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Bioconductor - periodicDNA (development version)

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 (3.22)

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] ORCID: 0000-0002-4295-0624

Maintainer: Jacques Serizay <jacquesserizay at gmail.com>

Citation (from within R, enter citation("periodicDNA")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 See More 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.

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