periodicDNA

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

Bioconductor version: Release (3.17)

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")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("periodicDNA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("periodicDNA")

Introduction to periodicDNA	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software
Version	1.10.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 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
Linking To
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
System Requirements
Enhances
URL	https://github.com/js2264/periodicDNA
Bug Reports	https://github.com/js2264/periodicDNA/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	periodicDNA_1.10.0.tar.gz
Windows Binary	periodicDNA_1.10.0.zip
macOS Binary (x86_64)	periodicDNA_1.10.0.tgz
macOS Binary (arm64)	periodicDNA_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/periodicDNA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/periodicDNA
Bioc Package Browser	https://code.bioconductor.org/browse/periodicDNA/
Package Short Url	https://bioconductor.org/packages/periodicDNA/
Package Downloads Report	Download Stats