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

## Documentation for package ‘motifbreakR’ version 2.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

calculatePvalue | Calculate the significance of the matches for the reference and alternate alleles for the for their PWM
encodemotif | MotifDb object containing motif information from the known and discovered motifs for the ENCODE TF ChIP-seq datasets.
example.results | Example Results from motifbreakR
exportMBbed | Export motifbreakR variants to bed file
exportMBtable | Export motifbreakR results to csv or tsv
factorbook | MotifDb object containing motif information from around the genomic regions bound by 119 human transcription factors in Factorbook.
findSupportingRemapPeaks | Find Corresponding TF Binding From The ReMap2022 Project
hocomoco | MotifDb object containing motif information from Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models
homer | MotifDb object containing motif information from motif databases included in HOMER.
motifbreakR | Predict The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
motifbreakR_motif | MotifDb object containing motif information from the motif databases of HOCOMOCO, Homer, FactorBook and ENCODE
plotMB | Plot a genomic region surrounding a genomic variant, and potentially disrupted motifs
shiny_motifbreakR | Run Shiny version of the motifbreakR package.
snps.from.file | Import SNPs from a BED file or VCF file for use in motifbreakR
snps.from.rsid | Import SNPs from rsid for use in motifbreakR
variants.from.file | Import SNPs from a BED file or VCF file for use in motifbreakR