Package: universalmotif
Title: Import, Modify, and Export Motifs with R
Version: 1.29.0
Authors@R: c(
      person(c("Benjamin", "Jean-Marie"), "Tremblay", role = c("aut", "cre"),
        email = "benjamin.tremblay@uwaterloo.ca",
        comment = c(ORCID = "0000-0002-7441-2951")),
      person("Spencer", "Nystrom", role = "ctb",
        comment = c(ORCID = "0000-0003-1000-1579"))
    )
URL: https://bioconductor.org/packages/universalmotif/
BugReports: https://github.com/bjmt/universalmotif/issues
Description: Allows for importing most common motif types into R for use by
    functions provided by other Bioconductor motif-related packages. Motifs can
    be exported into most major motif formats from various classes as defined
    by other Bioconductor packages. A suite of motif and sequence manipulation
    and analysis functions are included, including enrichment, comparison,
    P-value calculation, shuffling, trimming, higher-order motifs, and others.
Depends: R (>= 4.1.0)
License: GPL-3
Encoding: UTF-8
Imports: methods, stats, utils, MASS, ggplot2, yaml, IRanges, Rcpp,
        Biostrings, BiocGenerics, S4Vectors, rlang, grid,
        MatrixGenerics
Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
        testthat, BiocParallel, seqLogo, motifStack, dplyr, ape,
        ggtree, processx, ggseqlogo, cowplot, GenomicRanges, ggbio
Enhances: PWMEnrich, rGADEM
LinkingTo: Rcpp, RcppThread
VignetteBuilder: knitr
biocViews: MotifAnnotation, MotifDiscovery, DataImport, GeneRegulation
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE, old_usage = TRUE)
Language: en-GB
Collate: 'RcppExports.R' 'add_multifreq.R' 'compare_motifs.R'
        'universalmotif-class.R' 'convert_motifs.R' 'convert_type.R'
        'create_motif.R' 'create_sequences.R' 'data.R'
        'enrich_motifs.R' 'filter_motifs.R' 'get_bkg.R'
        'make_DBscores.R' 'merge_motifs.R' 'merge_similar.R'
        'motif_clusters.R' 'motif_finder.R' 'motif_peaks.R'
        'motif_pvalue.R' 'motif_rc.R' 'motif_tree.R' 'read_cisbp.R'
        'read_homer.R' 'read_jaspar.R' 'read_matrix.R' 'read_meme.R'
        'read_motifs.R' 'read_transfac.R' 'read_uniprobe.R'
        'run_meme.R' 'sample_sites.R' 'scan_sequences.R'
        'sequence_complexity.R' 'shuffle_motifs.R'
        'shuffle_sequences.R' 'switch_alph.R' 'trim_motifs.R'
        'universalmotif-methods.R' 'universalmotif.R'
        'universalmotif_df.R' 'utils-internal.R' 'utils-motif.R'
        'utils-sequence.R' 'view_logo.R' 'view_motifs.R'
        'write_homer.R' 'write_jaspar.R' 'write_matrix.R'
        'write_meme.R' 'write_motifs.R' 'write_transfac.R' 'zzz.R'
git_url: https://git.bioconductor.org/packages/universalmotif
git_branch: devel
git_last_commit: 6692d9a
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-10-31
NeedsCompilation: yes
Packaged: 2025-11-01 00:49:56 UTC; biocbuild
Author: Benjamin Jean-Marie Tremblay [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-7441-2951>),
  Spencer Nystrom [ctb] (ORCID: <https://orcid.org/0000-0003-1000-1579>)
Maintainer: Benjamin Jean-Marie Tremblay <benjamin.tremblay@uwaterloo.ca>
