coRdon

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see coRdon.

Codon Usage Analysis and Prediction of Gene Expressivity

Bioconductor version: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BiomedicalInformatics, GeneExpression, GenePrediction, GeneSetEnrichment, Genetics CellBiology, ImmunoOncology, KEGG, Metagenomics, Pathways, Software, Visualization

Version 1.26.0

In Bioconductor since BioC 3.8 (R-3.5) (7 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

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_1.26.0.tar.gz

Windows Binary (x86_64) coRdon_1.26.0.zip

macOS Binary (x86_64) coRdon_1.26.0.tgz

macOS Binary (arm64) coRdon_1.26.0.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