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

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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("motifbreakR")
AuthorSimon Gert Coetzee [aut, cre] Dennis J. Hazelett [aut]
Bioconductor views ChIPSeq MotifAnnotation Visualization
Date of publicationNone
MaintainerSimon Gert Coetzee <Simon.Coetzee@cshs.org>
LicenseGPL-2
Version1.6.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/data.R R/locus.from.rsid.R R/scoreMotif.R
README.md
build
build/vignette.rds
data
data/datalist
data/encodemotif.rda
data/example.results.rda
data/factorbook.rda
data/hocomoco.rda
data/homer.rda
data/motifbreakR_motif.rda
inst
inst/CITATION
inst/doc
inst/doc/motifbreakR-vignette.R
inst/doc/motifbreakR-vignette.Rmd
inst/doc/motifbreakR-vignette.html
inst/extdata
inst/extdata/danRer.bed
inst/extdata/example.pvalue.rda
inst/extdata/example.snpfrombed.rda
inst/extdata/pca.enhancer.snps
inst/extdata/pca.enhancer.snps.rda
inst/extdata/snps.bed
man
man/calculatePvalue.Rd man/encodemotif.Rd man/example.results.Rd man/factorbook.Rd man/hocomoco.Rd man/homer.Rd man/motifbreakR.Rd man/motifbreakR_motif.Rd man/plotMB.Rd man/snps.from.file.Rd man/snps.from.rsid.Rd
vignettes
vignettes/motifbreakR-vignette.Rmd
vignettes/motifbreakr-manuscript.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.