periodicDNA

DOI: 10.18129/B9.bioc.periodicDNA    

This package is for version 3.15 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: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 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
LinkingTo
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
SystemRequirements
Enhances
URL	https://github.com/js2264/periodicDNA
BugReports	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_1.6.0.tar.gz
Windows Binary	periodicDNA_1.6.0.zip
macOS Binary (x86_64)	periodicDNA_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/periodicDNA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/periodicDNA
Package Short Url	https://bioconductor.org/packages/periodicDNA/
Package Downloads Report	Download Stats