coRdon
Codon Usage Analysis and Prediction of Gene Expressivity
Bioconductor version: Release (3.19)
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 "4.4") 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 | 1.22.0 |
In Bioconductor since | BioC 3.8 (R-3.5) (6 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 | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | coRdon_1.22.0.tar.gz |
Windows Binary | coRdon_1.22.0.zip |
macOS Binary (x86_64) | coRdon_1.22.0.tgz |
macOS Binary (arm64) | coRdon_1.22.0.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 |