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Motif2Site

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

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

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
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")
Motif2Site HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, DifferentialPeakCalling, Epigenetics, SequenceMatching, Sequencing, Software
Version 1.5.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 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
Linking To
Suggests BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805
System Requirements
Enhances
URL
Bug Reports https://github.com/ManchesterBioinference/Motif2Site/issues
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Package Archives

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

Source Package Motif2Site_1.5.0.tar.gz
Windows Binary Motif2Site_1.5.0.zip
macOS Binary (x86_64) Motif2Site_1.5.0.tgz
macOS Binary (arm64) Motif2Site_1.5.0.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