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Motif2Site

This is the development version of Motif2Site; for the stable release version, see Motif2Site.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

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

DOI: 10.18129/B9.bioc.Motif2Site

Bioconductor version: Development (3.24)

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] ORCID: 0000-0003-4820-4101

Maintainer: Peyman Zarrineh <peyman.zarrineh at manchester.ac.uk>

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

Peyman Zarrineh. Motif2Site: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions. doi:10.18129/B9.bioc.Motif2Site, R package version 1.17.0, https://bioconductor.org/packages/Motif2Site.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("Motif2Site")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("Motif2Site")

Details

Package Archives

Follow Installation instructions to use this package in your R session.