DOI: 10.18129/B9.bioc.Motif2Site  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Motif2Site.

Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Bioconductor version: 3.16

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.

Author: Peyman Zarrineh [cre, aut]

Maintainer: Peyman Zarrineh <peyman.zarrineh at>

Citation (from within R, enter citation("Motif2Site")):


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biocViews ChIPSeq, DifferentialPeakCalling, Epigenetics, SequenceMatching, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.15 (R-4.2) (1 year)
License GPL-2
Depends R (>= 4.1)
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
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