Package: motifbreakR
Title: A Package For Predicting The Disruptiveness Of Single Nucleotide
        Polymorphisms On Transcription Factor Binding Sites
Version: 2.24.0
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.
        Lastly, it can be used to interrogate any genome curated within
        Bioconductor (currently there are 32 species, a total of 109 
        versions).
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
VignetteBuilder: knitr
Encoding: UTF-8
License: GPL-2
BugReports: https://github.com/Simon-Coetzee/motifbreakR/issues
biocViews: ChIPSeq, Visualization, MotifAnnotation, Transcription
NeedsCompilation: no
RoxygenNote: 7.3.2
git_url: https://git.bioconductor.org/packages/motifbreakR
git_branch: RELEASE_3_22
git_last_commit: 79ca231
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
Packaged: 2025-10-30 03:33:53 UTC; biocbuild
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>
Built: R 4.5.1; ; 2025-10-30 09:32:14 UTC; unix
