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)
