Package: periodicDNA
Type: Package
Title: Set of tools to identify periodic occurrences of k-mers in DNA
        sequences
Version: 1.23.0
Date: 2025-07-24
Encoding: UTF-8
Authors@R: 
    c(person(given = "Jacques",
           family = "Serizay",
           role = c("aut", "cre"),
           email = "jacquesserizay@gmail.com",
           comment = c(ORCID = "0000-0002-4295-0624")))
Description: This R package helps the user identify k-mers 
    (e.g. di- or tri-nucleotides) present periodically in a set of genomic 
    loci (typically regulatory elements). The functions of this package 
    provide a straightforward approach to find periodic occurrences 
    of k-mers in DNA sequences, such as regulatory 
    elements. It is not aimed at identifying motifs separated by a 
    conserved distance; for this type of analysis, please visit MEME website. 
URL: https://github.com/js2264/periodicDNA
BugReports: https://github.com/js2264/periodicDNA/issues
RoxygenNote: 7.1.0
Depends: R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome,
        BiocParallel
Imports: S4Vectors, rtracklayer, stats, Seqinfo, magrittr, zoo,
        ggplot2, methods, parallel, cowplot
Suggests: BSgenome.Scerevisiae.UCSC.sacCer3,
        BSgenome.Celegans.UCSC.ce11, BSgenome.Dmelanogaster.UCSC.dm6,
        BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Mmusculus.UCSC.mm10, reticulate, testthat, covr,
        knitr, rmarkdown, pkgdown
VignetteBuilder: knitr
biocViews: SequenceMatching, MotifDiscovery, MotifAnnotation,
        Sequencing, Coverage, Alignment, DataImport
License: GPL-3 + file LICENSE
git_url: https://git.bioconductor.org/packages/periodicDNA
git_branch: devel
git_last_commit: e77802f
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.24
Date/Publication: 2026-05-18
NeedsCompilation: no
Packaged: 2026-05-18 23:01:28 UTC; biocbuild
Author: Jacques Serizay [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4295-0624>)
Maintainer: Jacques Serizay <jacquesserizay@gmail.com>
Built: R 4.6.0; ; 2026-05-19 05:03:02 UTC; unix
