Man pages for cubar
Codon Usage Bias Analysis
| 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) |
