Package: periodicDNA
Type: Package
Title: Set of tools to identify periodic occurrences of k-mers in 
    DNA sequences
Version: 1.0.0
Date: 2020-05-03
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, 
    GenomeInfoDb,
    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
