Virus-Host Codon Usage Co-Adaptation Analysis

Documentation for package ‘vhcub’ version 1.0.0

vhcub-package	vhcub: A package to analysis the co-adaptation of codon usage between a virus and its host.
CAI.values	Codon Adaptation Index (CAI)
dinuc.base	Statistical dinucleotide over- and underrepresentation (base model).
dinuc.codon	Statistical dinucleotide over- and underrepresentation (codon model).
dinuc.syncodon	Statistical dinucleotide over- and underrepresentation (syncodon model).
ENc.GC3plot	ENc-GC3 scatterplot.
ENc.values	Effective Number of Codons (ENc).
fasta.read	Read fasta formate and convert it to data frame
GC.content	GC content
PR2.plot	Parity rule 2 (PR2) plot
RCDI.values	Relative Codon Deoptimization Index (RCDI)
RSCU.values	Relative Synonymous Codon Usage (RSCU)
SCUO.values	Synonymous codon usage eorderliness (SCUO)
SiD.value	Similarity Index (SiD)
vhcub	vhcub: A package to analysis the co-adaptation of codon usage between a virus and its host.