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coRdon

Codon Usage Analysis and Prediction of Gene Expressivity


Bioconductor version: Release (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
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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