coRdon

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see coRdon.

Codon Usage Analysis and Prediction of Gene Expressivity


Bioconductor version: 3.18

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 (from within R, enter citation("coRdon")):

Installation

To install this package, start R (version "4.3") 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 PDF
NEWS Text

Details

biocViews BiomedicalInformatics, GeneExpression, GenePrediction, GeneSetEnrichment, Genetics CellBiology, ImmunoOncology, KEGG, Metagenomics, Pathways, Software, Visualization
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package coRdon_1.20.0.tar.gz
Windows Binary coRdon_1.20.0.zip
macOS Binary (x86_64) coRdon_1.20.0.tgz
macOS Binary (arm64) coRdon_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/coRdon
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/coRdon
Bioc Package Browser https://code.bioconductor.org/browse/coRdon/
Package Short Url https://bioconductor.org/packages/coRdon/
Package Downloads Report Download Stats