R (>= 2.13.0), methods, Biobase (>= 2.3.3), affycomp
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 (>= 3.5), Biobase, GSEABase, hgu95a.db, SummarizedExperiment
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 (>= 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 (>= 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 (>= 3.6), limma, edgeR, ReactomeGSA, Seurat
doParallel, foreach, parallel, iterators, data.table, stringr,
survival, arm, stats, utils, methods
R (>= 4.1), SingleCellExperiment, BiocFileCache, data.table,
utils, S4Vectors, zellkonverter
AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment,
SingleCellExperiment, SummarizedExperiment
R (>= 4.2.0), ExperimentHub, AnnotationHub
R (>= 4.1), ExperimentHub, SummarizedExperiment
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
beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2,
glmnet, graphics, grDevices, grid, gtable, ipflasso, methods,
RColorBrewer, reshape2, scales, stats, SummarizedExperiment,
survival, tibble
dplyr, utils, purrr, stringr, tidyr, tidyselect,
BiocFileCache, httr2, tools, S4Vectors
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
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
BiocFileCache, HiCExperiment, GenomicRanges, IRanges,
S4Vectors, utils, tools
RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools
ExperimentHub (>= 1.14.0), AnnotationHub, AnnotationFilter,
data.table, utils, BSgenome, GenomeInfoDb, GenomicFeatures,
GenomicRanges, ensembldb
ExperimentHub, SingleCellExperiment, SpatialExperiment,
HDF5Array, SummarizedExperiment, S4Vectors, htmltools,
rmarkdown, base64enc, utils
AnnotationHub, ExperimentHub, S4Vectors, assertthat, dplyr,
kableExtra, knitr, magrittr, methods, readr, stringr, tibble,
utils
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
animalcules, data.table, dplyr, ggplot2, magrittr,
MultiAssayExperiment, plyr, rlang, S4Vectors, stringr,
SummarizedExperiment, tibble, tidyr, tidyselect
grDevices, AnnotationHub, BumpyMatrix, ExperimentHub,
S4Vectors, SingleCellExperiment, SummarizedExperiment,
HDF5Array
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, dplyr, forcats, ggdist, gghalves, ggplot2,
purrr, queryup, spdl, tidyr, tidyselect
ExperimentHub, Rsamtools, BiocGenerics, rtracklayer,
SingleCellExperiment
AzureStor, GenomicRanges, HDF5Array, S4Vectors, checkmate,
methods, rhdf5, alabaster.matrix
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
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
rmarkdown, knitr, BiocStyle, testthat, SummarizedBenchmark,
dplyr, ggplot2, rlang
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
DT, forcats, ggplot2, htmltools, knitr, rmarkdown,
sessioninfo, testthat, EnrichmentBrowser,
MicrobiomeBenchmarkData, mia, stats, rlang, limma, mgsub,
methods, readr, crayon, tibble, magrittr, tidytext, 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
BiocStyle, DT, knitr, readr, rmarkdown, scater, testthat,
utils, uwot, vegan
survival, RUnit, metafor, genefilter, logging, sva, xtable,
futile.logger, BiocStyle
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
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
BiocStyle, knitr, rmarkdown, RefManageR, planet, mixOmics
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
rtracklayer, dplyr, testthat, methods, BiocStyle, knitr,
rmarkdown
BiocStyle, gDRstyle (>= 1.1.5), knitr, qs, reshape2,
rmarkdown, SummarizedExperiment, testthat, yaml
limma, rtracklayer, GenomicRanges, Rsamtools,
VariantAnnotation, tools, BiocStyle, knitr, testthat
ExperimentHub, BiocStyle, RefManageR, knitr, rmarkdown,
testthat, minfi, tibble, sessioninfo
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
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
BiocStyle, broom, broom.mixed, circlize, ComplexHeatmap,
emmeans, geepack, ggalluvial, ggeffects, grDevices, knitr,
lme4, lmerTest, methods, RColorBrewer, rmarkdown, spelling,
TBSignatureProfiler, testthat (>= 3.0.0),
TreeSummarizedExperiment, usethis, vegan
LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat
knitr, rmarkdown, ExperimentHubData, testthat (>= 3.0.0)
grid, ggplot2, ggpubr, knitr, rmarkdown, scater, scattermore,
terra, testthat, BiocStyle, DropletUtils
testthat, xtable, rmarkdown, knitr, BiocStyle, markdown
testthat, knitr, BiocStyle, rmarkdown, markdown
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
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
knitr, rmarkdown, markdown, BiocStyle, preciseTAD
ComplexHeatmap, AnnotationHub, tibble, stringr, BiocStyle,
knitr, testthat (>= 3.0.0)
rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
knitr, testthat, BiocStyle, rcellminer, rmarkdown
RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr,
Biobase, GEOquery, biomaRt, survminer, survey, rmarkdown
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
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, kableExtra, magrittr, dplyr
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