Package: Motif2Site
Type: Package
Title: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
Version: 1.15.0
Depends: R (>= 4.1)
Authors@R: person("Peyman Zarrineh", email="peyman.zarrineh@manchester.ac.uk", role=c("cre", "aut"), comment = c(ORCID = "0000-0003-4820-4101"))
Description: Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.
BugReports: https://github.com/fls-bioinformatics-core/Motif2Site/issues
License: GPL-2
LazyData: false
Encoding: UTF-8
Imports: S4Vectors, stats, utils, methods,  grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools
Suggests: BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805
biocViews: Software, Sequencing, ChIPSeq, DifferentialPeakCalling, Epigenetics, SequenceMatching 
RoxygenNote: 7.1.2
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/Motif2Site
git_branch: devel
git_last_commit: c1fd6d7
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
