Codon Usage Bias Analysis
Quality control of CDS
Differential codon usage analysis
Optimize codons
Count occurrences of different codons
create custom codon table from a data frame
Estimate Codon Stabilization Coefficient
Estimate optimal codons
Estimate RSCU
Estimate tRNA weight w
Calculate CAI
get codon table by NCBI gene code ID
Mean Codon Stabilization Coefficients
Deviation from Proportionality
Calculate ENC
Fraction of optimal codons (Fop)
GC contents
GC contents at synonymous 3rd codon positions
GC contents at 4-fold degenerate sites
Calculate TAI
Plot codon-anticodon pairing relationship
Reverse complement
Convert CDS to codons
show available codon tables
apply a cub index to a sliding window
sliding window of codons
plot sliding window codon usage
slide window interval generator
A suite of functions for rapid and flexible analysis of codon usage bias. It provides in-depth analysis at the codon level, including relative synonymous codon usage (RSCU), tRNA weight calculations, machine learning predictions for optimal or preferred codons, and visualization of codon-anticodon pairing. Additionally, it can calculate various gene- specific codon indices such as codon adaptation index (CAI), effective number of codons (ENC), fraction of optimal codons (Fop), tRNA adaptation index (tAI), mean codon stabilization coefficients (CSCg), and GC contents (GC/GC3s/GC4d). It also supports both standard and non-standard genetic code tables found in NCBI, as well as custom genetic code tables.
Useful links