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 (3.21)
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:
Maintainer: Jacques Serizay <jacquesserizay at gmail.com>
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")| Introduction to periodicDNA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Coverage, DataImport, MotifAnnotation, MotifDiscovery, SequenceMatching, Sequencing, Software |
| Version | 1.17.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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.
| Source Package | periodicDNA_1.17.0.tar.gz |
| Windows Binary (x86_64) | periodicDNA_1.17.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |