# Codon Usage Bias Analysis

## Documentation for package ‘cubar’ version 1.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

aa2codon | amino acids to codons
ca_pairs | Generate codon-anticodon pairing relationship
check_cds | Quality control and preprocessing of coding sequences
codon_diff | Differential codon usage analysis
codon_optimize | Optimize codon usage in coding sequences
count_codons | Count codon frequencies in coding sequences
create_codon_table | Create custom codon table from amino acid-codon mapping
est_aau | Estimate Amino Acid Usage Frequencies of CDSs.
est_csc | Estimate Codon Stabilization Coefficient
est_optimal_codons | Identify optimal codons using statistical modeling
est_rscu | Estimate Relative Synonymous Codon Usage (RSCU)
est_trna_weight | Estimate tRNA weights for TAI calculation
extract_trna_gcn | Extract tRNA gene copy numbers from nature tRNA sequences
get_aau | Amino Acid Usage
get_cai | Calculate Codon Adaptation Index (CAI)
get_codon_table | Retrieve codon table by NCBI genetic code ID
get_cscg | Mean Codon Stabilization Coefficients
get_dp | Deviation from Proportionality
get_enc | Calculate effective number of codons (ENC)
get_fop | Calculate fraction of optimal codons (Fop)
get_gc | Calculate GC content of coding sequences
get_gc3s | GC contents at synonymous 3rd codon positions
get_gc4d | GC contents at 4-fold degenerate sites
get_tai | Calculate tRNA Adaptation Index (TAI)
human_mt | human mitochondrial CDS sequences
plot_ca_pairs | Plot codon-anticodon pairing relationship
rev_comp | Generate reverse complement sequences
seq_to_codons | Convert a coding sequence to a codon vector
show_codon_tables | Display available genetic code tables
slide | Generate sliding window intervals
slide_apply | apply a cub index to a sliding window
slide_codon | Generate sliding windows for codon-level analysis
slide_plot | plot sliding window codon usage
yeast_cds | yeast CDS sequences
yeast_exp | yeast mRNA expression levels
yeast_half_life | Half life of yeast mRNAs
yeast_trna | yeast tRNA sequences
yeast_trna_gcn | yeast tRNA gene copy numbers (GCN)