Package: motifbreakR
Title: A Package for Predicting the Disruptiveness of Single Nucleotide
        Polymorphisms on Transcription Factor Binding Sites
Version: 2.27.4
Authors@R: c(person(given="Simon Gert", family="Coetzee",
        email="coetzee@uthscsa.edu", role = c("aut", "cre"),
        comment=c(ORCID="0000-0003-4267-5930")),
        person(given="Dennis J.", family="Hazelett",
        email="dennis.hazelett@cshs.org", role = c("aut")))
Description: 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.
        Both single nucleotide variants and small insertions and
        deletions (indels) are supported. Lastly, it can be used to
        interrogate any genome curated within Bioconductor as a
        BSgenome package.
Depends: R (>= 4.4.0), grid, MotifDb
Imports: methods, grDevices, stringr, 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, testthat (>= 3.0.0), withr
VignetteBuilder: knitr
Encoding: UTF-8
License: GPL-2
BugReports: https://github.com/Simon-Coetzee/motifbreakR/issues
biocViews: ChIPSeq, Visualization, MotifAnnotation, Transcription
NeedsCompilation: no
Config/testthat/edition: 3
Config/roxygen2/version: 8.1.0
Config/pak/sysreqs: cmake make libgsl0-dev libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-07 04:30:20 UTC
RemoteUrl: https://github.com/bioc/motifbreakR
RemoteRef: HEAD
RemoteSha: 79191d66d267418c562dc812ba622ad3c1e6ac85
Packaged: 2026-10-11 12:08:26 UTC; root
Author: Simon Gert Coetzee [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-4267-5930>),
  Dennis J. Hazelett [aut]
Maintainer: Simon Gert Coetzee <coetzee@uthscsa.edu>