Package: periodicDNA
Type: Package
Title: Set of tools to identify periodic occurrences of k-mers in DNA
        sequences
Version: 1.20.0
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
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:01:58 UTC
RemoteUrl: https://github.com/bioc/periodicDNA
RemoteRef: RELEASE_3_22
RemoteSha: 4feee90ff3d5fbefd4632a14203ae9abea919f62
NeedsCompilation: no
Packaged: 2026-03-04 08:40:24 UTC; root
Author: Jacques Serizay [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4295-0624>)
Maintainer: Jacques Serizay <jacquesserizay@gmail.com>
Built: R 4.5.2; ; 2026-03-04 08:44:27 UTC; windows
