DOI: 10.18129/B9.bioc.periodicDNA    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see periodicDNA.

Set of tools to identify periodic occurrences of k-mers in DNA sequences

Bioconductor version: 3.12

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.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at>

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biocViews Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (0.5 years)
License GPL-3 + file LICENSE
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
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