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

• R (>= 4.1.0)

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:

install.packages("cubar")

The latest developmental version of cubar can be installed with:

devtools::install_github("mt1022/cubar", dependencies = TRUE)

Usage

Documentation can be found within R (by typing ?function_name). The following tutorials are available from our website:

• Get Started
• Non-standard Genetic Code
• Theories behind cubar

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.