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motifbreakR

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


Bioconductor version: Release (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")
motifbreakR: an Introduction HTML R Script
Reference Manual PDF

Details

biocViews ChIPSeq, MotifAnnotation, Software, Transcription, Visualization
Version 2.18.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-2
Depends R (>= 4.3.0), 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, pwalign
System Requirements
URL
Bug Reports https://github.com/Simon-Coetzee/motifbreakR/issues
See More
Suggests BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle
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Package Archives

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

Source Package motifbreakR_2.18.0.tar.gz
Windows Binary motifbreakR_2.18.0.zip
macOS Binary (x86_64) motifbreakR_2.18.0.tgz
macOS Binary (arm64) motifbreakR_2.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/motifbreakR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/motifbreakR
Bioc Package Browser https://code.bioconductor.org/browse/motifbreakR/
Package Short Url https://bioconductor.org/packages/motifbreakR/
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