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().
| Version: | 1.0.0 |
| Imports: | Biostrings, coRdon , ggplot2, seqinr, stringr |
| Suggests: | testthat |
| Published: | 2019-11-15 |
| DOI: | 10.32614/CRAN.package.vhcub |
| Author: | Ali Mostafa Anwar [aut, cre], Mohamed Soudy [aut] |
| Maintainer: | Ali Mostafa Anwar <ali.mo.anwar at std.agr.cu.edu.eg> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| CRAN checks: | vhcub results |
| Reference manual: | vhcub.pdf |
| Package source: | vhcub_1.0.0.tar.gz |
| Windows binaries: | r-devel: vhcub_1.0.0.zip, r-release: vhcub_1.0.0.zip, r-oldrel: vhcub_1.0.0.zip |
| macOS binaries: | r-release (arm64): vhcub_1.0.0.tgz, r-oldrel (arm64): vhcub_1.0.0.tgz, r-release (x86_64): vhcub_1.0.0.tgz, r-oldrel (x86_64): vhcub_1.0.0.tgz |
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