Package index • cubar

All functions

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)