vhcub
Virus-Host Codon Usage Co-Adaptation Analysis
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().
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.0.0 |
rolling linux/jammy R-4.5 | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
rolling linux/noble R-4.5 | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
rolling source/ R- | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
latest linux/jammy R-4.5 | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
latest linux/noble R-4.5 | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
latest source/ R- | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
2026-04-26 source/ R- | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
2026-04-23 source/ R- | vhcub_1.0.0.tar.gz |
1.8 MiB |
1.0.0 |
2025-04-20 source/ R- | vhcub_1.0.0.tar.gz |
1.8 MiB |