R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
R (>= 4.1), minfi(>= 1.36.0), ExperimentHub
R (>= 3.6.0), SummarizedExperiment, ExperimentHub
R (>= 3.6), SummarizedExperiment, ExperimentHub
R (>= 3.0.0), XML, ggplot2, impute, Biobase, BiocStyle
R (>= 4.1.0), SummarizedExperiment, TreeSummarizedExperiment
R (>= 4.4.0), S4Vectors (>= 0.23.18), MultiAssayExperiment,
RaggedExperiment
R (>= 2.10), Biobase (>= 2.5.5), tilingArray, GO.db
GenomicRanges (>= 1.5.42), ShortRead, rtracklayer
R (>= 3.3), Biobase, metagenomeSeq(>= 1.12.0)
R (>= 3.5), minfi(>= 1.21.2), ExperimentHub
R (>= 3.5), Biobase, GSEABase, hgu95a.db
R (>= 2.10.0), tools, utils, IRanges, Biobase (>= 2.5.5),
Biostrings
R (>= 2.10.0), RColorBrewer, gplots, geneplotter, splots,
limma, vcd, LSD,EBImage
R (>= 3.0.0), affy, Biobase, boot, clue, cluster, genefilter,
geneplotter, gplots, gtools, KEGGREST, MASS, mouse4302.db,
RColorBrewer, xtable
R (>= 4.4.0), SingleCellExperiment, SpatialExperiment,
cytomapper,
R (>= 2.15.0), Biobase, Rsamtools (>= 0.1.50), BSgenome
R (>= 4.2.0), EBImage, SpatialExperiment
R (>= 3.6.0), Biobase, AnnotationHub, ExperimentHub
Biobase, AnnotationHub, ExperimentHub, SummarizedExperiment, R
(>= 3.6.0)
SummarizedExperiment, ExperimentHub, R (>= 3.6.0)
R (>= 4.2), SummarizedExperiment, TreeSummarizedExperiment
R (>= 4.1), SummarizedExperiment, TreeSummarizedExperiment,
MultiAssayExperiment
R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylation450kmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19
R (>= 3.5.0), minfi (>= 1.21.2),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
R (>= 4.1), SingleCellExperiment, SummarizedExperiment,
SpatialExperiment
R (>= 3.6), ExperimentHub, SingleCellExperiment
R (>= 3.6), AnnotationHub (>= 2.15), ExperimentHub (>= 1.0),
Biostrings (>= 2.51), gplots (>= 3.0), protViz (>= 0.4),
ShortRead (>= 1.41)
R (>= 2.14.0), tools, methods, utils, Biobase (>= 1.14.0),
hgu133a.db, annotate
R (>= 4.1.0), ExperimentHub, GenomicRanges, InteractionSet
R (>= 4.1), SummarizedExperiment, ExperimentHub
R (>= 2.10.0), methods, PREDA, Biobase, affy, annotate
R (>= 3.3), xcms, CAMERA, LOBSTAHS, methods, utils
R (>= 3.6), limma, edgeR, ReactomeGSA, Seurat
doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, stats, utils, methods
R (>= 3.4), SummarizedExperiment, ExperimentHub, DelayedArray
(>= 0.21.2), HDF5Array (>= 1.23.2)
R (>= 3.6), ExperimentHub, ExperimentHubData (>= 1.9.2)
R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table,
utils, S4Vectors
AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment,
SingleCellExperiment, SummarizedExperiment
R (>= 4.2.0), ExperimentHub, AnnotationHub
R (>= 4.1), ExperimentHub, SummarizedExperiment
SpatialExperiment (>= 1.3.3), R (>= 3.6)
R (>= 4.1), AnnotationHub (>= 2.16), ExperimentHub (>= 1.0)
R (>= 4.1), SingleCellExperiment, BiocFileCache
R (>= 2.4.0), affy , ath1121501cdf , tinesath1cdf ,
RColorBrewer , methods, grid
ExperimentHub, AnnotationHub, markdown, rmarkdown, EBImage,
magick, magrittr, filesstrings, animation, einsum
BiocFileCache, GenomicRanges, GenomeInfoDb, GEOquery, graph,
methods, utils
beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2,
glmnet, graphics, grDevices, grid, gtable, ipflasso, methods,
RColorBrewer, reshape2, scales, stats, SummarizedExperiment,
survival, tibble
utils, methods, Matrix, ExperimentHub, AnnotationHub,
AnnotationDbi, S4Vectors, DelayedArray, DelayedMatrixStats,
gypsum, alabaster.base, alabaster.matrix, alabaster.se, DBI,
RSQLite, jsonlite
AnnotationDbi, BiocGenerics, methods, GenomicRanges,
GenomeInfoDb, IRanges, readr, rtracklayer, S4Vectors, utils
AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr, mia,
purrr, rlang, stringr, tibble, tidyr, tidyselect
ExperimentHub, AnnotationHub, utils, methods, rlang, stats,
reshape2
AnnotationHub, ExperimentHub, MultiAssayExperiment, rlang,
stats
AnnotationHub, ExperimentHub, HDF5Array, methods, S4Vectors,
stats, SummarizedExperiment, utils
tibble, utils, stats, tools, sesame, methods, sesameData,
BiocParallel, BiocManager
utils, ExperimentHub, AnnotationHub, BiocFileCache, httr2,
curl, tibble
affy, frma, frmaTools, hgu133plus2.db, hgu133plus2frmavecs,
sva, rgl, ConsensusClusterPlus, cluster, siggenes, ROCR, pamr,
survival, gplots, AnnotationDbi, Biobase
grid, TSP, limma, rhdf5, knitr, abind, gplots, igraph,
grDevices, graphics, stats
GenomicFeatures, Gviz, readxl, plyr, rtracklayer,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
BiocFileCache, S4Vectors, rjson, utils, tools
ExperimentHub, utils, magrittr, dplyr, tidyr, mclust, ggplot2,
purrr, reshape2, viridis, ggthemes, stats, methods
BiocStyle, RUnit, SummarizedExperiment, ExperimentHub (>=
0.99.6), AnnotationHub, DESeq2
genefilter, nlme, quadprog, graphics, stats, utils,
AnnotationHub, SummarizedExperiment, S4Vectors
SummarizedExperiment,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19, utils,
AnnotationHub
BiocFileCache, HiCExperiment, GenomicRanges, IRanges,
S4Vectors, utils, tools
RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools
utils, rtracklayer, GenomicFeatures (>= 1.56.0), txdbmaker
ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter,
data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures,
GenomicRanges, ensembldb
ExperimentHub, SingleCellExperiment, SpatialExperiment,
HDF5Array, SummarizedExperiment, S4Vectors, htmltools,
rmarkdown, base64enc, utils
dplyr, FlowSorted.Blood.EPIC, tibble, FlowSorted.DLPFC.450k,
minfi, utils, AnnotationHub, SummarizedExperiment
AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr,
kableExtra, knitr, magrittr, methods, readr, stringr, tibble,
utils
AnnotationHub, assertthat, dplyr, ExperimentHub, kableExtra,
knitr, magrittr, methods, readr, S4Vectors,
SummarizedExperiment, phyloseq, MultiAssayExperiment,
data.table
Rtsne (>= 0.15), utils(>= 3.5.0), ExperimentHub, BiocGenerics,
DESeq2, S4Vectors, SummarizedExperiment, getDEE2,
MatrixGenerics
Rcpp, stats, splines, methods, utils, DESeq2,
SummarizedExperiment, fdrtool, genefilter, qvalue, Biobase,
BiocGenerics, BiocParallel, dplyr, grid, ggplot2, cowplot
methods, utils, ExperimentHub, S4Vectors, DelayedArray,
HDF5Array
ExperimentHub, BiocParallel, checkmate, dplyr, stats, stringr,
tidyr, purrr, utils
GenomicRanges, GenomicAlignments, methods, S4Vectors,
parallel, IRanges
grDevices, AnnotationHub, BumpyMatrix, ExperimentHub,
S4Vectors, SingleCellExperiment, SummarizedExperiment
BiocFileCache, Biostrings, data.table, dplyr, ggplot2,
magrittr, Matrix, MultiAssayExperiment, Rbowtie2, readr, rlang,
Rsamtools, S4Vectors, stringr, SummarizedExperiment, taxize,
tibble, tidyr, tools
ExperimentHub, HDF5Array, rhdf5, GenomeInfoDb, S4Vectors,
GenomicRanges, stats, IRanges, utils
BiocFileCache, tools, S4Vectors, ape, utils
methods, utils, BiocGenerics, ExperimentHub, Biostrings, ape
methods, ExperimentHub, BiocGenerics, S4Vectors, BumpyMatrix
ExperimentHub, utils, GSEABase, org.Mm.eg.db, org.Hs.eg.db,
AnnotationDbi, methods, stats, AnnotationHub
AnnotationHub, BiocFileCache, ExperimentHub, HDF5Array,
stringr, SummarizedExperiment
Biostrings (>= 2.21.11), IRanges (>= 1.11.31), S4Vectors
ExperimentHub, Rsamtools, BiocGenerics, rtracklayer,
SingleCellExperiment
grid, gdata, MASS, genefilter, methods, fields, utils,
lattice, Biobase
AzureStor, DelayedArray, GenomicRanges, HDF5Array, S4Vectors,
checkmate, methods, rhdf5
utils, methods, Matrix, BiocGenerics, S4Vectors, SparseArray,
DelayedArray, GenomicRanges, SummarizedExperiment,
ExperimentHub (>= 2.3.4), AnnotationHub (>= 3.3.6),
AnnotationDbi, ensembldb, GenomicFeatures, alabaster.base,
alabaster.matrix, alabaster.sce, gypsum, jsonlite, DBI, RSQLite
utils, readr, stringr, GenomicRanges, S4Vectors, IRanges,
GenomeInfoDb
ExperimentHub, utils, affy, limma, Biobase, magrittr, dplyr,
R.utils, stats, rhdf5
AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub,
graphics, HDF5Array, S4Vectors, SingleCellExperiment,
SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
shiny, golem, ggplot2, cowplot, plotly, viridisLite,
shinyWidgets, sessioninfo, grid, grDevices, methods,
AnnotationHub, utils, png, scater, DT, ExperimentHub,
RColorBrewer, SummarizedExperiment, stats, graphics, S4Vectors,
IRanges, fields, benchmarkme, SingleCellExperiment,
BiocFileCache, jsonlite, tibble, rtracklayer, Matrix,
BiocGenerics, GenomicRanges, magick, paletteer, scuttle, edgeR,
limma, statmod, MatrixGenerics, rlang
dplyr, hexbin, Matrix, SpatialExperiment, stats
methods, Biostrings, BiocGenerics, jsonlite, remotes
ExperimentHub, SingleCellExperiment, HDF5Array,
SummarizedExperiment, gdata, AnnotationHub
SpatialExperiment, SpatialFeatureExperiment, BumpyMatrix,
SummarizedExperiment, utils
ggplot2, grid, gridExtra, deSolve, dplyr, locfit
AnnotationHub, ExperimentHub, S4Vectors, dplyr, magrittr,
purrr, rlang, stringr, tibble, tidyr
ExperimentHub, GenomicRanges, HDF5Array, R.utils, rhdf5
Biostrings, GenomicRanges, illuminaHumanv1.db,
illuminaHumanv2.db, illuminaHumanv3.db
rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark,
dplyr, ggplot2, rlang
AnnotationDbi, AnnotationHub, BiocStyle, DEXSeq,
ExperimentHub, GenomicFeatures, S4Vectors, depmap, knitr,
rmarkdown
BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt,
broom, colorspace, cowplot, dendsort, doParallel, foreach,
forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin,
IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db,
pheatmap, piano, readxl, Rtsne, tidyr, xtable
minfi, MultiAssayExperiment, knitr, rmarkdown, rexposome,
BiocStyle
testthat, knitr, rmarkdown, BiocStyle, DT, jsonvalidate,
BiocManager, ensembldb
BiocStyle, knitr, rmarkdown, ExperimentHubData, testthat (>=
3.0.0)
BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat,
GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db,
org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Drerio.UCSC.danRer10.refGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Rnorvegicus.UCSC.rn4.ensGene,
TxDb.Rnorvegicus.UCSC.rn5.refGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene
clustifyr, Seurat, usethis, rmarkdown, knitr, tidyr,
BiocStyle
knitr, rmarkdown, GenomicFeatures, ChIPseeker, AnnotationDbi,
S4Vectors, DESeq2, fastqcr, devtools, testthat, readr, dplyr,
tidyr, ggplot2
knitr, rmarkdown, DESeq2, fastqcr, devtools, testthat, readr,
dplyr, tidyr, ggplot2, S4Vectors
BiocStyle, survival, xtable, sva, genefilter, logging
survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle
BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat,
utils, uwot, vegan
BiocStyle, knitr, ggplot2, rmarkdown, survival, survminer,
ComplexHeatmap, corrplot, formatR
BiocStyle, DT, dplyr, HGNChelper, knitr, methods, rmarkdown,
SummarizedExperiment, sva, testthat
BiocStyle, knitr, RaggedExperiment, readr, rmarkdown,
TCGAutils, testthat
BiocStyle, randomForest, testthat, knitr, rmarkdown, e1071,
xgboost, keras, tensorflow
knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2,
readr, stringr, tidyverse, magick
sessioninfo, knitr (>= 1.6), RefManageR, rmarkdown (>=
0.3.3), BiocStyle
BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, hwriter,
xtable, beeswarm
dplyr, testthat, methods, BiocStyle, knitr, rmarkdown
Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap,
pkgdown, rmarkdown, Seurat, SingleCellExperiment,
SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils
BiocStyle, knitr, rmarkdown, testthat, DropletUtils
knitr, rmarkdown, BiocStyle, iSEE, scater,
SingleCellExperiment, SummarizedExperiment, plyr
knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
BiocStyle, knitr, dplyr, devtools, DT, rmarkdown
testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle,
Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr
rmarkdown, BiocStyle, knitr, ExperimentHub, minfi
affy, hgu95av2.db, hgu95av2cdf, vsn, knitr, genefilter
knitr, BiocStyle, ggplot2, cowplot, rmarkdown, markdown,
testthat (>= 3.0.0)
knitr, rmarkdown, BiocGenerics, sva, BiocManager
knitr,rmarkdown, FlowSorted.CordBlood.450k,
FlowSorted.Blood.450k(>= 1.0.1),
EpiDISH,FlowSorted.CordBloodNorway.450k, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICmanifest,
IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1),
IlluminaHumanMethylationEPICanno.ilm10b4.hg19
FlowSorted.Blood.EPIC, knitr, rmarkdown, testthat,
IlluminaHumanMethylation450kmanifest(>= 0.2.0),
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
rtracklayer, dplyr, testthat, methods, BiocStyle, knitr,
rmarkdown
BiocStyle, gDRstyle (>= 1.1.3), knitr, qs, reshape2,
rmarkdown, SummarizedExperiment, testthat, yaml
limma, rtracklayer, GenomicRanges, Rsamtools,
VariantAnnotation, tools, BiocStyle, knitr, testthat
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown,
SummarizedExperiment, SingleCellExperiment
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown
ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown,
testthat, minfi, tibble, sessioninfo
ExperimentHub (>= 0.99.6), knitr, BiocStyle, rmarkdown,
DESeq2
BiocGenerics, BiocStyle, knitr, rmarkdown, Harman (>= 1.23.3)
AnnotationHub, knitr, rmarkdown, igraph, survival, ANF,
stats, testthat
knitr, rmarkdown, BiocStyle, scran (>= 1.11.4), BiocSingular,
scater, scuttle, Rtsne, igraph, iSEE, testthat
knitr, ggplot2, testthat (>= 3.0.0), scater, Seurat, Signac,
zellkonverter, iSEE, ggspavis, kableExtra, BiocStyle
BiocStyle, knitr, rmarkdown, Rtsne, umap, ggplot2, FlowSOM,
mclust
RUnit, BiocGenerics, markdown, BiocStyle, knitr, rmarkdown
testthat, methods, BiocStyle, knitr, rmarkdown
Biobase, BiocCheck, BiocManager, BiocStyle, circlize,
cowplot, dendextend, devtools, ggplot2, gridExtra, haven,
phyloseq, rmarkdown, roxygen2, stats, testthat, tidyr
Biobase, BiocCheck, BiocManager, BiocStyle, cowplot,
devtools, ggplot2, gridExtra, haven, rmarkdown, roxygen2,
stats, testthat, tibble, UpSetR
knitr, rmarkdown, devtools, Biobase (>= 2.39.1), BiocManager,
AnnotationHubData, ExperimentHubData, AnnotationHub, CellScore
(>= 1.21.4)
testthat, RColorBrewer, wesanderson, scales, gridExtra,
BiocStyle, knitr, rmarkdown, airway, locfdr, tidyr, latex2exp
BiocStyle, knitr, rmarkdown, markdown, testthat
knitr, BiocStyle, ExperimentHubData, testthat (>= 3.0.0),
rmarkdown
LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat
knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0)
grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle,
DropletUtils
testthat, xtable, rmarkdown, knitr, BiocStyle, markdown
testthat, knitr, BiocStyle, rmarkdown, markdown
animalcules, BiocStyle, biomformat, GenomicRanges, IRanges,
knitr, lintr, plyr, qlcMatrix, rBLAST, rmarkdown, R.utils,
Rsubread, spelling, sys, testthat, usethis
BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC
BiocFileCache, BiocStyle, data.table, knitr, rmarkdown
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0), mia,
ggplot2, tidyr, dplyr, magrittr, tibble, purrr
knitr, rmarkdown, BiocStyle, SingleCellExperiment, testthat
knitr, rmarkdown, BiocStyle, roxygen2, seqinr, readr
singscore, vissE, knitr, prettydoc, BiocStyle, rmarkdown,
testthat (>= 3.0.0), BiocFileCache, GO.db, stringr, limma
BiocStyle, knitr, rmarkdown, testthat, specL (>= 1.2)
xcms (>= 3.13.8), CAMERA, Risa (>= 1.0.0), knitr, Heatplus,
pcaMethods, sp, rmarkdown
BiocStyle, knitr, multiWGCNA, rmarkdown, SummarizedExperiment
BiocStyle, dplyr, DropletUtils, knitr, GEOquery, Matrix,
matrixStats, methods, muscat, rmarkdown, R.utils, readxl,
scater, scds, Seurat
knitr, bambu, ggbio, BSgenome.Hsapiens.NCBI.GRCh38, circlize,
ComplexHeatmap, apeglm, rlang, rmarkdown, GenomicAlignments,
Rsamtools
knitr, rmarkdown, BiocStyle, GenomicRanges, rtracklayer,
CAGEfightR
BiocStyle (>= 2.2), DT, ggplot2, knitr, rmarkdown, testthat,
specL, lattice, scales
knitr, rmarkdown, BiocManager, GenomicFeatures, S4Vectors,
devtools, testthat
BiocStyle, ggplot2, knitr, rmarkdown, testthat
Rsamtools, GenomicAlignments, GEOquery, SRAdb,
GenomicFeatures, BiocStyle
knitr, rmarkdown, markdown, BiocStyle, preciseTAD
pRoloc (>= 1.13.8), testthat, SummarizedExperiment
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
knitr, testthat, BiocStyle, rcellminer, rmarkdown
RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown
AnnotationDbi, rpx (>= 2.0.3), DT, knitr, rmarkdown,
BiocStyle, mzR, xcms, msdata, MALDIquant (>= 1.12),
MALDIquantForeign, readBrukerFlexData, Rdisop, OrgMassSpecR,
SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db,
e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable,
lattice, mzID, pRoloc, pRolocdata, MSnID, msmsTests, msmsEDA,
DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram,
protViz, genefilter, plotly, gridExtra, dplyr, lubridate,
magick, cleaver
knitr, DT, rmarkdown, testthat, BiocStyle
knitr, rmarkdown, BiocStyle, GenomicRanges, sessioninfo,
testthat
knitr, rmarkdown, markdown, SingleCellAlleleExperiment,
Matrix, BiocStyle
BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0)
BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi,
testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData
scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown,
testthat
BiocStyle, knitr, rmarkdown, testthat, jsonvalidate,
BiocManager
BiocGenerics, sesame, testthat, knitr, rmarkdown
Biobase, limma, breastCancerNKI, knitr, rmarkdown, readxl,
BiocStyle
BiocStyle, knitr, rmarkdown, SeuratObject,
SpatialFeatureExperiment, testthat (>= 3.0.0)
DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod,
gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid,
gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap,
BiocStyle, knitr, BiocParallel
BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown,
scater, scran, UpSetR, uwot
ExperimentHub, AnnotationHubData, BiocStyle, covr,
ExperimentHubData, knitr, RefManageR, rmarkdown, sessioninfo,
testthat (>= 3.0.0)
knitr, RefManageR, rmarkdown, BiocStyle, testthat (>= 2.1.0),
covr, here, BiocManager, lobstr, DropletUtils
BiocStyle, knitr, rmarkdown, BumpyMatrix, HDF5Array
BiocStyle, ExperimentHub, ggplot2, knitr, prettydoc,
rmarkdown, testthat (>= 3.0.0)
GenomicFeatures, GenomicRanges, IRanges, Rsamtools,
ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown,
systemPipeR
knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran,
scater, iSEE, testthat
ggplot2, testthat, knitr, rmarkdown, iSEE, BiocStyle
BiocStyle, knitr, rmarkdown, testthat, tools
knitr, rmarkdown, pander, testthat, BiocStyle
knitr, BiocStyle, snow, BiocFileCache, BiocParallel,
data.table, rmarkdown
rmarkdown, knitr, BiocStyle, snow, BiocFileCache,
BiocParallel
testthat (>= 1.0.0), knitr, rmarkdown, markdown, covr,
BiocStyle
BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq,
SummarizedExperiment, ggplot2, reshape2
BiocStyle, knitr, rmarkdown, RefManageR, sessioninfo,
testthat, ExperimentHub
BiocStyle, ggplot2, hrbrthemes, knitr, readr, rmarkdown,
scater, usethis, utils
VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle