Package: universalmotif
Title: Import, Modify, and Export Motifs with R
Version: 1.8.3
Authors@R: c(
      person(c("Benjamin", "Jean-Marie"), "Tremblay", role = c("aut", "cre"),
        email = "b2tremblay@uwaterloo.ca",
        comment = c(ORCID = "0000-0002-7441-2951")),
      person("Spencer", "Nystrom", role = "ctb")
    )
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, ggseqlogo, yaml,
        IRanges, Rcpp, Rdpack (>= 0.7), Biostrings, BiocGenerics,
        S4Vectors, rlang, grid
Suggests: spelling, knitr, bookdown, TFBSTools, rmarkdown, MotifDb,
        testthat, Logolas, BiocParallel, seqLogo, motifStack, dplyr,
        ape, ggtree, processx
Enhances: MotIV, PWMEnrich, rGADEM, motifRG
LinkingTo: Rcpp, RcppThread
RdMacros: Rdpack
VignetteBuilder: knitr
biocViews: MotifAnnotation, MotifDiscovery, DataImport, GeneRegulation
RoxygenNote: 7.1.1
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' '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' 'shuffle_motifs.R' 'shuffle_sequences.R'
        'switch_alph.R' 'trim_motifs.R' 'universalmotif-methods.R'
        'universalmotif.R' 'utils-internal.R' 'utils-motif.R'
        'utils-sequence.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: RELEASE_3_12
git_last_commit: 3f4e9ef
git_last_commit_date: 2020-12-20
Date/Publication: 2020-12-20
NeedsCompilation: yes
Packaged: 2020-12-21 04:03:51 UTC; biocbuild
Author: Benjamin Jean-Marie Tremblay [aut, cre]
    (<https://orcid.org/0000-0002-7441-2951>),
  Spencer Nystrom [ctb]
Maintainer: Benjamin Jean-Marie Tremblay <b2tremblay@uwaterloo.ca>
Built: R 4.0.3; x86_64-apple-darwin13.4.0; 2021-03-29 02:21:39 UTC; unix
