cubar
Overview
cubar is a package for codon usage bias analysis in R. Main features are listed as follows:
- Codon level analyses
- Support NCBI and custom genetic codes
- Calculate tRNA weights
- Calculate relative synonymous codon usage (RSCU)
- Machine learning-based inference of optimal codons
- Visualization codon-anticodon pairing relationships
- Gene level analyses
- Codon frequency matrix
- Codon Adaptation Index (CAI)
- Mean Codon Stabilization Coefficients (CSCg)
- Effective number of codons (ENC)
- Fraction of optimal codons (Fop)
- GC content at 4-fold degenerate sites (GC4d)
- tRNA Adaptation Index (tAI)
Dependencies
Depends
Imports
Biostrings
(>= 2.60.0),
IRanges
(>= 2.34.0),
data.table
(>= 1.14.0),
ggplot2
(>= 3.3.5),
rlang
(>= 0.4.11)
Installation
The latest release of cubar
can be installed with:
The latest developmental version of cubar
can be installed with:
Usage
Documentation can be found within R (by typing ?function_name
). The following tutorials are available from our website:
Suggests
- Biostrings for sequence input/output and manipulation.
- Peptides for peptide- or protein-related indices.
Getting help
Please use GitHub issues for bug reports, questions, and feature requests.