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 (>= 3.5.0)
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
