Codon Usage Bias Analysis


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Documentation for package ‘cubar’ version 1.2.0

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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)