Codon Usage Bias Analysis
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Documentation for package ‘cubar’ version 0.6.0
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_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 |
| 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) |