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).

Author
Simon Gert Coetzee [aut, cre] Dennis J. Hazelett [aut]
Date of publication
None
Maintainer
Simon Gert Coetzee <Simon.Coetzee@cshs.org>
License
GPL-2
Version
1.4.0

View on Bioconductor

Man pages

calculatePvalue
Calculate the significance of the matches for the reference...
encodemotif
MotifDb object containing motif information from the known...
example.results
Example Results from motifbreakR
factorbook
MotifDb object containing motif information from around the...
hocomoco
MotifDb object containing motif information from Homo Sapiens...
homer
MotifDb object containing motif information from motif...
motifbreakR
Predict The Disruptiveness Of Single Nucleotide Polymorphisms...
motifbreakR_motif
MotifDb object containing motif information from the motif...
plotMB
Plot a genomic region surrounding a genomic variant, and...
snps.from.file
Import SNPs from a BED file or VCF file for use in...
snps.from.rsid
Import SNPs from rsid for use in motifbreakR

Files in this package

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