Imports
BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR,
data.table, formula.tools, Seqinfo, GenomicAlignments (>=
1.45.1), GenomicFeatures (>= 1.61.4), GenomicRanges (>=
1.61.1), ggplot2 (>= 4.0.0), gtools, IRanges (>= 2.18.0),
KernSmooth, Matrix, memoise, plyr, rlang, Rsamtools (>=
2.25.1), reshape2, rtracklayer (>= 1.69.1), S4Vectors (>=
0.27.5), scales, som, stringdist, stringi, SummarizedExperiment
(>= 1.39.1), utils, vegan, VGAM
Suggests
BSgenome.Dmelanogaster.UCSC.dm3,
BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9,
DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown