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vhcub  

Virus-Host Codon Usage Co-Adaptation Analysis
View on CRAN: Click here


Download and install vhcub package within the R console
Install from CRAN:
install.packages("vhcub")

Install from Github:
library("remotes")
install_github("cran/vhcub")

Install by package version:
library("remotes")
install_version("vhcub", "1.0.0")



Attach the package and use:
library("vhcub")
Maintained by
Ali Mostafa Anwar
[Scholar Profile | Author Map]
First Published: 2019-11-15
Latest Update: 2019-11-15
Description:
Analyze the co-adaptation of codon usage between a virus and its host, calculate various codon usage bias measurements as: effective number of codons (ENc) Novembre (2002) <doi:10.1093/oxfordjournals.molbev.a004201>, codon adaptation index (CAI) SharpandLi (1987) <doi:10.1093/nar/15.3.1281>, relativecodon deoptimization index (RCDI) Puigbò et al (2010) <doi:10.1186/1756-0500-3-87>, similarity index (SiD) Zhou et al (2013) <doi:10.1371/journal.pone.0077239>,synonymous codon usage orderliness (SCUO) Wan et al (2004) <doi:10.1186/1471-2148-4-19> and, relative synonymouscodon usage (RSCU) Sharp et al (1986) <doi:10.1093/nar/14.13.5125>. Also, it provides a statistical dinucleotide over- and underrepresentation with three different models. Implement several methods for visualization of codon usage as ENc.GC3plot() and PR2.plot().
How to cite:
Ali Mostafa Anwar (2019). vhcub: Virus-Host Codon Usage Co-Adaptation Analysis. R package version 1.0.0, https://cran.r-project.org/web/packages/vhcub. Accessed 10 May. 2025.
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