Imports
futile.logger, checkmate, patchwork (>= 1.2.0), reshape2,
data.table, matrixStats, Matrix, GenomicRanges, RColorBrewer,
ComplexHeatmap, DESeq2, circlize, progress, utils, methods,
stringr, tools, scales, igraph, S4Vectors, ggplot2, rlang,
Biostrings, GenomeInfoDb (>= 1.34.8), SummarizedExperiment,
forcats, gridExtra, limma, tidyselect, readr, grid, tidyr (>=
1.3.0), dplyr, stats, grDevices, graphics, magrittr, tibble,
viridis, colorspace, biomaRt, topGO, AnnotationHub, ensembldb
Suggests
knitr, BSgenome.Hsapiens.UCSC.hg19,
BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm39,
BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9,
BSgenome.Rnorvegicus.UCSC.rn6, BSgenome.Rnorvegicus.UCSC.rn7,
BSgenome.Dmelanogaster.UCSC.dm6,
BSgenome.Mmulatta.UCSC.rheMac10,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
TxDb.Mmusculus.UCSC.mm39.knownGene,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm9.knownGene,
TxDb.Rnorvegicus.UCSC.rn6.refGene,
TxDb.Rnorvegicus.UCSC.rn7.refGene,
TxDb.Dmelanogaster.UCSC.dm6.ensGene,
TxDb.Mmulatta.UCSC.rheMac10.refGene, org.Hs.eg.db,
org.Mm.eg.db, org.Rn.eg.db, org.Dm.eg.db, org.Mmu.eg.db, IHW,
clusterProfiler, ReactomePA, DOSE, BiocFileCache, ChIPseeker,
testthat (>= 3.0.0), BiocStyle, csaw, BiocParallel, WGCNA,
variancePartition, purrr, EDASeq, JASPAR2022, JASPAR2024,
RSQLite, TFBSTools, motifmatchr, rbioapi, LDlinkR