Depends
R (>= 3.5), methods, IRanges (>= 2.13.12), GenomicRanges (>=
1.31.8), S4Vectors (>= 0.17.25)
Imports
AnnotationDbi, BiocGenerics (>= 0.1.0), Biostrings (>=
2.47.6), pwalign, DBI, dplyr, GenomeInfoDb, GenomicAlignments,
GenomicFeatures, RBGL, Rsamtools, SummarizedExperiment,
VennDiagram, biomaRt, ggplot2, grDevices, graph, graphics,
grid, InteractionSet, KEGGREST, matrixStats, multtest,
regioneR, rtracklayer, stats, utils, universalmotif, stringr,
tibble, tidyr, data.table, scales, ensembldb
Suggests
AnnotationHub, BSgenome, limma, reactome.db, BiocManager,
BiocStyle, BSgenome.Ecoli.NCBI.20080805,
BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db,
BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7,
BSgenome.Hsapiens.UCSC.hg38, DelayedArray, idr, seqinr,
EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, EnsDb.Hsapiens.v86,
TxDb.Hsapiens.UCSC.hg18.knownGene,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene, GO.db, gplots, UpSetR,
knitr, rmarkdown, reshape2, testthat, trackViewer, motifStack,
OrganismDbi, BiocFileCache