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 (3.24)
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("periodicDNA")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.0), Biostrings, GenomicRanges, IRanges, BSgenome, BiocParallel |
| Imports | S4Vectors, rtracklayer, stats, Seqinfo, 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | periodicDNA_1.23.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | periodicDNA_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | periodicDNA_1.23.0.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 |