Science Score: 10.0%
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Low similarity (12.0%) to scientific vocabulary
Repository
Codon Usage Analysis and Prediction of Gene Expressivity
Statistics
- Stars: 22
- Watchers: 2
- Forks: 1
- Open Issues: 11
- Releases: 0
Metadata Files
README.md
coRdon 
Codon Usage Analysis and Prediction of Gene Expressivity
R package for analysis and visualization of codon usage in DNA sequences.
Main functionalities: * calculates different measures of CU bias and CU-based predictors of gene expressivity * performs gene set enrichment analysis for unannotated or KEGG/COG annotated DNA sequences * implements several methods for visualization of codon usage and enrichment analysis results.
Although specifically aimed at the analysis of metagenomic samples, coRdon allows for the inspection and quantification of codon usage in DNA sequences using any of the 20 different variants of genetic code, with the additional options to include stop codons and alternative start codons in calculations.
The following statistics are implemented in the package:
- ENC, effective number of codons
(Wright, 1990),
- its modified version ENC'
(Novembre, 2002),
- a measure of codon bias, termed B
(Karlin and Mrazek, 1996),
- and related measure of expression, E
(Karlin and Mrazek, 2000),
- maximum likelihood codon bias, MCB
(Urrutia and Hurst, 2001),
- MILC, Measure Independent of Length and Composition, and
- MELP, MILC-based Expression Level Predictor (Supek and Vlahovicek, 2005),
- SCUO, synonymous codon usage orderliness (Wan et al., 2004),
- Codon Adaptation Index, CAI
(Sharp and Li, 1987),
- frequency of optimal codons, Fop
(Ikemura 1981),
- gene codon bias, GCB (Merkl, 2003).
The package also implements B plot for visualization of CU bias, both within a single sample and between different samples for which CU bias statistics are calculated.
Additionally, if the input sequences are annotated in either KEGG or COG orthology database, functional analysis can be performed in order to determine significantly enriched functions in the imput sample. This is aimed particularly at metagenomic samples, as a way of determining functional fingerprint of a microbial community. There are also several methods for visualisation of enrichment analysis results, including MA-like plot and bar plot.
Geting started
To install coRdon, run the following in R:
{r}
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("coRdon")
The developmental version can be installed directly from from GitHub:
{r}
devtools::install_github("BioinfoHR/coRdon")
For worked example on how to do analysis of codon usage with coRdon, please see the package vignette.
GitHub Events
Total
- Watch event: 3
- Issue comment event: 2
- Member event: 1
Last Year
- Watch event: 3
- Issue comment event: 2
- Member event: 1
Committers
Last synced: almost 3 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Anamaria Elek | a****k@g****m | 83 |
| BioinfoHR | B****R | 27 |
| BioinfoHR | m****c@b****r | 8 |
| vobencha | v****a@g****m | 2 |
| Maja Kuzman | 3****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 18
- Total pull requests: 0
- Average time to close issues: 26 days
- Average time to close pull requests: N/A
- Total issue authors: 18
- Total pull request authors: 0
- Average comments per issue: 1.22
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
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- CongLiu37 (1)
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 19,834 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: coRdon
Codon Usage Analysis and Prediction of Gene Expressivity
- Homepage: https://github.com/BioinfoHR/coRdon
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/coRdon/inst/doc/coRdon.pdf
- License: Artistic-2.0
-
Latest release: 1.26.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.5 depends
- Biobase * imports
- Biostrings * imports
- data.table * imports
- dplyr * imports
- ggplot2 * imports
- methods * imports
- purrr * imports
- stats * imports
- stringr * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests