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cubar

Comprehensive Codon Usage Bias Analysis in R

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Version

Install

install.packages('cubar')

Monthly Downloads

308

Version

1.2.0

License

MIT + file LICENSE

Issues

1

Pull Requests

0

Stars

8

Forks

2

Maintainer

Hong Zhang

Last Published

August 19th, 2025

Functions in cubar (1.2.0)

rev_comp

Generate reverse complement sequences
human_mt

human mitochondrial CDS sequences
seq_to_codons

Convert a coding sequence to a codon vector
plot_ca_pairs

Plot codon-anticodon pairing relationship
show_codon_tables

Display available genetic code tables
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)
get_gc

Calculate GC content of coding sequences
slide

Generate sliding window intervals
slide_plot

plot sliding window codon usage
yeast_cds

yeast CDS sequences
slide_codon

Generate sliding windows for codon-level analysis
slide_apply

apply a cub index to a sliding window
yeast_trna

yeast tRNA sequences
yeast_exp

yeast mRNA expression levels
yeast_trna_gcn

yeast tRNA gene copy numbers (GCN)
yeast_half_life

Half life of yeast mRNAs
create_codon_table

Create custom codon table from amino acid-codon mapping
est_csc

Estimate Codon Stabilization Coefficient
ca_pairs

Generate codon-anticodon pairing relationship
codon_diff

Differential codon usage analysis
count_codons

Count codon frequencies in coding sequences
est_optimal_codons

Identify optimal codons using statistical modeling
est_aau

Estimate Amino Acid Usage Frequencies of CDSs.
check_cds

Quality control and preprocessing of coding sequences
aa2codon

amino acids to codons
codon_optimize

Optimize codon usage in coding sequences
get_enc

Calculate effective number of codons (ENC)
get_aau

Amino Acid Usage
get_dp

Deviation from Proportionality
get_cscg

Mean Codon Stabilization Coefficients
extract_trna_gcn

Extract tRNA gene copy numbers from nature tRNA sequences
est_rscu

Estimate Relative Synonymous Codon Usage (RSCU)
est_trna_weight

Estimate tRNA weights for TAI calculation
get_cai

Calculate Codon Adaptation Index (CAI)
get_codon_table

Retrieve codon table by NCBI genetic code ID
get_fop

Calculate fraction of optimal codons (Fop)