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>
citation("coRdon")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
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) (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 | |
| 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_1.2.0.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 [email protected]:packages/coRdon |
| Bioc Package Browser | https://code.bioconductor.org/browse/coRdon/ |
| Package Short Url | https://bioconductor.org/packages/coRdon/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |