Motif2Site

DOI: 10.18129/B9.bioc.Motif2Site  

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

Bioconductor version: Release (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 manchester.ac.uk>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Motif2Site
PDF		Reference Manual
Text		NEWS

Details

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
LinkingTo
Suggests	BiocStyle, rmarkdown, knitr, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Ecoli.NCBI.20080805
SystemRequirements
Enhances
URL
BugReports	https://github.com/ManchesterBioinference/Motif2Site/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	Motif2Site_1.2.0.tar.gz
Windows Binary	Motif2Site_1.2.0.zip
macOS Binary (x86_64)	Motif2Site_1.2.0.tgz
macOS Binary (arm64)	Motif2Site_1.2.0.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