma, mvtnorm, utils, methods, arm, HTqPCR (>= 1.16.0)
vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods,
utils, stats, SummarizedExperiment, matrixStats, ggforce
BiocGenerics, BiocParallel, dplyr, futile.logger, methods,
openxlsx, S4Vectors, scales, stringr, tidyr, utils
BiocGenerics, cowplot, devEMF, dplyr, ggbeeswarm, ggdendro,
ggrepel, grDevices, methods, notame, scales, stringr, stats,
tibble, tidyr, utils
dplyr, tidyr, BiocParallel, broom, MASS, rlang, magrittr,
stats, methods
Biobase, methods, BiocGenerics, graphics, stats
stats, IRanges, S4Vectors, graphics, methods
multtest (>= 1.7.3), graphics, grDevices, stats, interp
affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1),
ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>=
1.0.0), splines, stats, stats4, utils, bit
graphics, grDevices, limma, marray, methods, stats
graphics, marray, OLIN, tcltk, tkWidgets, widgetTools
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
checkmate, crayon, curl, digest, dplyr(>= 1.1.0), fs, httr2,
igraph, jsonlite, later, logger, lubridate, magrittr, progress,
purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown,
RSQLite, R.utils, rvest, sessioninfo, stats, stringi, stringr,
tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML,
xml2, yaml, zip
ggplot2, ggrepel, RColorBrewer, mclust, stats,
SummarizedExperiment
biomaRt, grDevices, graphics, utils, methods,
Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz,
gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr,
smatr, ggplot2, ggrepel, stringr
Biobase, S4Vectors, methods, stats, utils, BiocFileCache,
shiny, graph, Rgraphviz, ontologyPlot, dplyr, magrittr, DT,
igraph, AnnotationHub, SummarizedExperiment, reticulate,
R.utils, httr, basilisk, jsonlite, RBGL, ellmer
methods, Biobase, BiocGenerics, flowCore(>= 1.99.17), flowViz,
ncdfFlow(>= 2.11.34), flowWorkspace(>= 3.99.1), flowClust(>=
3.11.4), RBGL, graph, data.table, RColorBrewer, grDevices
MASS, jsonlite, Hmisc, methods, knitr, AICcmodavg, car, rlist,
summarytools, graphics, stats, utils
fastICA, tsne, scatterplot3d, pixmap, fdrtool, ape, biomaRt,
Biobase, RcppParallel, Rcpp, methods, graph, XML, png, RCurl
transport, parallel, Rfast, robustbase, dbscan, randomForest,
foreach, graphics, doParallel, stats, flowMeans, rgl, ellipse
dplyr, methods, stats, utils, Matrix, jsonlite, homologene,
gprofiler2, babelgene, data.table, parallel, ggplot2, ggpubr,
patchwork, DelayedArray, grr, repmis, ggtree, tools
stats, utils, methods, BiocParallel, SummarizedExperiment,
limma, fdrtool, Rcpp
e1071, gplots, gtools, limma, MASS, mRMRe, randomForest, ROCR,
sva
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
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
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
data.table, MultiAssayExperiment, ConsensusClusterPlus,
igraph, ggplotify, matrixStats, RColorBrewer, clusterRepro,
CoreGx, caret, survminer, methods, S4Vectors, BiocGenerics,
survival, stats, plyr, dplyr, MatrixGenerics, BiocParallel,
rlang, piano, scales, survcomp, genefu, ggplot2, switchBox,
reportROC, pROC, verification, utils
circlize, ComplexHeatmap, flowCore, flowWorkspace, ggplot2,
grDevices, grid, gridExtra, methods, plyr, stats, utils
ROTS, limma, affy, genefilter, preprocessCore,
aroma.affymetrix, aroma.core
assertthat, circular, conicfit, doParallel, foreach, genlasso
(>= 1.4), graphics, methods, parallel, scater,
SingleCellExperiment, SummarizedExperiment, stats, utils
graphics, stats, methods, ggplot2, utils, grDevices, stringr,
plyr, dplyr, tidyr, quadprog, Matrix, S4Vectors, shiny, readxl,
DT, igraph, shinycssloaders, shinyhelper, shinyjs, shinyjqui,
shinyWidgets, htmlwidgets, plotly, colourpicker, shinytoastr
dplyr, limma, lme4, MASS, matrixStats, reshape2, stats,
tibble, SummarizedExperiment, methods
Matrix, ptw, ggplot2, gridExtra, matrixStats, reshape2,
methods, graphics, stats
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
ape, phangorn, tidyr, ggplot2, ggtree, methods
plyr, stats, graphics, matrixStats, methods
ruv, e1071, dendextend, limma, pcaMethods, stats,
RColorBrewer, circlize, dplyr, igraph, pheatmap,
preprocessCore, tidyr, rlang, graphics, grDevices, utils,
SummarizedExperiment, methods, S4Vectors, BiocGenerics,
ggplot2, GGally, ggdendro, ggpubr, network, reshape2, ggtext,
stringi
ape, bioDist, BiocStyle, Biostrings, bsplus, colourpicker,
data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra,
htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast,
scattermore, shiny, shinycssloaders, shinyFiles, shinyjs,
stringr, tsne, svglite, umap, xml2, zoo, yaml
BiocGenerics, Biobase, gplots, igraph, relations, marray,
fgsea, shiny, DT, htmlwidgets, shinyjs, shinydashboard,
visNetwork, scales, grDevices, graphics, stats, utils, methods
BSgenome, digest, visNetwork, magrittr, methods, Biostrings,
Seqinfo, parallel, stats, utils, rmarkdown
utils, Biobase (>= 2.5.5), MASS, methods
mixOmics, scales, Rdpack, ggplot2, gridExtra, ggpubr,
lmerTest, performance, grid, stats, pheatmap, vegan, Biobase,
BiocStyle, TreeSummarizedExperiment
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
aricode, BiocNeighbors, BiocParallel, bluster, clevr, clue,
cluster, elsa, fclust, igraph, Matrix, matrixStats, mclustcomp,
methods, pdist, sp, spdep, stats, utils, SpatialExperiment,
SummarizedExperiment
methods, S4Vectors, utils, shiny, ontoProc, ggplot2, graphics
stats, utils, grDevices, mvtnorm, sn, dplyr, flowPeaks,
ggplot2, tidyverse, cowplot, mlrMBO, DiceKriging, smoof,
ParamHelpers, lhs, rgenoud, BiocManager
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
graphics, grDevices, Icens, stats, utils
methods, stats, graphics, S4Vectors, Biostrings, utils
Biobase, stats, dplyr, tidyr, ggplot2, ggrepel, gridExtra,
decoupleR, reshape2
SingleCellExperiment, methods, cluster, stats, limma, NMF,
ROCR, ggalluvial, RColorBrewer, dplyr, fgsea, reshape2,
viridis, scales, Matrix, MatrixModels, msigdbr, ggplot2,
cowplot, ggrepel, umap, tsne
stats4, Biobase, mclust (>= 4.3), caret, e1071, sampling,
class, kernlab, lattice, nnet, randomForest, proxy, FNN,
hexbin, BiocGenerics, stats, dendextend, RColorBrewer, scales,
MASS, knitr, mvtnorm, LaplacesDemon, coda, mixtools, gtools,
plyr, ggplot2, biomaRt, utils, grDevices, graphics, colorspace
shiny (>= 0.9.1), scales, dplyr, DT (>= 0.1.40), graphics,
utils, ggplot2, shinydashboardPlus (>= 2.0.0), colourpicker,
shinyhelper, shinyWidgets, shinyjs, colorspace, stats,
grDevices, grid, BiocGenerics, shinydashboard
dplyr, magrittr, data.table, RColorBrewer, ggplot2, S4Vectors,
ComplexHeatmap, stringr, NormalyzerDE, tibble, limma, MASS,
edgeR, matrixStats, preprocessCore, stats, gtools, methods,
ROTS, ComplexUpset, tidyr, purrr, circlize, gprofiler2,
plotROC, MSnbase, UpSetR, dendsort, vsn, Biobase, reshape2,
POMA, ggtext, scales, DEqMS, vegan
bnlearn, reshape2, sva, stats, utils, Biobase
DAPAR (>= 1.35.1), DAPARdata (>= 1.30.0), rhandsontable,
data.table, shiny, shinyBS, shinyAce, highcharter, htmlwidgets,
webshot, shinythemes, later, shinycssloaders, future, promises,
shinyjqui, tibble, ggplot2, gplots, shinyjs, vioplot, Biobase,
DT, R.utils, RColorBrewer, XML, colourpicker, gtools, markdown,
rclipboard, sass, shinyTree, shinyWidgets
gdata, biomaRt, ggplot2, ggrepel, gtools, stats, matrixStats,
graphics
AnnotationDbi, AnnotationHub, BiocFileCache, cluster,
colourpicker, data.table, digest, dplyr, DT (>= 0.2), edgeR,
fastICA, fastmatch, ggplot2, ggrepel, graphics, grDevices,
highcharter (>= 0.5.0), htmltools, httr, jsonlite, limma,
pairsD3, plyr, purrr, Rcpp (>= 0.12.14), recount, Rfast,
R.utils, reshape2, shinyjs, stringr, stats,
SummarizedExperiment, survival, tools, utils, XML, xtable,
methods
utils, stats, igraph, methods, Spectra (>= 1.17.10), Matrix,
BiocParallel, BiocGenerics, ProtGenerics (>= 1.27.1),
QFeatures, MsCoreUtils, IRanges
Biobase, bit64, chron, data.table, doParallel, DT, enviPat,
foreach, ggplot2, graphics, grDevices, ggpubr, gridExtra,
Hmisc, methods, minpack.lm, MSnbase, parallel, plotly, rhdf5,
rlang, Rcpp, shiny, shinyscreenshot, signal, scales, stats,
utils
Biobase (>= 2.5.5), affy (>= 1.46.0), affyio, oligoClasses
Biobase, methods, knitr, tools, xtable, pander, S4Vectors
methods, stats, utils, S4Vectors, IRanges,
SummarizedExperiment, BiocGenerics (>= 0.53.4), ProtGenerics
(>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils
(>= 1.7.2), igraph, grDevices, plotly, tidyr, tidyselect,
reshape2
rlang, ggplot2, patchwork, heatmaply, methods, MsCoreUtils,
stats, igraph, VIM, scales, grDevices, graphics, limma
MASS, pscl, arrangements, hitandrun, assertthat, dplyr,
BiocParallel
SummarizedExperiment, utils, sva, stats, methods, graphics,
Hmisc
dplyr, sva, stats, ggplot2, rlang, methods
methods, rlang, checkmate, dplyr, collapse, vroom, tidyr,
tibble, utils, stats, ashr, S4Vectors, BiocGenerics
Biobase, limSolve, MASS, methods, preprocessCore, stats,
SummarizedExperiment, ggplot2, tidyr, rlang, utils
Biobase, minfi, doParallel, foreach, iterators, ggplot2,
methods, RColorBrewer
SummarizedExperiment, BiocGenerics, data.table, S4Vectors,
Biobase, parallel, BiocParallel, RColorBrewer, caTools,
magicaxis, methods, reshape2, scales, grDevices, graphics,
stats, utils, assertthat, matrixStats, downloader
methods, graphics, utils, stats, Rdpack (>= 0.7)
curl, jsonlite, methods, paws.storage, R.utils, utils
dplyr, ggplot2 (>= 3.4), grDevices, hexbin, htmltools,
BiocManager, BiocParallel, rawrr (>= 1.15.5), rlang, reshape2,
scales, shiny (>= 1.5), stats, utils
EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats
stringr, gplots, ggplot2, methods, stats, utils, shiny
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
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
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
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
vroom, org.At.tair.db, AnnotationDbi, clusterProfiler,
ComplexHeatmap, data.table, DT, edgeR, enrichplot, FactoMineR,
ggpubr, ggrepel, grDevices, grid, httr, limma, magrittr,
methods, mixOmics, MOFA2, plotly, purrr, RColorBrewer,
reshape2, reticulate, rmarkdown, S4Vectors, shiny,
shinydashboard, shinyWidgets, stats, stringr, tidyr, tibble,
tidyselect, UpSetR,
dplyr, ggplot2, hash, methods, rhdf5, rlang, stats, S4Vectors,
tidyr, tools, yaml
plyr, dplyr, DBI, data.table, reshape2, methods, sqldf, tools,
utils, RSQLite
graphics, methods, stats, utils, grid, gridExtra, reshape2,
gplots, ggplot2, plotrix, RColorBrewer, STRINGdb, MCL,
dynamicTreeCut, gsubfn, hash, png, sqldf, igraph, BgeeDB,
knitr, RITANdata, GenomicFeatures, ensembldb, AnnotationFilter,
EnsDb.Hsapiens.v86
glmnet, pROC, ggplot2, graphics, stats, Biobase, methods,
utils
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
ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
stats, utils, methods
Biobase, BiocGenerics, BiocParallel, stats, limma, dplyr,
magrittr, rlang, edgeR, foreach, mice
affy, boot, impute, splines, graphics, qvalue, reshape2
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
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
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
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
dplyr, fastDummies, ggplot2, stringr, tibble, Matrix,
ComplexHeatmap, grid, circlize, SingleCellExperiment,
SummarizedExperiment, tidyverse, tidyr, magrittr, S4Vectors
corrplot, MASS, stats, lattice, grDevices, gridExtra,
snowfall, psych, BiocParallel, grid, bladderbatch, reshape2,
graphics
GENLIB, gRain, snpStats, kinship2, methods, stats, utils,
R.utils
httr, utils, XML, rjson, data.table, RCurl, dplyr, tidyr,
readr, stringr, purrr, lubridate
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
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
grid, ggplot2, plyr, spatstat.geom, stats, grDevices
reshape2, BiocParallel, ape, scales, Seurat, ggplot2, ggtree,
patchwork, proxy, methods, stats, base, utils, dplyr
S4Vectors, limma, ggraph, igraph, methods, cluster,
minpack.lm, mixtools, BiocParallel, proxy, proxyC, Matrix,
ggplot2, hopach, diptest, mgcv, stats, graphics, statmod, Cepo
stats, boot, utils, scales, lifecycle, rlang, tidyselect,
magrittr, crayon, cli, fansi, dplyr, tidyr, purrr, tibble,
ggplot2, ggrepel, patchwork, forcats, readr, stringr, glue,
SingleCellExperiment
ggplot2, ggrepel, flowCore, umap, Seurat, reshape2, scales,
RColorBrewer, corrplot, stats, grDevices, graphics, utils,
MASS, matrixStats, methods
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, umap, ggplot2, irlba, viridis,
BiocParallel, matrixStats, Matrix, sparseMVN, coop
SingleCellExperiment, methods, isotree, FNN, igraph, ggplot2,
GGally, ggridges, SummarizedExperiment, ranger, transport,
cramer, rlang, bluster, scales, MASS, stringr, Matrix,
grDevices
aplot, BiocGenerics, cli, dplyr, ggplot2, ggsci, ggtree,
grDevices, magrittr, purrr, rlang, scales, scater, Seurat,
SingleCellExperiment, stats, stringr, tibble, tidyr
Matrix, S4Vectors, SingleCellExperiment, SummarizedExperiment,
xgboost, methods, stats, dplyr, pROC
matrixStats, BiocParallel, torch (>= 0.3.0), coro, igraph,
Matrix, cluster, psych, glmnet, RhpcBLASctl, stats, utils,
methods, survival
BiocBaseUtils, BiocParallel (>= 1.30.0), doParallel, doRNG,
GENIE3, Matrix, MultiAssayExperiment, SingleCellExperiment,
SummarizedExperiment, distributions3, dplyr, grDevices,
graphics, httr, igraph, jsonlite, methods, parallel,
reticulate, tidyr, glmnet, MASS, utils, stats, S4Vectors,
graph, mpath
hexbin, stats, methods, cluster, dplyr, entropy, ggforce,
grid, rlang, concaveman
grDevices, graphics, stats, utils, dplyr, ggplot2, gtools,
HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix,
tidyr, rlang, data.table, BiocParallel
S4Vectors (>= 0.24.3), SingleCellExperiment, Matrix,
SummarizedExperiment, IRanges, methods, stats, BiocParallel,
reshape, ggplot2, igraph, grDevices, ggforce, graphics
SpatialExperiment, SummarizedExperiment, spatstat.geom,
spatstat.explore, sf, lwgeom, SpatialPack, ggplot2, stats,
pheatmap, plotly, shiny, igraph, janitor, knitr, methods,
utils, isoband, S4Vectors, grDevices, dbscan, hexDensity,
hexbin, uwot, SingleCellExperiment, BiocNeighbors, irlba
dplyr, rmarkdown, data.table, Biostrings, stats, plyr, knitr,
ggplot2, gridExtra, DECIPHER, stringr, sangerseqR, kableExtra,
tibble, scales, rlang, flowCore, methods, basilisk,
basilisk.utils, reticulate, here, pwalign, utils
geeM, MASS, mpath, dplyr, stats, utils, withr, purrr, tidyr,
furrr, doSNOW, gamlss, scales, future, Matrix, ggplot2,
splines, foreach, glmmTMB, parallel, RcppEigen, bigstatsr,
tidyselect, broom.mixed, Rcpp
Biobase, SingleCellExperiment, SummarizedExperiment,
BiocGenerics, S4Vectors, dplyr, reshape2, matrixStats, proxy,
utils, googleVis, ggplot2, methods, stats, e1071, randomForest,
Rcpp (>= 0.12.12)
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
data.table, Rcpp, magrittr, plyr, stringr, utils, stats,
methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr,
parallel, grDevices
foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats,
phytools, KernelKnn, gplots, zeallot, crayon, assertthat,
igraph, methods, grDevices, graphics, stats, utils, markdown,
SummarizedExperiment, BiocParallel
SingleCellExperiment, SummarizedExperiment, stats, methods,
graphics, grDevices, parallel, quantreg, cluster, moments,
data.table, BiocParallel, S4Vectors, ggplot2, forcats,
BiocGenerics
graphics, stats, utils, aroma.light, BiocParallel, class,
cluster, compositions, diptest, edgeR, fpc, gplots, grDevices,
hexbin, limma, matrixStats, mixtools, RColorBrewer, boot,
rhdf5, RUVSeq, rARPACK, MatrixGenerics, SingleCellExperiment,
DelayedMatrixStats, sparseMatrixStats, SparseArray (>= 1.7.6)
tibble, dplyr, FNN, flowCore, Rtsne, ggplot2, magrittr, utils,
stats, readr
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
methods, Rcpp, beachmat (>= 2.25.1), DelayedArray,
BiocNeighbors (>= 1.99.0), parallel
randomForest, e1071, stats, SummarizedExperiment,
SingleCellExperiment, methods
stats, utils, methods, graphics, doParallel, foreach,
parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS
(>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>=
4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), BiocParallel (>=
1.12.0)
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
S4Vectors, seriation, circlize, methods, randomcoloR, stats,
grid, grDevices, matrixStats
ggplot2, grid, igraph, utils, yulab.utils
BiocParallel, ggplot2, Matrix, methods, rearrr, sf,
SpatialExperiment, SummarizedExperiment
dplyr, MASS, Matrix, SingleCellExperiment (>= 1.30.1), stats,
tidygraph, rlang, utils
httr, jsonlite, yaml, objectProperties, stringr, S4Vectors,
docopt, curl, uuid, data.table
AnnotationHub, BiocGenerics, bsicons, bslib, circlize,
ComplexHeatmap, cowplot, dplyr, DT, edgeR, ExperimentHub,
ggplot2, ggpubr, ggrepel, grDevices, grid, htmltools, limma,
magrittr, pals, readr, S4Vectors, scales, scater, shiny,
shinycssloaders, shinyjs, shinyvalidate, shinyWidgets,
SingleCellExperiment, standR, stats, stringr,
SummarizedExperiment, tibble, tidyr, utils, withr
Biobase, BiocGenerics, graphics, grDevices, htmltools,
MatrixGenerics, methods, minfi, RColorBrewer, shiny, stats,
utils
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
parallel, Matrix, stats, methods, Rcpp, pracma, RcppAnnoy,
RSpectra
methods, Rcpp, matrixStats, GetoptLong, grid, GlobalOptions,
igraph, Polychrome, S4Vectors, xml2 (>= 1.3.3), circlize,
ComplexHeatmap, grDevices, stats, utils, shiny, fastmatch
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
stats, utils, methods, ggplot2, matrixTests, matrixStats,
foreach, BulkSignalR
methods, Matrix, S4Vectors, DelayedArray, DelayedMatrixStats,
BiocParallel, BiocNeighbors, stats, utils, Rcpp, beachmat (>=
2.25.1)
methods, stats, graphics, ggplot2, grDevices, ggrepel,
GSEABase, plotly, tidyr, plyr, magrittr, reshape, edgeR,
RColorBrewer, Biobase, BiocParallel, SummarizedExperiment,
matrixStats, reshape2, S4Vectors
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
SpatialExperiment, SummarizedExperiment, BiocNeighbors,
Matrix, methods, utils
basilisk, reticulate, irlba, stats, assertthat
terra, sf, smoothr, spatstat.explore, spatstat.geom,
SpatialExperiment, SingleCellExperiment, dplyr, ggplot2,
patchwork, SummarizedExperiment, stats, rlang, parallel,
EBImage, spatstat.random, S4Vectors
matrixStats, matrixTests, rstatix, spatstat.explore,
spatstat.geom, ape, hdf5r, nanoparquet, jsonlite, Matrix,
qvalue, stats, utils, methods, ggplot2, reshape2, RColorBrewer,
circlize, mixtools, dplyr, readbitmap, rlang, effsize, viridis
ggplot2, Matrix, parallel, quadprog, httr, methods, memoise,
BiocParallel, BiocFileCache, SummarizedExperiment, scatterpie,
SpatialExperiment
Rcpp, stats, Matrix, SpatialExperiment, SummarizedExperiment,
BiocParallel (>= 1.0)
babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet,
checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>=
1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>=
2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix,
methods, plotly (>= 4.9.0), stats, utils, viridis
utils, stats, matrixStats, IRanges, XVector
Rcpp, Matrix, matrixStats (>= 0.60.0), methods
methods, glmnet, huge, stats, graphics, utils
ggplot2, methods, stats, dplyr, spatstat.geom,
spatstat.random, SpatialExperiment, SummarizedExperiment, RANN
grDevices, stats, utils, graphics, SeuratObject, Biobase,
GeomxTools, repmis, methods, Matrix, logNormReg (>= 0.4)
rjson, grDevices, magick, utils, S4Vectors,
SummarizedExperiment, BiocGenerics, BiocFileCache
dplyr, ggplot2, parallel, patchwork, purrr, refund,
SpatialExperiment, spatstat.explore, spatstat.geom,
SummarizedExperiment, methods, stats, fda, tidyr, graphics,
ExperimentHub, scales, S4Vectors
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
Spectra (>= 1.5.6), MsCoreUtils, methods
Spectra (>= 1.19.9), IRanges, S4Vectors, MsCoreUtils,
ProtGenerics, 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
BiocParallel, ClassifyR, S4Vectors, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, cli, concaveman,
coxme, data.table, dplyr, ggforce, ggh4x, ggnewscale, ggplot2,
ggthemes, grDevices, lifecycle, lmerTest, magrittr, methods,
pheatmap, rlang, scales, scam, simpleSeg, spatstat.explore,
spatstat.geom, stats, survival, tibble, tidyr
stats, methods, graphics, grDevices, huge (>= 1.3.2), pulsar
(>= 0.3.11), MASS, VGAM, Matrix (>= 1.5), glmnet, phyloseq
dplyr, tibble, tidyselect, stats, ggplot2, tidyr,
spatstat.univar, S4Vectors, parallel
Biobase (>= 2.5.5), graphics, grDevices, gtools, methods,
RColorBrewer, stats, utils
Biobase, stats, ppcor, logging, foreach, doRNG, data.table,
MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse,
caret, dplyr, biomaRt, randomForest, ggridges, cvms,
ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr,
stringr, tidyr
stats, methods, utils, dplyr, S4Vectors, SummarizedExperiment,
SpatialExperiment, Matrix, rhdf5, ggplot2, grid, readbitmap,
rjson, tibble, viridis, grDevices, RColorBrewer, Seurat, rlang
ggplot2, Matrix, SingleCellExperiment, sparseMatrixStats,
stats
SpatialExperiment, SummarizedExperiment, BiocNeighbors,
SingleCellExperiment, stats, escheR, MASS, ggplot2, spatialEco,
grDevices, BiocParallel
stats, methods, SingleCellExperiment, fitdistrplus, graphics,
edgeR, Hmisc, WGCNA, limma, mvtnorm, phyloseq, utils
xcms, MSnbase, MsExperiment, RaMS, dplyr, tidyr, tibble,
ggplot2, shiny, plotly, data.table, caret, stats, graphics,
utils, keys
ggplot2, reshape2, MASS, RColorBrewer, gridExtra,visNetwork,
gplots, umap, htmlwidgets, S4Vectors, BiocGenerics, grDevices,
stats, utils, graphics, doFuture, doRNG, future, foreach
dplyr (>= 1.1), magrittr, rlang, stats, graphite, tibble,
ggraph, igraph, reshape2, org.Hs.eg.db, SummarizedExperiment,
edgeR, methods, ggforce, pheatmap, utils, stringr, gtools,
tidyr
dplyr, SpatialExperiment (>= 1.5.2), SummarizedExperiment,
SingleCellExperiment, edgeR, rlang, readr, tibble, ggplot2,
tidyr, ruv, limma, patchwork, S4Vectors, Biobase, BiocGenerics,
grDevices, stats, methods, ggalluvial, mclustcomp, RUVSeq
Biobase, gridExtra, ggplot2, methods, stats, grid, MASS,
calibrate, gplots, edgeR, limma, foreach, affy
BiocParallel, spatstat.geom, concaveman, data.table,
spatstat.explore, dplyr, tidyr, SingleCellExperiment, tibble,
stringr, tidyselect, ggplot2, methods, stats,
SummarizedExperiment, S4Vectors, plotly, purrr, ranger,
magrittr, limma, SpatialExperiment, cluster, treekoR, edgeR
graphics, stats, dplyr, magrittr, sp, raster, spdep, ggplot2,
pheatmap, grDevices, Seurat, SpatialExperiment,
SummarizedExperiment
png, sqldf, plyr, igraph, httr, methods, RColorBrewer, gplots,
hash, plotrix
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
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
Rcpp, RcppParallel, methods, cli, dplyr, rlang, S4Vectors,
SummarizedExperiment, SingleCellExperiment, SpatialExperiment,
BiocGenerics, BiocParallel, fastmatch, pracma, stats, withr,
Matrix, DelayedMatrixStats, deldir, utils, BiocNeighbors,
ggplot2, ggstar, ggtree, ggfun
SummarizedExperiment, dplyr, ggplot2, methods, stats
methods, Biostrings, S4Vectors, IRanges, utils, stats,
parallel, graphics, grDevices, RSQLite, DBI
data.table, ggplot2, grDevices, magrittr, methods, patchwork,
RankProd, RColorBrewer, stats, utils
seqinr, methods, Biostrings, stringr, BiocGenerics
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 (>= 2.12), rlang, utils, methods, dplyr
ggplot2, ggpubr, methods, miniUI, mzID, mzR, shiny, stats
graphics, grDevices, methods, ncdf4, stats, utils, assertthat
methods, ontoProc (>= 0.99.7), SummarizedExperiment,
AnnotationDbi, matrixStats, org.Mm.eg.db, stats, utils,
BiocFileCache
utils, igraph, methods, graphics, stats, BiocParallel
Biobase, dplyr, flowCore, ggplot2, methods, purrr, rlang,
stats, stringr, tibble, tidyr
tidySummarizedExperiment, tidySingleCellExperiment,
tidySpatialExperiment, tidyseurat, plyranges, purrr, rlang,
stringr, cli,
dplyr, tidyr, SummarizedExperiment, tibble, ggplot2, magrittr,
rlang, purrr, pkgconfig, lifecycle, methods, utils, S4Vectors,
tidyselect, ellipsis, vctrs, pillar, stringr, cli, fansi,
Matrix, stats
SummarizedExperiment, SingleCellExperiment, BiocGenerics,
S4Vectors, methods, utils, pkgconfig, tibble, dplyr, tidyr,
ggplot2 (>= 4.0.0), plotly, rlang, purrr, stringr, vctrs,
tidyselect, pillar, cli, fansi, lifecycle, magick, tidygate (>=
1.0.13), shiny
dplyr, tibble (>= 3.0.4), magrittr, tidyr, ggplot2, rlang,
purrr, lifecycle, methods, utils, S4Vectors, tidyselect,
ellipsis, vctrs, pillar, stringr, cli, fansi, stats, pkgconfig,
plyxp
methods, AnnotationDbi, gplots, graphics, grDevices, stats,
utils, annotate, DBI, RSQLite
strucchange, affy, vsn, genefilter, RColorBrewer, grid, stats4
Biobase, graphics, limma (>= 1.8.6), MASS, marray, methods,
stats
dplyr, tidyr, tibble, purrr, magrittr, ggplot2, stringr,
ggrepel, lmtest, plyr, checkmate
gss, mvtnorm, stats, zoo, cluster, utils, BiocParallel,
flexclust, grDevices, graphics, Biobase, SPEM
circlize, ComplexHeatmap, data.table, grDevices, grid,
GSEABase, Matrix, methods, stats, utils
stats, methods, SummarizedExperiment, corpcor, doParallel,
parallel, ggplot2, tidyr, GGally
methods, stats, grDevices, reshape2, Rtsne, umap,
RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
grDevices, graphics, animation, tibble, dplyr, stringr, purrr,
methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2
assertthat, caret, ClassifyR, directPA, doParallel, dplyr,
ggnewscale, ggplot2, ggraph, ggrepel, ggthemes, glmnet, Hmisc,
igraph, latex2exp, limma, magrittr, methods, plotly, pROC,
purrr, reshape2, stats, stringr, survival, tibble, tidygraph,
tidyr, statmod
methods, utils, stats, assertthat, ggplot2, scales, grid,
grDevices
grDevices, stats, tools, utils, Biobase, Matrix (>= 1.4-2),
MSnbase (>= 2.33.5), PSMatch (>= 1.11.4), ggplot2 (>= 2.2.1),
mzR (>= 2.27.5)
SummarizedExperiment, BiocGenerics, S4Vectors, Biobase,
BiocParallel, ggplot2, tibble, dplyr, caTools, downloader,
magrittr, methods, reshape2, tidyr, data.table, assertthat,
scales, graphics, grDevices, parallel, stats, utils, limma,
jsonlite
biobroom, broom, data.table, doParallel, foreach,
futile.logger, ggplot2, grDevices, gridExtra, grid, knitr,
limma, MASS, mefa, nls2, openxlsx (>= 2.4.0), parallel, plyr,
purrr, RColorBrewer, RCurl, reshape2, rmarkdown, splines,
stats, stringr, tibble, utils, VennDiagram, VGAM
ggplot2, tidyr, foreach, doParallel, openxlsx, stringr, RCurl,
parallel, MASS, BiocParallel, limma
stats, BiocParallel, MatrixGenerics, methods,
SingleCellExperiment, SummarizedExperiment, SpatialExperiment
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
RCy3, KEGGREST, dplyr, purrr, tibble, pbapply
TreeSummarizedExperiment (>= 1.99.0), edgeR, methods,
SummarizedExperiment, S4Vectors, dirmult, dplyr, tibble, tidyr,
ape, diffcyt, ggnewscale, ggplot2 (>= 3.4.0), viridis, ggtree,
stats, utils, rlang
ape, dplyr, jsonlite, magrittr, methods, rlang, stats, tibble,
tidytree (>= 0.4.5), utils, yulab.utils (>= 0.1.6)
stats, utils, tidyr, dplyr, data.table, ggiraph, ggplot2,
hopach, ape, ggtree, patchwork, SingleCellExperiment, diffcyt,
edgeR, lme4, multcomp
methods, BiocGenerics, utils, ape, rlang, dplyr,
SummarizedExperiment, BiocParallel, IRanges, treeio
stats, utils, graphics, grDevices, segmented, gplots,
parallel, magrittr, BiocParallel, DT, S4Vectors,
SummarizedExperiment, methods, shiny, shinyFiles
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
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
Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn,
grDevices, graphics, stats, utils
Biobase, graphics, grDevices, splines, stats
class, ggplot2, hexbin, methods, scales, shiny, stats, utils,
RColorBrewer, S4Vectors
methods, data.table(>= 1.13.6), Matrix, stats, BiocParallel,
BiocNeighbors, SingleCellExperiment, SummarizedExperiment
methods, stats, httr, jsonlite, S4Vectors (>= 0.47.6)
AnnotationDbi, BiocFileCache, BiocBaseUtils, BiocGenerics,
httr2, jsonlite, methods, progress, rjsoncons, rlang, utils
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
MASS, pbkrtest (>= 0.4-4), lmerTest, Matrix (>= 1.4.0),
iterators, gplots, corpcor, matrixStats, RhpcBLASctl, reshape2,
gtools, remaCor (>= 0.0.15), fANCOVA, aod, scales, Rdpack,
rlang, lme4 (>= 1.1.33), grDevices, graphics, Biobase, methods,
utils, stats
BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix,
methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment,
stats, SummarizedExperiment, utils
Rcpp, Matrix, igraph, mgcv, RSpectra, grDevices, graphics,
stats
dplyr, DT, methods, ggplot2, grDevices, magrittr, patchwork,
plotly, purrr, rlang, shiny, stats, tibble, tidyr, htmlwidgets,
utils
utils, data.tree, ape, parallel, Rfast, stats
mixtools, stats, parallel, e1071, KernSmooth
data.table, AnnotationDbi, dendextend, dynamicTreeCut,
GOSemSim, GO.db, heatmaply, topGO, AnnotationForge, DT,
DiagrammeR, R.utils, RColorBrewer, UpSetR, biomaRt, fgsea,
ggplot2, htmlwidgets, igraph, methods, plotly, scales,
ComplexHeatmap, circlize
BiocBaseUtils, BiocGenerics, BiocIO (>= 1.15.1), jsonlite,
methods, S4Vectors, SingleCellExperiment, SpatialExperiment,
SummarizedExperiment
igraph, methods, plyr, ggplot2, scico, RColorBrewer, tm,
ggwordcloud, GSEABase, reshape2, grDevices, ggforce, msigdb,
ggrepel, textstem, tidygraph, stats, scales, ggraph
BiocParallel, bluster, DelayedArray, ggnewscale, ggplot2 (>=
3.4.0), grDevices, grid, lifecycle, Matrix, MatrixGenerics,
memuse, methods, patchwork, rlang, RSpectra, S4Vectors, scales,
scico, sf, SingleCellExperiment, SpatialExperiment, spdep,
stats, SummarizedExperiment, terra, utils, zeallot
matrixStats, limma, parallel, shiny, qvalue, grDevices, stats,
MultiAssayExperiment, clusterProfiler, DOSE, httr, 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
limma, randomForest, kernelshap, caret, lime, DT, methods,
SummarizedExperiment, ggplot2
SummarizedExperiment, SingleCellExperiment, Rfast, singscore,
AnnotationHub, ontologyIndex, tibble, dplyr, BiocParallel,
Matrix, minpack.lm, pracma, methods, readr, magrittr, progress,
quadprog
MSnbase (>= 2.33.3), mzR (>= 2.25.3), methods, Biobase,
BiocGenerics, ProtGenerics (>= 1.37.1), lattice,
MassSpecWavelet (>= 1.66.0), S4Vectors, IRanges,
SummarizedExperiment, MsCoreUtils (>= 1.19.2), MsFeatures,
MsExperiment (>= 1.5.4), Spectra (>= 1.16.1), progress,
RColorBrewer, MetaboCoreUtils (>= 1.11.2), data.table
BiocGenerics, genefilter, graphics, grDevices, gtools,
methods, stats, utils, mvtnorm, RColorBrewer, GeneMeta,
siggenes
BiocBaseUtils, BiocGenerics, BiocIO, jsonlite, methods,
S4Vectors, SingleCellExperiment, SpatialExperiment,
SummarizedExperiment, VisiumIO
SpatialExperiment, BiocFileCache, Matrix, S4Vectors,
SummarizedExperiment, methods, utils, EBImage, shiny,
HDF5Array, arrow, ggplot2, SingleCellExperiment, TENxIO, dplyr,
graphics, stats
methods, stats, utils, BBmisc, Biobase, grDevices, ggplot2,
scales, ComplexHeatmap, parallel, doParallel, Rmisc, grid,
nlme, PharmacoGx, downloader
mclust, plyr, alluvial, ggplot2, igraph, gridExtra, tools,
grDevices, graphics, utils, STRINGdb
methods, utils, stats, 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
variancePartition (>= 1.26.0), EnrichmentBrowser (>= 2.22.0),
GSEABase (>= 1.54.0), msigdbr, Rfast, ggplot2, tidyr, dplyr,
reshape2, progress, utils, Rdpack, stats
checkmate, dplyr, ggplot2, tidyr, SummarizedExperiment
BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
cpp11, BH(>= 1.62.0-1), RProtoBufLib, cytolib, Rhdf5lib,
flowWorkspace
cpp11, BH(>= 1.81.0.0), cytolib, RProtoBufLib
IRanges, XVector, Biostrings, Rcpp, S4Vectors
Rcpp, RcppArmadillo (>= 0.7.2), Rhdf5lib, beachmat, ClusterR
Rcpp, assorthead (>= 1.5.1), beachmat, BiocNeighbors,
Rigraphlib
Rcpp, beachmat, assorthead (>= 1.3.5), BiocNeighbors
Rcpp, RcppArmadillo (>= 14.0), RcppParallel, RcppEigen,
dqrng
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)
BiocStyle, rmarkdown, knitr, testthat, digest, Matrix,
alabaster.matrix
BiocStyle, rmarkdown, knitr, testthat, jsonlite
testthat, knitr, SummarizedExperiment, BiocParallel,
BiocStyle, rmarkdown
testthat, knitr, BiocStyle, chihaya, BiocSingular,
ResidualMatrix
testthat, knitr, rmarkdown, BiocStyle, DropletUtils, magick,
png, digest
knitr, BiocStyle, testthat (>= 3.0.0), BiocManager
BiocManager, BiocGenerics, S4Vectors, Seqinfo, GenomeInfoDb,
GenomicRanges, AnnotationHub, ExperimentHub, ensembldb, httr,
tidyr, r3dmol, bio3d, shiny, shiny.gosling, ggdist, 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
BiocStyle, dplyr, tidyr, graph, mia, KEGGREST, testthat (>=
3.0.0), knitr, rmarkdown
mia (>= 1.6.0), DT, S4Vectors, SingleCellExperiment,
SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr,
magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr,
tidyverse
ExperimentHub, SNFtool, knitr, rmarkdown, testthat
batchelor, BiocStyle, bluster, knitr, magick, matrixStats,
patchwork, RcppArmadillo, rmarkdown, scater, scran, Seurat,
splatter, testthat (>= 3.0.0), UpSetR
BiocFileCache, BiocStyle, knitr, processx, rhdf5 (>= 2.52.1),
rmarkdown, S4Vectors, Seurat, SeuratObject,
SingleCellExperiment, spelling, SummarizedExperiment, testthat
(>= 3.0.0), vctrs, withr, yaml
hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges,
rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db,
org.Mm.eg.db, humanCHRLOC, Rgraphviz, RUnit, BiocStyle, knitr
utils, hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db,
RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db,
reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75,
BiocStyle, knitr
biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy,
hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db,
rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit
IRanges, Seqinfo, GenomeInfoDb, GenomicRanges,
VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr,
AnnotationForge, rBiopaxParser, RUnit, txdbmaker, MSnbase, mzR,
Biostrings, CompoundDb, keras, ensembldb, SummarizedExperiment,
ExperimentHub, gdsfmt, rmarkdown, HubPub
BiocStyle, dplyr, knitr, readr, rmarkdown, tinytest
AnVIL, AnVILAz, AnVILGCP, BiocStyle, GCPtools, knitr,
rmarkdown, testthat (>= 3.0.0), tinytest
AnVIL, BiocStyle, knitr, rmarkdown, testthat, withr
knitr, BiocStyle, GCPtools, testthat (>= 3.0.0)
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)
BiocStyle, knitr, formatR, rmarkdown, magick, devtools
Biobase, BiocStyle, doSNOW, dynamicTreeCut, DT, GEOquery,
knitr, NMF, plyr, R2HTML, rmarkdown, reshape2, plotly, Rtsne,
testthat, zoo
affy, AnnotationDbi, AnnotationHub, apcluster, Biobase,
BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071,
ensembldb, GenomicDataCommons, GenomicRanges, GEOquery,
ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite,
knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme,
OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork,
pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite,
remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer,
statmod, testthat, UniProt.ws, writexl, XML
AWAggregatorData, BiocStyle, ExperimentHub, knitr, rmarkdown,
testthat (>= 3.0.0)
airway, ggplot2, testthat, EDASeq, knitr, BiocStyle,
RefManageR, sessioninfo, rmarkdown
BiocStyle, knitr, rmarkdown, testthat, roxygen2
knitr, rmarkdown, testthat, tximport, BiocStyle,
GenomicFeatures, Biostrings
testthat, interp, fields, pheatmap, viridis, rmarkdown,
spelling
knitr, rmarkdown, pals, scuttle, scater, scran, cowplot,
ggplot2, testthat (>= 3.0.0), harmony, Seurat, ExperimentHub,
spatialLIBD, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), BiocStyle
knitr, rmarkdown, BiocStyle, testthat, callr
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD
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
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
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, MultiAssayExperiment, RUnit
BiocManager, BiocStyle, curl, glue, knitr, rmarkdown,
sessioninfo, shinytest2
BiocParallel, testthat, BiocStyle, knitr, rmarkdown
airway, BiocStyle, boot, DESeq2, ggplot2 (>= 3.4.1),
GOSemSim, Hmisc, knitr (>= 1.43), org.Hs.eg.db, reactome.db,
rmarkdown, spelling, testthat (>= 3.1.5), WGCNA
BiocGenerics, tools, foreach, BBmisc, doParallel,
GenomicRanges, RNAseqData.HNRNPC.bam.chr14,
TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation,
Rsamtools, GenomicAlignments, ShortRead, RUnit, BiocStyle,
knitr, batchtools, data.table
BiocStyle, knitr, rmarkdown, testthat, tm, networkD3,
visNetwork, clipr, blastula, kableExtra, DiagrammeR,
SummarizedExperiment
BiocStyle, here, knitr, rmarkdown, testthat (>= 3.0.0)
GSEABase, airway, org.Hs.eg.db, DESeq2, limma, BiocFileCache,
GO.db, testthat, knitr, rmarkdown, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, ResidualMatrix
testthat, HDF5Array, BiocStyle, rmarkdown, knitr
BiocStyle, covr, devtools, knitr, pkgdown, RefManageR,
rmarkdown, sessioninfo, testthat, utils
BiocGenerics, BiocPkgTools, knitr, commonmark, BiocStyle
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, xml2
BiocStyle, roxygen2, devtools, testthat (>= 2.0.0), knitr,
rmarkdown, lgr
BiocStyle, httptest2, knitr, mockery, rmarkdown, testthat (>=
3.0.0)
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
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
testthat, knitr, rmarkdown, BiocStyle, arm, earth, ranger,
SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1)
testthat (>= 2.1.0), knitr, BiocStyle, rmarkdown, curl
knitr, rmarkdown, testthat (>= 3.2.3), covr, tradeSeq, scran,
slingshot, tools, ami, reshape2, plyr, fs, sparseMatrixStats,
ggVennDiagram, uwot, BiocStyle, DelayedMatrixStats, limma
RUnit, devtools, BiocGenerics, knitr, rmarkdown
knitr, rmarkdown, testthat, BiocStyle, dynamicTreeCut,
scRNAseq, scuttle, scater, scran, pheatmap, viridis, mbkmeans,
kohonen, apcluster, DirichletMultinomial, vegan, fastcluster
knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
lifecycle, tidyverse, shiny (>= 1.9.1), bslib (>= 0.8.0),
BiocStyle, knitr, rmarkdown, testthat
testthat, BiocStyle, knitr, rmarkdown, devtools
BiocStyle, knitr, ontologyIndex, rmarkdown, testthat (>=
3.0.0)
knitr, markdown, rmarkdown, STexampleData, testthat (>=
3.0.0), codetools, Matrix, lattice, cluster, survival, MASS,
nlme
BiocManager, devtools, knitr, pheatmap, rmarkdown, testthat
(>= 3.1.6)
BiocStyle, knitr, msqc1, RefManageR, rmarkdown, sessioninfo,
testthat, vdiffr
testthat (>= 3.1), knitr, rmarkdown, BiocStyle
BiocStyle, testthat, knitr, rmarkdown, emmeans, lme4,
lmerTest
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
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
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, rmarkdown, RUnit, BiocGenerics, magick, BiocStyle
limma, parallel, knitr, rmarkdown, ExperimentHub, testthat
BiocStyle, covr, knitr, rmarkdown, testthat, limma, ggplot2
knitr, rmarkdown, BiocStyle, testthat, tidyverse, ggpubr,
destiny, ggrepel
BiocStyle, caret, knitr, testthat, rmarkdown
CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle,
ExperimentHub
knitr, rmarkdown, dplyr, ggplot2, RUnit, BiocGenerics,
BiocManager, kableExtra, rgl
BiocStyle, knitr, rmarkdown, testthat, limma, Rtsne
data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics,
AnnotationDbi, destiny, RUnit, scater, scran, knitr,
org.Mm.eg.db, rmarkdown
zellkonverter, SingleCellExperiment, HDF5Array, tidyr,
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), mockery
BiocStyle, knitr, rmarkdown, testthat, ggplot2
knitr, rmarkdown, BiocStyle, testthat, covr, UpSetR, scater,
scMerge, fgsea, escape, pheatmap
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,
GenomeInfoDb, Rsamtools, GenomicInteractions, GenomicRanges,
IRanges, AnnotationHub
BiocGenerics, S4Vectors, BiocSingular, ResidualMatrix,
BiocStyle, testthat, rmarkdown, knitr
mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit,
BiocGenerics
msdata (>= 0.19.3), roxygen2, BiocStyle (>= 2.5.19),
testthat, knitr (>= 1.1.0), rmarkdown, mzR (>= 2.41.4),
MsBackendMetaboLights (>= 1.3.1), vdiffr, RColorBrewer
Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14,
BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown,
BiocStyle
BiocStyle, knitr, rmarkdown, testthat, webshot
limma, edgeR, car, Rmixmod, gridExtra (>= 2.0.0), cowplot,
BiocStyle, pamr, PoiClaClu, knitr, htmltools, gtable, scales,
e1071, rmarkdown, IRanges, robustbase, glmnet, class,
randomForestSRC, MatrixModels, xgboost, data.tree, ggnewscale,
TOP, BiocNeighbors
testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), rmarkdown,
BRAIN, UniProt.ws (>= 2.36.5)
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, BiocManager, jsonlite, readr, org.Hs.eg.db,
quarto, testthat
knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics,
covr
ComplexHeatmap, covr, knitr, rmarkdown, testthat, ggrepel,
BiocStyle, BiocManager, remotes, shiny, gprofiler2, purrr,
data.table, R.utils
BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork
knitr, BiocStyle, testthat (>= 3.0.0), aricode, ggplot2,
patchwork, dplyr, scattermore
MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics,
gbm, mgcv, corpcor, limma, st, mvtnorm
minet, Rgraphviz, RUnit, BiocGenerics, igraph
testthat, knitr, rmarkdown, BiocStyle, SeuratObject,
BiocFileCache, xml2
testthat (>= 3.0.0), sessioninfo, knitr, BiocStyle,
rmarkdown, covr
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
testthat (>= 1.0.0), knitr, markdown, dendsort, jpeg, tiff,
fastcluster, EnrichedHeatmap, dendextend (>= 1.0.1), grImport,
grImport2, glue, GenomicRanges, gridtext, pheatmap (>= 1.0.12),
gridGraphics, gplots, rmarkdown, Cairo, magick
knitr, rmarkdown, testthat, BiocStyle (>= 2.5.19),
MsBackendMgf
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
BiocManager, BiocStyle, ggplot2, glue, knitr, mbkmeans,
patchwork, rmarkdown, scater, SFEData,
SpatialFeatureExperiment, TENxPBMCData, testthat (>= 3.0.0)
knitr, testthat, rmarkdown, covr, viridis, ggplot2,
RColorBrewer, randomForest, tidyr, TSCAN, DelayedMatrixStats
BiocStyle, ggplot2, knitr, rmarkdown, 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,
SummarizedExperiment, S4Vectors
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
ReportingTools, BiocStyle
BiocStyle, BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown,
testthat
hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats, RUnit
BiocStyle, RUnit, knitr, rmarkdown, dreamlet, muscat,
ExperimentHub, scater, HMP, reshape2, glue, tidyverse,
BiocGenerics, compositions
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle, magrittr,
igraph, dplyr
BiocStyle, knitr, patchwork, rmarkdown, scRNAseq, scuttle,
stringr, testthat (>= 3.0.0)
testthat (>= 3.0.0), DT, BiocStyle, knitr, rmarkdown,
SummarizedExperiment, SingleCellExperiment
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
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, fields, knitr, rmarkdown, RColorBrewer, scater,
scRepertoire, DelayedMatrixStats, slingshot, testthat
EBcoexpress, testthat, EBarrays, GeneNet, mclust, minqa,
SummarizedExperiment, Biobase, knitr, rmarkdown, BiocStyle,
edgeR
testthat (>= 3.0.0), knitr, Seurat, SeuratObject, tidyverse,
rmarkdown, BiocStyle
Biobase, BiocManager, BiocSet, edgeR, DESeq2, GEOquery, GSA,
knitr, limma, readxl, rmarkdown, S4Vectors,
SummarizedExperiment, testthat, covr
glmnet (>= 4.1-7), GSVA, viper, fgsea (>= 1.15.4), AUCell,
SummarizedExperiment, rpart, ranger, BiocStyle, covr, knitr,
pkgdown, RefManageR, rmarkdown, roxygen2, sessioninfo,
pheatmap, testthat, OmnipathR, Seurat, ggplot2, ggrepel,
patchwork, magick
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
sessioninfo, knitr (>= 1.6), BiocStyle (>= 2.5.19),
RefManageR, rmarkdown (>= 0.3.3), testthat, 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
lattice, parallel, MASS, RColorBrewer, DT, knitr, rmarkdown,
BiocStyle
knitr, rmarkdown, testthat, UpSetR, BiocStyle
plotly, testthat, Seurat (>= 2.2), DESeq2, edgeR,
ggplot.multistats, knitr, rmarkdown, BiocStyle, scRNAseq,
ggrastr (>= 0.2.0), ComplexHeatmap, bluster, scater, scran,
MASS
msigdbr, org.Hs.eg.db, org.Mm.eg.db, minfi, knitr, rmarkdown,
GO.db, KEGGREST, testthat,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19,
IlluminaHumanMethylation450kanno.ilmn12.hg19, BiocStyle, RUnit
BiocStyle, ggplot2, Hmisc, kableExtra, knitr, pheatmap,
rmarkdown, testthat (>= 3.0.0), withr, airway
BiocStyle, airway, tidyverse, knitr, rmarkdown, testthat (>=
3.0.0), dominatRData
knitr, patchwork, rmarkdown, Seurat, testthat, formatR,
BiocFileCache, SingleCellExperiment
BiocStyle, knitr, rmarkdown, curatedOvarianData, testthat
prettydoc, clusterProfiler, gson (>= 0.0.5), knitr, memoise,
org.Hs.eg.db, rmarkdown, testthat
BiocStyle, knitr, pander, rmarkdown, muscat, ExperimentHub,
RUnit, muscData, scater, scuttle
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, digest, knitr, rmarkdown, shiny
ecoliLeucine, ecolicdf, graph, multtest, affy
arrow, jsonlite, knitr, Matrix, readr, rhdf5, SeuratObject,
splines, AnnotationDbi, Biobase, BiocStyle, org.Hs.eg.db,
SummarizedExperiment
knitr, tximportData, testthat (>= 3.0.0)
SummarizedExperiment, testthat, Biobase, survminer,
affycoretools, knitr, plotROC, limma, rmarkdown
minfiData, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
ALL, BiocStyle, ComplexHeatmap, DESeq2, ReportingTools,
airway, biocGraph, hgu95av2.db, geneplotter, knitr, msigdbr,
rmarkdown, statmod
clusterProfiler, dplyr, europepmc, ggarchery, glue, ggforce,
ggHoriPlot, ggtreeExtra, ggupset, ggplotify, ggridges,
grDevices, gridExtra, ggstar, org.Hs.eg.db, quarto, scales,
tibble, tidyr
BiocStyle, knitr, rmarkdown, ggplot2, scatterpie, ggtangle,
ggrepel, testthat, ggnetwork, magick
roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase,
testthat
knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown,
GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle
knitr, rmarkdown, testthat (>= 3.0.0), sessioninfo
BiocStyle, knitr, rmarkdown, magrittr, kableExtra, testthat
(>= 3.0.0)
testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors,
IRanges, SummarizedExperiment, antiProfilesData,
hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny,
minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr,
AnnotationHub
testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9),
Mus.musculus, Biobase, BiocStyle
STexampleData, BumpyMatrix, knitr, rmarkdown, BiocStyle,
ggpubr, scran, scater, scuttle, Seurat, hexbin
ggplot2, ggvis, plotly, ggrepel, knitr, rmarkdown, ALL,
hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment, GO.db
rworkflows, remotes, knitr, BiocStyle, rmarkdown, testthat
(>= 3.0.0), readxl, memoise, markdown, sctransform, DESeq2,
MAST, DelayedMatrixStats, ggdendro, scales, patchwork
knitr, BiocStyle, rmarkdown, HubPub, GenomicAlignments
GenomeInfoDb, RUnit, knitr, BiocStyle, rmarkdown, HubPub
BiocStyle, knitr, rmarkdown, testthat, covr, stats, scran,
scater, scds, TENxPBMCData, airway
testthat (>= 2.1.0), knitr, rmarkdown, htmltools, BiocStyle
BiocStyle, countrycode, knitr, rmarkdown, testthat (>= 3.0.0)
BiocFileCache, BiocStyle, ggtree, graphics, knitr, memuse,
rmarkdown, spelling, testthat (>= 3.0.0)
rmarkdown, Seurat, ggpubr, knitr, testthat (>= 3.0.0),
BiocStyle
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
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, 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
oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM,
hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf,
hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData
knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment,
SummarizedExperiment, airway
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
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, BumpyMatrix, futile.logger, gDRstyle (>= 1.7.1),
gDRtestData (>= 1.7.1), kableExtra, knitr, markdown, purrr,
rmarkdown, SummarizedExperiment, testthat, yaml
BiocStyle, gDRstyle (>= 1.7.1), gDRimport (>= 1.7.1),
gDRtestData (>= 1.7.1), IRanges, knitr, pkgbuild, qs, testthat,
yaml
BiocStyle, gDRtestData (>= 1.7.1), gDRstyle (>= 1.7.1),
knitr, purrr, qs, testthat
BiocManager, BiocStyle, futile.logger, gDRstyle (>= 1.7.1),
gDRtestData (>= 1.7.1), IRanges, knitr, lintr, mockery, purrr,
rcmdcheck, rmarkdown, scales, testthat, tools, withr, yaml
parallel, digest, Matrix, crayon, RUnit, knitr, markdown,
rmarkdown, BiocGenerics
knitr, rmarkdown, testthat (>= 3.0.0), DESeq2, mosdef,
GeneTonic, htmltools, AnnotationDbi, macrophage, topGO,
biomaRt, ReactomePA, clusterProfiler, BiocStyle, org.Hs.eg.db
knitr, RUnit, testthat, BiocGenerics, rmarkdown, markdown
testthat (>= 2.0.0), rmarkdown, knitr, dplyr, covr, ggplot2,
ggrepel, BiocStyle, microbenchmark, magick, purrr, pheatmap,
viridis, poolr, listviewer, shiny
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
knitr, rmarkdown, foreach, doRNG, doParallel, Biobase,
SummarizedExperiment, testthat, methods, BiocStyle
GenomeInfoDbData, R.utils, data.table, GenomicRanges,
Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2,
BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr
knitr, rmarkdown, devtools, roxygen2, pkgdown, usethis,
BiocStyle, testthat, forcats, stats, wordcloud, circlize,
EnrichmentBrowser, clusterProfiler, msigdbr, cluster,
RColorBrewer, reshape2, tibble, BiocManager, bcellViper, readr,
utils
BiocCheck, roxygen2, knitr, rmarkdown, testthat
knitr, rmarkdown, dplyr, dbplyr, tm, wordcloud
rmarkdown, knitr, testthat (>= 3.0.0), parallel, ggiraph,
Seurat, SpatialExperiment (>= 1.4.0), SpatialDecon, patchwork
knitr, rmarkdown, BiocGenerics, testthat, covr, markdown,
quarto, DropletUtils, SingleCellExperiment
knitr, rmarkdown, DESeq2, S4Vectors, ChAMP, impute, tidyr,
clusterProfiler, org.Hs.eg.db, edgeR, limma, quantreg, minfi,
IlluminaHumanMethylation450kanno.ilmn12.hg19, dearseq, NOISeq,
testthat (>= 3.0.0), CATT, TCGAbiolinks, enrichplot, GEOquery,
BiocGenerics
devtools, knitr, rmarkdown, roxygen2, limma, topGO, testthat
(>= 3.0.0)
airway, knitr, DESeq2, 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)
ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl,
ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat
(>= 3.0.0), yulab.utils
aplot, BiocParallel, forcats, ggforce, ggnewscale, igraph,
knitr, ks, Matrix, prettydoc, rmarkdown, scran, scater,
scatterpie (>= 0.2.4), scuttle, shadowtext, sf, SeuratObject,
SpatialExperiment, STexampleData, testthat (>= 3.0.0), MASS
Biostrings, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
BiocStyle, rmarkdown, knitr, OSTA.data, VisiumIO, arrow,
STexampleData, BumpyMatrix, scater, scran, uwot, testthat,
patchwork
emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr,
prettydoc, rmarkdown, testthat, tibble, glue, Biostrings
aplot, cluster, knitr, MASS, mdendro, prettydoc, pvclust,
rmarkdown, testthat (>= 3.0.0), treeio, yulab.utils
treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc,
markdown, testthat (>= 3.0.0), pillar
knitr, prettydoc, rmarkdown, BiocStyle, testthat (>= 3.0.0)
roxygen2, knitr, rmarkdown, testthat, BiocStyle
testthat (>= 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
knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat
AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr,
org.Hs.eg.db, prettydoc, readr, rmarkdown, testthat, tidyr,
tidyselect, ROCR
BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db,
org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db,
org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db,
org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db,
org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db,
ggplot2, ggrepel, DT, magick
hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter,
RColorBrewer, xtable, SparseM, GSEABase, geneplotter,
org.Hs.eg.db, RUnit, BiocGenerics, BiocStyle, knitr
SparseM (>= 0.36), XML, RBGL, RUnit, cluster, BiocStyle,
knitr
checkmate, a4Preproc, ALL, BiocStyle, clipper, codetools,
hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db,
parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat,
topologyGSA (>= 1.4.0)
MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate,
org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR,
BiocStyle
hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools,
testthat, BiocStyle, knitr, RUnit
BiocStyle, GSE62944, knitr, rappdirs, rmarkdown
GSEABase,Category, multtest, ALL, annotate, hgu95av2.db,
genefilter, GOstats, RColorBrewer
knitr, rmarkdown, BiocStyle, clusterProfiler, testthat, tm
SummarizedExperiment, pasilla, org.Dm.eg.db, AnnotationDbi,
knitr, plotly, WGCNA, rmarkdown
knitr, rmarkdown, ggplot2, BiocStyle, genefu, survcomp,
Biobase, survminer, breastCancerTRANSBIG, breastCancerUPP,
iC10TrainingData, pamr, testthat
RUnit, BiocStyle, knitr, rmarkdown, limma, RColorBrewer,
org.Hs.eg.db, genefilter, edgeR, GSVAdata, sva, ggplot2,
TENxPBMCData, scuttle, scran, igraph, shiny, shinydashboard,
ggplot2, data.table, plotly, future, promises, shinybusy,
shinyjs
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
HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit,
RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA,
affydata, minfiData, sva
RColorBrewer, pheatmap, MASS, patchwork, testthat
BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
parallel, ggplot2, reshape2, gdsfmt, SNPRelate, SeqArray,
knitr, markdown, rmarkdown, Rsamtools
knitr, annotate, gwascat, testthat, rmarkdown
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
testthat (>= 3.0.0), knitr, ggplot2, rmarkdown, BiocStyle,
pryr
AnnotationHubData, ExperimentHubData, GenomeInfoDbData,
testthat, knitr, rmarkdown, BiocStyle,
SingleCellExperiment, SummarizedExperiment, Seurat,
SeuratObject, ggplot2, progress, testthat, splatter, scater,
devtools, knitr, rmarkdown, BiocStyle, ExperimentHub
knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot,
DescTools, RColorBrewer
knitr, rmarkdown, pwalign, msa, ape, testthat, seqinr
knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
GenomicAlignments, parallel, testthat, knitr, rmarkdown,
BiocStyle, ggplot2, dplyr, scales, ggseqlogo
BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
ggforce, ggrepel, patchwork
ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat,
Matrix, BiocStyle, knitr, rmarkdown, devtools
RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2),
BiocStyle
BiocManager, BiocStyle, knitr, curl, glue, rmarkdown,
sessioninfo, testthat, tibble, GenomicDataCommons
BiocStyle, dplyr, ggraph, ggplot2, igraph, knitr, markdown,
Peptides, randomForest, rmarkdown, scRepertoire, spelling,
testthat, tidygraph, viridis
BiocManager, BiocStyle, knitr, mockery, spelling, rmarkdown,
testthat (>= 3.0.0), withr
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), DT
BiocGenerics, rmarkdown, BiocStyle, knitr, testthat, DT
testthat (>= 3.0.0), ggfortify, shinyWidgets, pROC, tuneR,
knitr, curl, readxl, reshape2, vroom, here, enrichR, rmarkdown
knitr, rmarkdown, keras, tensorflow, glmnetUtils, e1071
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0),
SummarizedExperiment
knitr, rmarkdown, testthat, EnrichedHeatmap, GenomicRanges,
data.table, circlize, GenomicFeatures, tidyverse, tidyHeatmap,
cluster, org.Hs.eg.db, simplifyEnrichment, GO.db, SC3,
GOexpress, SingleCellExperiment, scater, gplots, pheatmap,
airway, DESeq2, DT, cola, BiocManager, gridtext, HilbertCurve
(>= 1.21.1), shinydashboard, SummarizedExperiment, pkgndep, ks
testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite,
processx, attempt, BiocStyle, httr
gProfileR, topGO, org.Dm.eg.db, rmarkdown, testthat
XVector, GenomicRanges, Rsamtools, GenomicAlignments,
GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset,
RUnit, BiocStyle
testthat, covr, knitr, BiocStyle, sessioninfo, rmarkdown,
roxygen2, withr, extraDistr, ggalluvial, scales, gridExtra,
R.utils, RefManageR, flexdashboard, circlize, plotly, gtools,
eulerr, openxlsx, jsonlite, pheatmap, BiocParallel, progressr,
future, doFuture, foreach, psych, Rcapture
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)
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
BiocStyle, knitr, rmarkdown, spatstat, Seurat, statmod,
corrplot, ggplot2, ggraph, ggrepel, gridExtra, reshape2,
igraph, jsonlite, vdiffr, patchwork, ggpubr, tidyr,
SpatialFeatureExperiment, ExperimentHub, TENxXeniumData,
SingleCellExperiment, SFEData, Matrix, data.table, scran,
scater, grid, GenomeInfoDb, testthat (>= 3.0.0)
RBGL, testthat, RColorBrewer, org.Hs.eg.db, hgu133plus2.db,
SPIA
RUnit, BiocGenerics, BiocStyle, knitr, markdown
BiocManager, BiocStyle (>= 2.26), httptest, knitr, lattice,
msdata, OrgMassSpecR, protViz, S4Vectors, Spectra, testthat,
mzR
BiocGenerics, BiocStyle, testthat, knitr, rmarkdown
BSgenome.Hsapiens.UCSC.hg19, BiocStyle, Cairo, rmarkdown,
knitr, R.utils, tinytest, GenomeInfoDb, GenomicRanges, IRanges,
MutationalPatterns, magick
RUnit, knitr, BiocStyle, gwascat, rmarkdown, snpStats,
VariantAnnotation, GenomeInfoDb, ensembldb, EnsDb.Hsapiens.v75,
Rsamtools, GenomicFiles (>= 1.13.6)
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
BiocStyle, devtools, knitr, roxygen2, rmarkdown, testthat (>=
3.0.0), S4Vectors,
SpatialDatasets, BiocStyle, knitr, rmarkdown, testthat (>=
3.0.0)
knitr, rmarkdown, Seurat, parallelDist, uwot, NMF, fpc,
dendextend, cluster, Rtsne, scRNAseq, Matrix
LRcellTypeMarkers, BiocStyle, knitr, rmarkdown, roxygen2,
testthat
ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat,
Biobase
knitr, testthat (>= 2.1.0), rmarkdown, markdown, kableExtra
testthat, knitr, rmarkdown, BiocStyle, MACSdata
berryFunctions, Biostrings, BSgenome,
BSgenome.Hsapiens.UCSC.hg19, GenomicRanges, IRanges, knitr,
mclust, MultiAssayExperiment, NMF, R.utils, RaggedExperiment,
rmarkdown, S4Vectors
gridExtra, VennDiagram, qqman, LOLA, RUnit, rmutil,
rmarkdown, JASPAR2018, TFBSTools, seqLogo, knitr, devtools,
BiocGenerics, BiocManager
BiocStyle, covr, knitr, rmarkdown, ggplot2, sessioninfo,
testthat (>= 3.0.0)
devtools, markdown, renv, testthat, BiocManager, knitr,
rmarkdown, roxygen2, mockery, covr, magick, BiocStyle
knitr, rmarkdown, BiocStyle, testthat, covr
biomaRt (>= 2.34.1), circlize (>= 0.4.11), STRINGdb (>=
2.2.0), httr (>= 1.2.1), IRanges (>= 2.8.2), S4Vectors (>=
0.12.2), knitr, testthat, readr, rmarkdown
signal, waveslim, BiocStyle, knitr, rmarkdown, RUnit, bench
knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(>
6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF,
TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer,
BiocStyle, scater, DelayedArray, HDF5Array, zinbwave, dplyr
BiocManager, BiocStyle, clusterProfiler, ComplexHeatmap,
depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite,
knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore,
splatter, testthat (>= 3.0.0), UpSetR
Matrix, sparseMatrixStats, SparseArray, DelayedArray,
DelayedMatrixStats, SummarizedExperiment, testthat (>= 2.1.0)
knitr, markdown, BiocStyle, testthat (>= 3.0.0)
beachmat, HDF5Array, Rhdf5lib, BiocStyle, TENxPBMCData,
scater, DelayedMatrixStats, bluster, knitr, testthat, rmarkdown
gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr,
pander, devtools, testthat, GSVA
testthat, knitr, rmarkdown, fgsea, BiocManager
knitr, markdown, rmarkdown, BiocStyle, testthat (>= 2.1.0)
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, msentropy, DT, microbenchmark, mzR
BiocStyle, testthat, knitr, rmarkdown, robustbase
RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown
BiocStyle, knitr, rmarkdown, DT, ggraph, tidyverse, testthat
(>= 3.0.0)
BiocGenerics, graphics (>= 4.4), grDevices (>= 4.4), knitr
(>= 1.48), testthat (>= 3.2.1.1)
BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC,
RUnit
BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0)
BiocStyle, doParallel, testthat, knitr, rmarkdown
BiocStyle, knitr, rmarkdown, devtools, R.utils
ape, cluster, foreach, doParallel, dplyr, GGally, ggplot2,
igraph, network, reshape2, sna, vegan, rmarkdown, knitr,
BiocStyle, testthat, mia, miaViz, colourvalues, philentropy
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, ggalluvial (>= 0.11.1), forcats, phyloseq,
aplot, ggnewscale, ggside, ggh4x, hopach, parallel, shadowtext,
DirichletMultinomial, ggpp, BiocManager
testthat (>= 3.0.0), rmarkdown, knitr, BiocStyle
testthat, mvtnorm, scater, scran, covr, knitr, rmarkdown,
uwot, scuttle, BiocStyle, MouseGastrulationData,
MouseThymusAgeing, magick, RCurl, MASS, curl, scRNAseq,
graphics, sparseMatrixStats
knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind,
affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1
scRNAseq, scater, BiocStyle, knitr, rmarkdown
BiocGenerics, RUnit, knitr, rtracklayer, utils, rmarkdown
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny
BiocStyle, knitr, rmarkdown, R.cache, SPONGE
BiocStyle, covr, earth, future, igraph (>= 1.2.7), iml,
kernlab, knitr, MASS, rmarkdown, RSNNS, testthat (>= 3.0.0),
xgboost
stringi, testthat (>= 2.1.0), HGNChelper,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Biobase, BiocStyle, GSVA, methods, rmarkdown, knitr,
SummarizedExperiment, testthat
BiocStyle, knitr, rmarkdown, mime, testthat, microbenchmark,
magick, vdiffr, kableExtra, devtools
class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL,
hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07),
golubEsets, ada, keggorthology, kernlab, mboost, party, klaR,
BiocStyle, knitr, testthat, airway
GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db,
org.Cf.eg.db, org.Mmu.eg.db, KEGGREST, annotate, Rgraphviz,
GOstats, graph, limma, mouse4302.db, reactome.db
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
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)
Biobase, knitr, seqinr, ape (>= 5.1), phangorn, pwalign
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, 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
MSnbase, testthat, xcms, BiocStyle, knitr, rmarkdown,
msPurityData, CAMERA, RPostgres, RMySQL
multcomp, gridExtra, knitr, BiocStyle, RefManageR,
sessioninfo, rmarkdown, testthat, tidyverse, plotly, MsDataHub,
MSnbase, matrixStats, MsCoreUtils, covr
BiocStyle, knitr, rmarkdown, tinytest, covr, markdown,
mockery, kableExtra
data.table, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0),
mockery, MSstatsConvert
BiocStyle, knitr, rmarkdown, covr, tinytest, gghighlight
BiocStyle, knitr, rmarkdown, covr, tinytest, dplyr
knitr, rmarkdown, tinytest, covr, mockery, testthat (>=
3.0.0)
MSstats, MSstatsTMT, tidyverse, boot, purrr, gridExtra,
knitr, rmarkdown, BiocStyle, testthat
rmarkdown, tinytest, sessioninfo, knitr, testthat (>= 3.0.0),
shinytest2,
HDF5Array, rmarkdown, knitr, fs, testthat, BiocStyle, covr,
SingleCellMultiModal, CiteFuse, scater
knitr, rmarkdown, gplots, RUnit, BiocGenerics,
preprocessCore, Biobase, GEOquery
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
msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19),
knitr, XML, rmarkdown
biovizBase, ggbio, RUnit, rmarkdown, knitr, qpdf
grid, kableExtra, knitr, NanoStringDiff, pheatmap, plotly,
rlang, rmarkdown, ruv, RUVSeq, shiny, testthat, xlsx
testthat, BiocStyle, knitr, rmarkdown, covr, scater, scran,
DropletUtils, igraph, BiocFileCache, Seurat
knitr, BiocGenerics, rmarkdown, RUnit, BiocStyle
rBiopaxParser (>= 2.1), RCurl, graph, knitr, rmarkdown,
BiocStyle
RUnit, BiocGenerics, org.Sc.sgd.db, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dr.eg.db, org.Ce.eg.db,
org.Cf.eg.db, org.Dm.eg.db, org.At.tair.db, rmarkdown, knitr,
markdown
knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI,
pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel, uwot
testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp,
BiocStyle, knitr
BiocStyle, Cairo, DT, knitr, pander, readr, testthat,
truncnorm
BiocFileCache, BiocStyle, circlize, ggpubr, KernSmooth,
knitr, piggyback, reshape2, rmarkdown, rpart, Seurat (>=
4.0.0), spatstat.explore, stringr, survival, tidyverse,
testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, STexampleData,
WeberDivechaLCdata, scran, ggplot2, testthat
knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics
(>= 0.8.0)
knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
BiocStyle, fpc, igraph, knitr, missForest, notameViz,
notameStats, pcaMethods, RUVSeq, testthat
batchCorr, BiocStyle, igraph, knitr, notameStats, pcaMethods,
Rtsne, testthat
testthat, devtools, knitr, rprojroot, rmarkdown, ggplot2,
BiocStyle
ALL, genefilter, limma, hgu95av2.db, ReportingTools,
BiocStyle
BiocStyle, BiocGenerics, knitr, rmarkdown, testthat
BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2,
pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr,
pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma,
RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt,
AnnotationDbi, ACME, RCurl
BiocStyle, knitr, rmarkdown, snpStats, brgedata
BiocStyle, knitr, rmarkdown, testthat, GEOquery,
VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges,
FDb.InfiniumMethylation.hg19, snpStats
knitr, rmarkdown, BiocStyle, magick, testthat
BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr,
mlrMBO, parallelMap, ParamHelpers, R.matlab, sigmajs, smoof,
testthat
RcppProgress, knitr, rmarkdown, roxygen2, devtools, usethis,
desc, testthat (>= 3.0.0)
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
rworkflows, remotes, knitr, BiocStyle, markdown, rmarkdown,
testthat (>= 3.0.0), piggyback, magick, GenomeInfoDbData, ape,
phytools, rphylopic (>= 1.0.0), TreeTools, ggimage, OmaDB
BiocStyle, DropletUtils, knitr, VisiumIO, SpatialExperimentIO
knitr, rmarkdown, BiocStyle, testthat, ggplot2, gridExtra,
grid, reshape2, scales
testthat, BiocStyle, knitr, rmarkdown, KEGGREST, missMDA,
ggplot2, ggrepel, car, cowplot, reshape2
RUnit, sandwich, MASS, knitr, GenomeInfoDb, GenomicRanges,
gwascat, BiocStyle, rmarkdown
AnnotationDbi, BiocStyle, biomaRt, covr, DESeq2, jsonlite,
knitr, org.Hs.eg.db, rmarkdown, scales, testthat (>= 3.0.0),
vdiffr
airway, circlize, grDevices, knitr, RCurl, reshape2,
rmarkdown, SummarizedExperiment, survminer, testthat, tidyverse
BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb
testthat (>= 3.0.0), msigdbr, BiocStyle, rmarkdown, knitr,
HDF5Array
testthat, devtools, faahKO, msdata, knitr, rmarkdown, pander,
BiocStyle
diffviewer, gridExtra, testthat (>= 3.0.0), vdiffr,
rmarkdown, BiocStyle, knitr, withr, qpdf, shinytest2, devtools,
R.devices, usethis, rlang, magick, cowplot
statmod, BiocStyle, knitr, rmarkdown, tidyr
knitr, markdown, rmarkdown, BiocStyle, PepsNMRData
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
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
BiocManager, knitr, rtracklayer, testthat,
BSgenome.Hsapiens.UCSC.hg19
ExperimentHub, mixOmics, ggplot2, testthat, tidyr, scales,
minfi, EpiDISH, knitr, rmarkdown
BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>=
3.0.0)
knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf,
BiocStyle, biocViews, testthat (>= 3.0.0)
knitr, htmltools, BiocStyle, rmarkdown, testthat
devtools, knitr, rmarkdown, testthat, airway, IRanges, here
testthat, covr, knitr, rmarkdown, BiocStyle, gridExtra,
magick
testthat (>= 3.0.0), BiocStyle, knitr, DT, dplyr, kableExtra,
scico, cowplot, ggnetwork, ggplot2, tidyr, STexampleData
knitr, DT, ontologyPlot, testthat, rmarkdown, BiocStyle
testthat (>= 3.0.0), knitr, rmarkdown, ddPCRclust
BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics
rmarkdown, knitr, testthat (>= 3.0.0), BiocStyle
quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
airway, biomaRt, BiocFileCache, broom, Seurat,
SingleCellExperiment, DESeq2, BiocStyle, knitr, readr, readxl,
pheatmap, tibble, rmarkdown, testthat (>= 2.1.0)
BiocStyle, CoGAPS, gridExtra, grid, testthat, devtools,
knitr, rmarkdown, ComplexHeatmap, gplots, SeuratObject
testthat, rmarkdown, pRolocdata (>= 1.43.2), roxygen2,
xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.41.0), dplyr,
akima, fields, vegan, GO.db, AnnotationDbi, Rtsne (>= 0.13),
nipals, reshape, magick, umap
pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown, testthat
(>= 3.0.0)
testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, DT
testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
car, rstudioapi, spelling
msdata, rpx, mzID, mzR, SummarizedExperiment, BiocStyle,
rmarkdown, knitr, factoextra, vdiffr (>= 1.0.0), testthat
knitr, rmarkdown, BiocStyle, testthat (>= 2.1.0), ptairData,
ropls
pumadata, affydata, snow, limma, ROCR,annotate
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
devtools, DESeq2, knitr, rmarkdown, testthat, BiocStyle
bodymapRat, quantro, knitr, rmarkdown, BiocStyle, testthat
BiocFileCache, BiocStyle, covr, knitr, limma, RefManageR,
rmarkdown, sessioninfo, testthat (>= 3.0.0)
testthat, BiocStyle, knitr, rmarkdown, covr
AnnotationDbi, BiocStyle, dplyr, ExperimentHub, GEOquery,
knitr, macrophage, org.Hs.eg.db, reshape2, rmarkdown, testthat,
tibble
rmarkdown, knitr, RUnit, BiocGenerics, BiocStyle
QUBICdata, qgraph, fields, knitr, rmarkdown
rmarkdown, BiocStyle, knitr, pander, markdown
knitr, BiocParallel, lme4, nlme, rmarkdown, BiocStyle,
testthat (>= 2.1.0), limma, sva
markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>=
3.0.0)
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), withr
BiocStyle (>= 2.28), ExperimentHub, tartare, knitr, testthat
BiocStyle (>= 2.5), ExperimentHub, knitr, protViz (>= 0.7),
rmarkdown, tartare (>= 1.5), testthat
Rgraphviz, XML, RUnit, BiocGenerics, BiocStyle, knitr
Rgraphviz, RCurl, graph, RUnit, BiocGenerics, RBGL, igraph
testthat, parallel, BiocStyle, knitr, rmarkdown
knitr, RColorBrewer, sqldf, BiocGenerics, testthat,
BiocStyle, jsonlite, heatmaply, glmnet, foreach, doSNOW,
parallel, rmarkdown
testthat, knitr, BiocStyle, rmarkdown, mclust, tidyverse,
tinytex
BiocStyle, testthat, knitr, rmarkdown, base64enc, graph
BiocStyle, knitr, rmarkdown, igraph, grDevices
devtools, knitr, ReactomeGSA.data, rmarkdown, scater, scran,
scRNAseq, scuttle, Seurat (>= 3.0), SingleCellExperiment,
testthat
BiocStyle, clusterProfiler, knitr, rmarkdown, org.Hs.eg.db,
prettydoc, testthat
testthat, igraph, XML, BiocManager, RCurl, bookdown,
rappdirs, yaml, BiocParallel, OSCA.intro, OSCA.workflows
minfiData, minfiDataEPIC, knitr, testthat, ggplot2,
gridExtra, rmarkdown, BiocStyle, GenomicRanges, limma,
ExperimentHub, AnnotationHub
knitr, rmarkdown, markdown, BiocStyle, TreeAndLeaf
knitr, rmarkdown, testthat, biocViews, BiocCheck, BiocStyle,
airway
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
testthat (>= 2.1.0), BiocStyle, knitr, rmarkdown, kableExtra,
BiocManager, stringr, stringi, ggplot2, tibble, lipidr
RUnit, BiocStyle, BiocGenerics, xtable, sna
bit64, BiocStyle, knitr, rmarkdown, testthat, bench, dplyr,
ggplot2, mockery, BiocParallel, curl
knitr, testthat, BiocStyle, DT, rmarkdown
BiocStyle, knitr, rmarkdown, tinytest, rhdf5 (>= 2.47.7)
BiocStyle, knitr, rmarkdown, tinytest, mockery
BiocStyle, knitr, rmarkdown, testthat, devtools
BiocStyle, CAMERA, gplots, knitr, magick, rmarkdown,
RMassBankData (>= 1.33.1), RUnit, xcms (>= 1.37.1)
readxl, knitr, rmarkdown, reshape2, pander, testthat
BiocStyle, knitr, PCAtools, rmarkdown, tidyr, stringr,
testthat (>= 3.0.0)
BiocStyle, knitr, rmarkdown, GSEABenchmarkeR,
EnrichmentBrowser, preprocessCore, DESeq2
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
testthat, BiocStyle, knitr, rmarkdown, ALL, RCy3, caret,
e1071, parallel, doParallel
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
RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown
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
knitr, rmarkdown, BiocManager, BiocStyle, remotes, ggpubr,
ggcorrplot, ggh4x, testthat (>= 3.0.0)
BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
knitr, rmarkdown, DESeq2, limma, SummarizedExperiment,
airway, BiocStyle, matrixTests, BiocManager
knitr, testthat, rmarkdown, BiocStyle, VariantAnnotation
BiocParallel, SparseArray (>= 0.0.4), DelayedArray,
HDF5Array, testthat, knitr, rmarkdown, BiocStyle
IRanges, GenomicRanges, SummarizedExperiment, Matrix,
DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle,
knitr
GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP,
survival, foreach, doRNG, Rgraphviz, GOstats
BiocGenerics, BioNet, formatR, knitr, msm, org.Sc.sgd.db,
markdown, rmarkdown, RUnit
knitr, rmarkdown, testthat, covr, BiocStyle, AnnotationHub,
ensembldb, edgeR, DEXSeq, stageR, DelayedArray
knitr, rmarkdown, mclust, scater, BiocStyle
testthat, BiocStyle, knitr, rmarkdown, BiocSingular,
DelayedMatrixStats
BiocGenerics, scater, scuttle, uwot, RUnit, knitr, markdown,
rmarkdown, rhdf5, HDF5Array
BiocStyle, knitr, testthat, cluster, SingleCellExperiment
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), markdown,
loo, prettydoc, SeuratObject, tidyseurat,
tidySingleCellExperiment, bayesplot, posterior
PCAtools, cowplot, BiocGenerics, RUnit, knitr, kableExtra,
rmarkdown
knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db,
rmarkdown
mvnfast, igraph, rvinecopulib, knitr, rmarkdown, testthat (>=
3.0.0), RefManageR, sessioninfo, BiocStyle
AUCell, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
SingleR, celldex, scuttle, scater, dplyr, ComplexHeatmap, grid,
testthat (>= 3.0.0)
AnnotationDbi, BiocStyle, knitr, rmarkdown, scran, scRNAseq,
scuttle, SeuratObject, testthat, vdiffr
BiocStyle, knitr, rsvd, Rtsne, scater, cowplot, rmarkdown
testthat, knitr, rmarkdown, BiocStyle, SingleCellExperiment,
SummarizedExperiment, scRNAseq, cowplot
AnnotationDbi, BiocStyle, clusterProfiler, DOSE, enrichplot,
fmsb, ggplot2, ggraph, gridExtra, INetTool, org.Hs.eg.db,
org.Mm.eg.db, patchwork, pROC, RColorBrewer, ReactomePA,
rentrez, robin, scales, Seurat, STRINGdb, testthat (>= 3.0.0),
knitr, rmarkdown, tidyverse, magick, celldex, SingleR,
TENxPBMCData, scater, GenomeInfoDb, GenomicRanges,
ggrepel, knitr, rmarkdown, testthat (>= 2.1.0), covr,
TENxPBMCData, scater, Seurat, shinydashboard, iSEE, igraph,
scran, tibble, scuttle
knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra
knitr, markdown, rmarkdown, scater, scattermore, scales,
matrixStats, deldir
BiocBaseUtils, fs, BiocStyle, testthat (>= 3.0.0)
covr, grid, coop, uwot, scran, ggh4x, knitr, UCell, irlba,
rlang, magick, igraph, scater, gtable, ggpubr, viridis,
bluster, cluster, circlize, speedglm, rmarkdown, gridExtra,
BiocStyle, slingshot, gprofiler2, GenomeInfoDb, BiocParallel,
BiocGenerics, BiocNeighbors, ComplexHeatmap, Seurat (>= 5.0.0),
testthat (>= 3.0.0), SingleCellExperiment, SummarizedExperiment
testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM,
R.utils
knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0)
BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2,
rmarkdown, scran, scRNAseq, shiny, testthat, DelayedArray,
visNetwork, doParallel, batchtools, splatter, scater,
kableExtra, mclust, TENxPBMCData
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, knitr, rmarkdown, BiocStyle, MatrixGenerics,
sparseMatrixStats, Matrix, S4Vectors, SummarizedExperiment,
SingleCellExperiment, scRNAseq, igraph
testthat, knitr, BiocStyle, rmarkdown, DT, mclust, dplyr
BiocGenerics, Biostrings, BiocStyle, knitr, rmarkdown,
testthat
BiocGenerics, covr, DuoClustering2018, ggplot2, HDF5Array,
knitr, markdown, rmarkdown, TENxPBMCData, testthat
testthat, LRBaseDbi, Seurat, scTGIF, Homo.sapiens
emojifont, knitr, rmarkdown, prettydoc, tibble
GenomeInfoDb, GenomicRanges, BSgenome, GenomicFeatures,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Dmelanogaster.UCSC.dm3.ensGene,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Celegans.UCSC.ce2, RUnit,
knitr, rmarkdown, BiocStyle
CooccurrenceAffinity, nnSVG, testthat (>= 3.0.0), knitr,
rmarkdown, BiocManager, remotes
BiocStyle, caret, glmnet, corrplot, ggplot2, ggraph, knitr,
methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat,
SummarizedExperiment, TabulaMurisSenisData, tidyr, tidytext,
testthat (>= 3.0.0)
testthat, parallel, knitr, rmarkdown, BiocStyle
BiocStyle, knitr, rmarkdown, shinytest2, spelling, svglite,
testthat (>= 3.0.0)
shinyMethylData, minfiData, BiocStyle, knitr, testthat
BiocStyle, testthat, knitr, rmarkdown, tidyverse, ggpubr
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
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, knitr, rmarkdown, BiocStyle, BiocGenerics,
SingleCellExperiment, scuttle, scrapper (>= 1.3.14), 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,
snifter, uwot, bluster, class
BiocGenerics, BiocStyle, clusterExperiment,
DelayedMatrixStats, knitr, mclust, mgcv, RColorBrewer, rgl,
rmarkdown, testthat, uwot, covr
BiocStyle, dbscan, ggpubr, knitr, rmarkdown, scater,
splatter, testthat (>= 3.0.0), tidytext, UpSetR
BiocStyle, knitr, STexampleData, scuttle, scran, scater,
ggspavis, testthat
knitr, rmarkdown, BiocStyle, ggplot2, testthat (>= 3.0.0)
parallel, Matrix, RUnit, knitr, markdown, rmarkdown, MASS,
BiocGenerics
knitr, rmarkdown, BiocStyle, ExperimentHub, lme4, lmerTest,
ggfortify, tidyr, testthat (>= 3.0.0)
data.table, devtools, knitr, cowplot, rjson, rmarkdown,
BiocStyle, testthat (>= 3.0.0), CoGAPS, ComplexHeatmap
FNN, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle,
DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin,
KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0),
orthogene, PANTHER.db (>= 1.0.3), R.utils, reactome.db,
rmarkdown, SummarizedExperiment, statmod, stringr, testthat,
webshot
HDF5Array, ExperimentHub, testthat, knitr, rmarkdown,
BiocStyle
testthat (>= 2.1.0), knitr, bench, rmarkdown, BiocStyle
testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>=
5.0.0)
RefManageR, BiocStyle, knitr, testthat (>= 3.0.0),
sessioninfo, rmarkdown, markdown
testthat, knitr, rmarkdown, qpdf, Seurat
knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix,
DropletUtils, VisiumIO
stringr, knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0),
mgcv
knitr, BiocStyle, rmarkdown, testthat (>= 3.0.0), stringi,
qpdf, pheatmap, viridis, cowplot, vdiffr, sf
testthat (>= 3.0.0), STexampleData, ggplot2, knitr
BiocStyle, knitr, rmarkdown, statmod, CellBench, scater,
patchwork, jsonlite, vdiffr, testthat (>= 3.0.0)
BiocGenerics, BiocStyle (>= 2.2), knitr (>= 1.15), rmarkdown,
RUnit (>= 0.4)
testthat, knitr (>= 1.1.0), msdata (>= 0.19.3), roxygen2,
BiocStyle (>= 2.5.19), mzR (>= 2.19.6), rhdf5 (>= 2.32.0),
rmarkdown, vdiffr (>= 1.0.0), msentropy, patrick
testthat, msdata (>= 0.19.3), roxygen2, rmarkdown, knitr,
S4Vectors, BiocStyle, mzR
testthat, quarto, MsBackendMgf, MsDataHub, mzR, knitr,
BiocStyle
BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown,
testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap,
elsa
SpatialDatasets, BiocStyle, knitr, rmarkdown, pkgdown,
imcRtools, testthat (>= 3.0.0)
parallel, boot, igraph, batchtools, testthat, covr, knitr,
BiocStyle, rmarkdown, RefManageR, sessioninfo, magick
knitr, rmarkdown, cowplot, testthat (>= 3.0.0), BiocStyle,
hexbin
testthat, knitr, rmarkdown, ggplot2, tidyr
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
BiocManager, BiocStyle, colorspace, cowplot, DT, htmltools,
knitr, pander, patchwork, rmarkdown, spelling, testthat (>=
3.0.0), tidyverse
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
limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr
devtools, MutationalPatterns, RUnit, BiocManager,
BiocGenerics, BiocStyle, knitr, rmarkdown
rmarkdown, markdown, knitr, testthat (>= 3.0.0)
flowCore, knitr, rmarkdown, usethis, testthat (>= 3.0.0),
BiocSingular, bluster, scater, scran, Seurat,
SingleCellExperiment, BiocStyle, magick, qs2
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)
rmarkdown, prettydoc, broman, RSpectra, BiasedUrn, knitr, ks,
igraph, testthat (>= 3.0.0), scuttle, magrittr, DropletUtils,
tibble, tidyr, harmony, aplot, scales, ggsc, scatterpie, scran,
scater, STexampleData, ape
dplyr, ggplot2, BiocStyle, knitr, qvalue, reshape2,
rmarkdown, testthat
knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr
knitr, rmarkdown, testthat (>= 3.0.0), ggplot2, tidyverse,
BiocStyle
BiocStyle, knitr, igraph, markdown, rmarkdown
BiocManager, knitr, rmarkdown, testthat, devtools, prettydoc,
glue
testthat, BiocStyle, knitr, rmarkdown, systemPipeR (>=
2.12.0), systemPipeRdata (>= 2.10.0), rhandsontable, zip,
callr, pushbar, fs, readr, R.utils, DESeq2,
SummarizedExperiment, glmpca, pheatmap, grid, ape, Rtsne,
UpSetR, tidyr, esquisse (>= 1.1.0), cicerone
BiocStyle, knitr, rmarkdown, microbenchmark, testthat, covr,
pheatmap, SpectralTAD, magick, qpdf
tinytest, BiocStyle, ggimage, knitr, rmarkdown
BiocStyle, knitr, msdata, sessioninfo, rmarkdown, gridExtra,
testthat (>= 3.0.0), covr
BiocStyle, bugsigdbr, fgsea, knitr, rmarkdown, testthat
org.Hs.eg.db, testthat, knitr, rmarkdown, BiocStyle
BiocStyle, HDCytoData, knitr, RefManageR, rmarkdown,
sessioninfo, testthat (>= 3.0.0)
utils, tidyr, dplyr, tibble, ggplot2, mockr (>= 0.2.0), knitr
(>= 1.41), rmarkdown (>= 2.20), testthat (>= 3.1.6),
nullranges, tidybulk, plyinteractions
rmarkdown, knitr, BiocStyle, biomaRt, RCy3, testthat (>=
3.0.0)
BiocStyle, testthat, knitr, markdown, rmarkdown,
SingleCellSignalR, SingleR, scater, scran, tidyHeatmap, igraph,
GGally, uwot, celldex, dittoSeq, plotly, rbibutils, prettydoc
BiocStyle, testthat, knitr, markdown, scater, igraph,
cowplot, DropletUtils, tidySummarizedExperiment
BiocStyle, testthat, knitr, markdown, rmarkdown, plotly,
rbibutils, prettydoc, airway
drosgenome1.db, puma, lumi, BiocStyle, BiocManager
knitr, Matrix, rmarkdown, BiocStyle, BiocParallel, testthat
BiocStyle, knitr, rmarkdown, testthat, snow, tidyverse,
igraph, gplots
knitr, aroma.light, affxparser, RUnit, BiocGenerics
BiocStyle, knitr, rmarkdown, gplots, matrixStats, Matrix
knitr, rmarkdown, BiocStyle, Biobase, curatedOvarianData,
ggbeeswarm, ggsci, survminer, tidyverse
limma, edgeR, statmod, DESeq2, ashr, NBPSeq, dplyr, testthat,
reshape2, tidyr, readr, org.At.tair.db, AnnotationDbi, knitr,
rmarkdown, BiocStyle
topdownrdata (>= 0.2), knitr, rmarkdown, ranger, testthat,
BiocStyle, xml2
ALL, hgu95av2.db, hgu133a.db, genefilter, multtest,
Rgraphviz, globaltest, knitr, BiocStyle, rmarkdown
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
knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics, stringr,
geneplast, ggtree, ggplot2, dplyr, dendextend, RColorBrewer
knitr, rmarkdown, scales, testthat (>= 3.0.0), BiocStyle,
GenomeInfoDb
Biostrings, cli, ggplot2, ggtree, igraph, knitr, rmarkdown,
phangorn, prettydoc, purrr, testthat, tidyr, vroom, xml2, yaml
knitr, rmarkdown, BiocStyle, CATALYST, testthat (>= 3.0.0)
ggtree, ggplot2, BiocStyle, knitr, rmarkdown, testthat
BiocFileCache, BiocStyle, dplyr, ggplot2, knitr, pheatmap,
sessioninfo, RefManageR, rmarkdown, testthat (>= 3.0.0),
tibble, tidyr, SingleCellExperiment
BiocStyle, knitr, rmarkdown, kableExtra, testthat (>= 3.0.0)
haplo.stats, mcbiopi, splines, logicFS (>= 1.28.1),
KernSmooth, VariantAnnotation
BiocGenerics, shinycssloaders, tidyverse, BiocManager,
Biostrings, xtable, rlist, motifStack, knitr, rmarkdown,
testthat (>= 3.0.0), fs, BiocStyle, RefManageR, biocthis, pryr
BiocGenerics, BiocStyle, testthat, knitr, rWikiPathways,
magick
knitr, testthat, scuttle, scran, metapod, BiocParallel,
BiocNeighbors, batchelor
devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle
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
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
BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend,
tximport, tximportData, ballgown, DESeq2, RUnit, cowplot,
Rfast, zenith, statmod, BiocGenerics, r2glmm, readr
breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
knitr, markdown, RColorBrewer, rmarkdown, rstudioapi,
testthat (>= 3.0.0)
htmltools, org.Mm.eg.db, limma, Rgraphviz, BiocStyle, knitr,
rmarkdown, corrplot, remotes, BiocManager, stats, utils,
grDevices, processx
arrow, BiocStyle, data.table, knitr, readr, rmarkdown, sf,
tinytest
testthat, org.Hs.eg.db, org.Mm.eg.db, patchwork, singscore,
knitr, rmarkdown, prettydoc, BiocStyle, pkgdown, covr
arrow, automap, BiocSingular, BiocStyle, cowplot, data.table,
DelayedMatrixStats, EBImage, ExperimentHub, ggh4x, gstat,
hexbin, knitr, matrixStats, pheatmap, RBioFormats, rhdf5,
rmarkdown, scater, scattermore, scran, sfarrow, SFEData,
testthat (>= 3.0.0), vdiffr, xml2
knitr, yaml, testthat (>= 3.0.0), rmarkdown, BiocStyle, httr
affydata, hgu95av2cdf, BiocStyle, knitr, rmarkdown, dplyr,
testthat
RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19,
BiocStyle, knitr, rmarkdown,
IlluminaHumanMethylationEPICmanifest, irlba,
FlowSorted.Blood.EPIC, FlowSorted.Blood.450k, preprocessCore
knitr, rmarkdown, BiocStyle, tidyverse, airway, edgeR,
EnsDb.Hsapiens.v86, org.Sc.sgd.db, AnnotationDbi,
ComplexHeatmap, patchwork, testthat (>= 2.1.0)
MSnbase, testthat, BiocStyle, knitr, rmarkdown
knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR
knitr, ggforce, shapr (>= 1.0.1), airway, xgboost,
BiocGenerics, RUnit, S4Vectors
testthat, knitr, rmarkdown, ggplot2, randomForest, tidyr,
EnhancedVolcano, BiocStyle
BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata (>=
0.25.1), ncdf4, testthat (>= 3.1.9), pander, rmarkdown,
MALDIquant, pheatmap, RANN, multtest, MsBackendMgf, signal,
mgcv, rhdf5
arrow, BiocFileCache, BiocStyle, knitr, rmarkdown, tinytest
knitr, testthat, BiocStyle, yesno, terra,
SpatialFeatureExperiment, SFEData, tiff
BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat
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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