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 Documentation: Reference manual: vhcub.html , vhcub.pdf Downloads: 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 Linking:Please use the canonical form https://CRAN.R-project.org/package=vhcub to link to this page.
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4