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                  Deviation 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)
