motifbreakR

DOI: 10.18129/B9.bioc.motifbreakR    

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

Bioconductor version: Release (3.13)

We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 22).

Author: Simon Gert Coetzee [aut, cre], Dennis J. Hazelett [aut]

Maintainer: Simon Gert Coetzee <simon.coetzee at cshs.org>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("motifbreakR")

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("motifbreakR")

 

HTML	R Script	motifbreakR: an Introduction
PDF		Reference Manual

Details

biocViews	ChIPSeq, MotifAnnotation, Software, Visualization
Version	2.6.1
In Bioconductor since	BioC 3.2 (R-3.2) (6 years)
License	GPL-2
Depends	R (>= 3.5.0), grid, MotifDb
Imports	methods, compiler, grDevices, grImport, stringr, BiocGenerics, S4Vectors(>= 0.9.25), IRanges, GenomeInfoDb, GenomicRanges, Biostrings, BSgenome, rtracklayer, VariantAnnotation, BiocParallel, motifStack, Gviz, matrixStats, TFMPvalue, SummarizedExperiment
LinkingTo
Suggests	BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/Simon-Coetzee/motifbreakR/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	motifbreakR_2.6.1.tar.gz
Windows Binary	motifbreakR_2.6.1.zip
macOS 10.13 (High Sierra)	motifbreakR_2.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/motifbreakR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/motifbreakR
Package Short Url	https://bioconductor.org/packages/motifbreakR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.13	Source Archive