R (>= 3.6.0), BiocStyle, knitr, readxl, CATALYST, diffcyt,
HDCytoData, uwot, cowplot
R (>= 3.3.0), BSgenome.Scerevisiae.UCSC.sacCer3, Biostrings,
GenomicFeatures, MotifDb, S4Vectors,
TxDb.Scerevisiae.UCSC.sacCer3.sgdGene, motifStack,
org.Sc.sgd.db, seqLogo
R (>= 4.0), NanoStringNCTools, GeomxTools
R (>= 3.3.0), flowCore, flowStats, flowWorkspace
R (>= 3.3.0), gwascat, GenomeInfoDb, GenomicRanges,
rtracklayer, Homo.sapiens, BiocGenerics
R (>= 3.3.0), Glimma (>= 1.1.9), limma, edgeR, gplots,
RColorBrewer, Mus.musculus, R.utils, TeachingDemos, statmod,
BiocWorkflowTools
R (>= 3.5.0), DRIMSeq, DEXSeq, stageR, DESeq2, edgeR, rafalib,
devtools
R (>= 3.3.0), edgeR (>= 4.3.6), gplots, org.Mm.eg.db, GO.db,
BiocStyle
R (>= 3.3.0), GenomicRanges, GenomicAlignments, Biostrings,
Rsamtools, ShortRead, BiocParallel, rtracklayer,
VariantAnnotation, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19,
RNAseqData.HNRNPC.bam.chr14
dplyr, fastqcr, stringr, tidyr, stats, utils, magrittr,
reticulate
AnnotationDbi, annotatr, Biobase, BiocParallel,
clusterProfiler, data.table, DESeq2, diffcoexp, DOSE, dplyr,
DT, edgeR, enrichit, enrichplot, FactoInvestigate, FactoMineR,
fastcluster, GenomicFeatures, GenomicRanges, ggplot2, ggrepel,
ggridges, GO.db, graphics, grDevices, heatmaply, knitr, limma,
magrittr, Matrix, matrixStats, miRBaseVersions.db, MKinfer,
NOISeq, plyr, ReactomePA, rlang, rmarkdown, ROCR, stats,
stringr, SummarizedExperiment, tidyr, topGO, tximport, utils,
txdbmaker, WGCNA
Biobase, S4Vectors, rjson, readxl, EnvStats, dplyr, reshape2,
methods, utils, stats, data.table, outliers, BiocGenerics,
ggplot2, ggrepel, ggforce, cowplot, scales, umap, Rtsne,
pheatmap, BiocStyle, networkD3
utils, methods, knitr, callr, rmarkdown, CodeDepends,
BiocStyle
affy, limma, hgfocuscdf, knitr, rmarkdown, BiocStyle
knitr, magick, rmarkdown, BiocStyle, BiocWorkflowTools,
pheatmap, ggseqlogo, viridis, magrittr, ggforce, ggthemes,
tidyverse, dplyr, GenomicRanges, SummarizedExperiment,
GenomicFeatures, BiocParallel, InteractionSet, Gviz, DESeq2,
limma, edgeR, statmod, BiasedUrn, sva, TFBSTools, motifmatchr,
pathview, BSgenome.Mmusculus.UCSC.mm9,
TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, JASPAR2016,
png
chipseqDBData, BiocStyle, BiocFileCache, ChIPpeakAnno, Gviz,
Rsamtools, TxDb.Mmusculus.UCSC.mm10.knownGene, csaw, edgeR,
knitr, org.Mm.eg.db, rtracklayer, rmarkdown
BiocGenerics, biomaRt, EnhancedVolcano, ggupset, naivebayes,
optparse, org.Hs.eg.db, org.Mm.eg.db, PerformanceAnalytics,
reshape2, testthat (>= 3.0.0)
benchmarkme (>= 0.6.0), DESeq2 (>= 1.18.1), GenomeInfoDb (>=
1.14.0), gginnards (>= 0.0.2), qqman (>= 0.1.8), rmarkdown,
BiocStyle, knitr, testthat, UpSetR (>= 1.4.0), venneuler,
R.utils, bigreadr, vroom
readxl, R.utils, SingleCellExperiment, scater, scran, limma,
BiocFileCache, org.Mm.eg.db