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vhcub
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]
[Scholar Profile | Author Map]
All associated links for this package
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 22 Sep. 2026.
Previous versions and publish date:
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Other R packages that vhcub depends,
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Complete documentation for vhcub
Functions, R codes and Examples using
the vhcub R package
Some associated functions: CAI.values . ENc.GC3plot . ENc.values . GC.content . PR2.plot . RCDI.values . RSCU.values . SCUO.values . SiD.value . dinuc.base . dinuc.codon . dinuc.syncodon . fasta.read . vhcub .
Some associated R codes: CAI.values.R . ENc.GC3plot.R . ENc.values.R . GC.content.R . PR2.plot.R . RCDI.values.R . RSCU.values.R . SCUO.values.R . SiD.value.R . dinuc.base.R . dinuc.codon.R . dinuc.syncodon.R . read.fasta.R . vhcub.R . Full vhcub package functions and examples
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