coRdon
This is the released version of coRdon; for the devel version, see coRdon.
Codon Usage Analysis and Prediction of Gene Expressivity
Bioconductor version: Release (3.23)
Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.
Author: Anamaria Elek [cre, aut], Maja Kuzman [aut], Kristian Vlahovicek [aut]
Maintainer: Anamaria Elek <anamariaelek at gmail.com>
citation("coRdon")):Anamaria Elek, Maja Kuzman, Kristian Vlahovicek. coRdon: Codon Usage Analysis and Prediction of Gene Expressivity. doi:10.18129/B9.bioc.coRdon, R package version 1.30.0, https://bioconductor.org/packages/coRdon.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("coRdon")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("coRdon")| coRdon | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, GeneExpression, GenePrediction, GeneSetEnrichment, Genetics CellBiology, ImmunoOncology, KEGG, Metagenomics, Pathways, Software, Visualization |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5) |
| Imports | methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table |
| System Requirements | |
| URL | https://github.com/BioinfoHR/coRdon |
| Bug Reports | https://github.com/BioinfoHR/coRdon/issues |
See More
| Suggests | BiocStyle, testthat, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | vhcub |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | coRdon_1.30.0.tar.gz |
| Windows Binary (x86_64) | coRdon_1.30.0.zip |
| macOS Binary (big-sur-x86_64) | coRdon_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | coRdon_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/coRdon |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/coRdon |
| Package Short Url | https://bioconductor.org/packages/coRdon/ |
| Package Downloads Report | Download Stats |