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periodicDNA

This is the development version of periodicDNA; for the stable release version, see periodicDNA.

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

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.11.0
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
See More
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_1.11.0.tar.gz
Windows Binary periodicDNA_1.11.0.zip
macOS Binary (x86_64) periodicDNA_1.11.0.tgz
macOS Binary (arm64) periodicDNA_1.11.0.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