Package: Motif2Site
Type: Package
Title: Detect binding sites from motifs and ChIP-seq experiments, and
        compare binding sites across conditions
Version: 1.10.0
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/ManchesterBioinference/Motif2Site/issues
License: GPL-2
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: RELEASE_3_20
git_last_commit: 12ad0b4
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Packaged: 2024-10-30 04:08:07 UTC; biocbuild
Author: Peyman Zarrineh [cre, aut] (<https://orcid.org/0000-0003-4820-4101>)
Maintainer: Peyman Zarrineh <peyman.zarrineh@manchester.ac.uk>
Built: R 4.4.1; ; 2024-10-30 16:17:53 UTC; windows
