Package: universalmotif
Title: Import, Modify, and Export Motifs with R
Version: 1.0.22
Authors@R: person(c("Benjamin", "Jean-Marie"), "Tremblay", role = c("aut",
    "cre"), email = "b2tremblay@uwaterloo.ca")
URL: https://github.com/bjmt/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, ggplot2, ape, ggtree, ggseqlogo, stats, utils,
        gtools, Rdpack (>= 0.7), Biostrings, BiocGenerics, Rcpp,
        processx
Suggests: knitr, BiocStyle, TFBSTools, MotIV, PWMEnrich, motifStack,
        seqLogo, rmarkdown, MotifDb, testthat, rGADEM, motifRG,
        motifbreakR, RcisTarget, motifcounter, Logolas, BiocParallel,
        BCRANK
LinkingTo: Rcpp
RdMacros: Rdpack
VignetteBuilder: knitr
biocViews: MotifAnnotation, MotifDiscovery, DataImport, GeneRegulation
RoxygenNote: 6.1.1
Roxygen: list(markdown = TRUE)
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' 'merge_motifs.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.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_8
git_last_commit: 34a663f
git_last_commit_date: 2019-03-06
Date/Publication: 2019-03-06
NeedsCompilation: yes
Packaged: 2019-03-07 05:18:45 UTC; biocbuild
Author: Benjamin Jean-Marie Tremblay [aut, cre]
Maintainer: Benjamin Jean-Marie Tremblay <b2tremblay@uwaterloo.ca>
Built: R 3.5.2; i386-w64-mingw32; 2019-03-07 12:52:09 UTC; windows
Archs: i386, x64
