coRdon

DOI: 10.18129/B9.bioc.coRdon    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see coRdon.

Codon Usage Analysis and Prediction of Gene Expressivity

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

HTML	R Script	coRdon
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, GeneExpression, GenePrediction, GeneSetEnrichment, Genetics CellBiology, ImmunoOncology, KEGG, Metagenomics, Pathways, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	Artistic-2.0
Depends	R (>= 3.5)
Imports	methods, stats, utils, Biostrings, Biobase, dplyr, stringr, purrr, ggplot2, data.table
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/BioinfoHR/coRdon
BugReports	https://github.com/BioinfoHR/coRdon/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	coRdon_1.2.0.tar.gz
Windows Binary	coRdon_1.2.0.zip
Mac OS X 10.11 (El Capitan)	coRdon_1.2.0.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