periodicDNA

This package is for version 3.14 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: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software

Version 1.4.0

In Bioconductor since BioC 3.12 (R-4.0) (3.5 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

System Requirements

URL https://github.com/js2264/periodicDNA

Bug Reports https://github.com/js2264/periodicDNA/issues

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

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

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

Source Package periodicDNA_1.4.0.tar.gz

Windows Binary periodicDNA_1.4.0.zip

macOS 10.13 (High Sierra) periodicDNA_1.4.0.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

Old Source Packages for BioC 3.14 Source Archive