motifbreakR
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
Bioconductor version: 3.23 · Package version: 2.26.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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).
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("motifbreakR")Details
| Maintainer | Simon Gert Coetzee <coetzee@uthscsa.edu> |
| Author | Simon Gert Coetzee [aut, cre] (ORCID: <https://orcid.org/0000-0003-4267-5930>), Dennis J. Hazelett [aut] |
| License | GPL-2 |
| Bug Reports | https://github.com/Simon-Coetzee/motifbreakR/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, MotifAnnotation, Software, Transcription, Visualization |
| Package Short Url | https://bioconductor.org/packages/motifbreakR/ |
Citation
From within R, enter citation("motifbreakR"):
Simon Gert Coetzee, Dennis J. Hazelett. motifbreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites. doi:10.18129/B9.bioc.motifbreakR, R package version 2.26.0, https://bioconductor.org/packages/motifbreakR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Dependencies
Depends: R (>= 4.4.0), 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, DT, bsicons, BiocFileCache, biomaRt, bslib, shiny, vroom
Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP155.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle, BSgenome.Hsapiens.1000genomes.hs37d5, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Hsapiens.NCBI.GRCh38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Hsapiens.UCSC.hg38