Package: vhcub
Title: Virus-Host Codon Usage Co-Adaptation Analysis
Version: 1.0.0
Authors@R: c(
    person(given = "Ali",family = "Mostafa Anwar",role = c("aut", "cre"),email = "ali.mo.anwar@std.agr.cu.edu.eg"),
    person(given = "Mohamed",family = "Soudy",email = "MohmedSoudy2009@gmail.com", role = "aut"))
Author: Ali Mostafa Anwar [aut, cre],
  Mohamed Soudy [aut]
Maintainer: Ali Mostafa Anwar <ali.mo.anwar@std.agr.cu.edu.eg>
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) Sharp  and  Li (1987) <doi:10.1093/nar/15.3.1281>, relative  codon 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 synonymous    codon 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().
License: GPL-3
Encoding: UTF-8
LazyData: true
biocViews:
Imports: Biostrings, coRdon , ggplot2, seqinr, stringr
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2019-11-07 17:12:46 UTC; ali
Repository: CRAN
Date/Publication: 2019-11-15 12:00:02 UTC
Built: R 4.4.3; ; 2025-10-21 13:28:15 UTC; windows
