# Codon Usage Bias Analysis

## Documentation for package ‘cubar’ version 1.0.0

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

## Help Pages

aa2codon | amino acids to codons
check_cds | Quality control of CDS
codon_diff | Differential codon usage analysis
codon_optimize | Optimize codons
count_codons | Count occurrences of different codons
create_codon_table | create custom codon table from a data frame
est_csc | Estimate Codon Stabilization Coefficient
est_optimal_codons | Estimate optimal codons
est_rscu | Estimate RSCU
est_trna_weight | Estimate tRNA weight w
get_cai | Calculate CAI
get_codon_table | get codon table by NCBI gene code ID
get_cscg | Mean Codon Stabilization Coefficients
get_dp | Deviaiton from Proportionality
get_enc | Calculate ENC
get_fop | Fraction of optimal codons (Fop)
get_gc | GC contents
get_gc3s | GC contents at synonymous 3rd codon positions
get_gc4d | GC contents at 4-fold degenerate sites
get_tai | Calculate TAI
human_mt | human mitochondrial CDS sequences
plot_ca_pairing | Plot codon-anticodon pairing relationship
rev_comp | Reverse complement
seq_to_codons | Convert CDS to codons
show_codon_tables | show available codon tables
slide | slide window interval generator
slide_apply | apply a cub index to a sliding window
slide_codon | sliding window of codons
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)