coRdon

DOI: 10.18129/B9.bioc.coRdon    

Codon Usage Analysis and Prediction of Gene Expressivity

Bioconductor version: Release (3.8)

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 "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("coRdon", version = "3.8")

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 GeneExpression, GenePrediction, GeneSetEnrichment, KEGG, Metagenomics, Pathways, Software, Visualization
Version 1.0.0
License Artistic-2.0
Depends R (>= 3.5)
Imports methods, stats, utils, Biostrings, Biobase, dplyr, 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_1.0.0.tar.gz
Windows Binary coRdon_1.0.0.zip
Mac OS X 10.11 (El Capitan) coRdon_1.0.0.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 http://bioconductor.org/packages/coRdon/
Package Downloads Report Download Stats

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