Other packages > Find by keyword >

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 05 Apr. 2025.
Previous versions and publish date:
No previous versions
Other packages that cited vhcub R package
View vhcub citation profile
Other R packages that vhcub depends, imports, suggests or enhances
Complete documentation for vhcub
Downloads during the last 30 days
03/0603/0703/0803/1003/1103/1203/1303/1403/1503/1603/1703/1803/1903/2003/2103/2203/2403/2503/2603/2703/2803/3003/3104/0104/0204/0304/04Downloads for vhcub1234567TrendBars

Today's Hot Picks in Authors and Packages

whitestrap  
White Test and Bootstrapped White Test for Heteroskedasticity
Formal implementation of White test of heteroskedasticity and a bootstrapped version of it, develope ...
Download / Learn more Package Citations See dependency  
IGST  
Informative Gene Selection Tool
Mining informative genes with certain biological meanings are important for clinical diagnosis of di ...
Download / Learn more Package Citations See dependency  
TrendInTrend  
Odds Ratio Estimation and Power Calculation for the Trend in Trend Model
Estimation of causal odds ratio and power calculation given trends in exposure prevalenceand outcome ...
Download / Learn more Package Citations See dependency  
leapp  
Latent Effect Adjustment After Primary Projection
These functions take a gene expression value matrix, a primary covariate vector, an additional know ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
gllvm  
Generalized Linear Latent Variable Models
Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation i ...
Download / Learn more Package Citations See dependency  

23,990

R Packages

207,311

Dependencies

64,809

Author Associations

23,991

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA