README.md

In CCDM-Programming-Club/codonfriend: Analyse Codon Usage With Your Pals

codonfriend

Deviations from normal codon usage may indicate some compartmentalisation of mutational load (e.g. RIP) or presence of foreign DNA (e.g. horizontal transfer). Codonfriend is a small library for working with codon data and facilitating analyses of codon usage.

Quick Install

This is a working project so for now I suggest you clone the repository and use devtools or rstudio to work with it. You should also be able to install using devtools.

devtools::install_github("https://github.com/CCDM-Programming-Club/codonfriend.git")

Roadmap

• [ ] A way to calculate CUT and CAIs for input fasta files.
• [x] Parse existing tables from EMBOSS
• [ ] Write our own version
• [ ] Plot CAI/CUT distributions (Histograms etc.)
• [ ] Basic statistical properties of CAI distributions (e.g. quartiles, fitting a model etc)
• [ ] Define what an “interesting” gene is wrt CAI or CUT e.g 5th percentile
• [ ] Validation - where are the known effectors and LGT candidates?
• [ ] Compare codon usage between genomes.
• [ ] Clustering 3-mers of “interesting” genes, are there differences between LGT candidates and RIPd candidates.
• [ ] Identify RIP-like codon changes.
• [ ] Regional biases in codon usage or CAI.

Contributing

Please see the contribution guide

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

CCDM-Programming-Club/codonfriend documentation built on May 9, 2019, 3:20 a.m.