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
biocViews:
Imports: Biostrings, coRdon , ggplot2, seqinr, stringr
RoxygenNote: 6.1.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2026-07-04 21:25:45 UTC; root
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://aliyoussef96.r-universe.dev
Date/Publication: 2025-07-05 11:02:55 UTC
RemoteUrl: https://github.com/aliyoussef96/vhcub
RemoteRef: HEAD
RemoteSha: 49f58dab1d0abd4e5700686f1e10f0c21d702137