periodicDNA
This is the development version of periodicDNA; for the stable release version, see periodicDNA.
All Bioconductor versions of periodicDNA
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12
Set of tools to identify periodic occurrences of k-mers in DNA sequences
Bioconductor version: 3.24 · Package version: 1.23.0
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 gmail.com>
Citation
From within R, enter citation("periodicDNA"):
Jacques Serizay. periodicDNA: Set of tools to identify periodic occurrences of k-mers in DNA sequences. doi:10.18129/B9.bioc.periodicDNA, R package version 1.23.0, https://bioconductor.org/packages/periodicDNA.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("periodicDNA")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.23.0 |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/js2264/periodicDNA |
| Bug Reports | https://github.com/js2264/periodicDNA/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.12 (R-4.0) (5 years) |
| Downloads rank | 980 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/periodicDNA/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("periodicDNA")| periodicDNA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | periodicDNA_1.23.0.tar.gz |
| Windows binary (x86_64) | periodicDNA_1.23.0.zip |
| macOS binary (arm64) | periodicDNA_1.23.0.tgz |
| macOS binary (x86_64) | periodicDNA_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/periodicDNA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/periodicDNA |
| Package Downloads Report | Download Stats |
Dependencies
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