motifbreakR

DOI: 10.18129/B9.bioc.motifbreakR  

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

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

Bioconductor version: Development (3.18)

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 32 species, a total of 109 versions).

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("motifbreakR")

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

Documentation

PDF		Reference Manual

Details

biocViews	ChIPSeq, MotifAnnotation, Software, Transcription, Visualization
Version	2.15.0
In Bioconductor since	BioC 3.2 (R-3.2) (7.5 years)
License	GPL-2
Depends	R (>= 4.1.0), grid, MotifDb
Imports	methods, grDevices, stringr, parallel, 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.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/Simon-Coetzee/motifbreakR/issues
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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/
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