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Motif2Site

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


Bioconductor version: Release (3.18)

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 manchester.ac.uk>

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

Installation

To install this package, start R (version "4.3") and enter:


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

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")
Motif2Site HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, DifferentialPeakCalling, Epigenetics, SequenceMatching, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-2
Depends R (>= 4.1)
Imports S4Vectors, stats, utils, methods, grDevices, graphics, BiocGenerics, BSgenome, GenomeInfoDb, MASS, IRanges, GenomicRanges, Biostrings, GenomicAlignments, edgeR, mixtools
System Requirements
URL
Bug Reports https://github.com/ManchesterBioinference/Motif2Site/issues
See More
Suggests BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805
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Package Archives

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

Source Package Motif2Site_1.6.0.tar.gz
Windows Binary Motif2Site_1.6.0.zip
macOS Binary (x86_64) Motif2Site_1.6.0.tgz
macOS Binary (arm64) Motif2Site_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/Motif2Site
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Motif2Site
Bioc Package Browser https://code.bioconductor.org/browse/Motif2Site/
Package Short Url https://bioconductor.org/packages/Motif2Site/
Package Downloads Report Download Stats