The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
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 |
Please use the canonical form https://CRAN.R-project.org/package=vhcub to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.