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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) &lt;<a href="https://doi.org/10.1093%2Foxfordjournals.molbev.a004201" target="_top">doi:10.1093/oxfordjournals.molbev.a004201</a>&gt;, codon adaptation index (CAI) Sharp and Li (1987) &lt;<a href="https://doi.org/10.1093%2Fnar%2F15.3.1281" target="_top">doi:10.1093/nar/15.3.1281</a>&gt;, relative codon deoptimization index (RCDI) Puigbò et al (2010) &lt;<a href="https://doi.org/10.1186%2F1756-0500-3-87" target="_top">doi:10.1186/1756-0500-3-87</a>&gt;, similarity index (SiD) Zhou et al (2013) &lt;<a href="https://doi.org/10.1371%2Fjournal.pone.0077239" target="_top">doi:10.1371/journal.pone.0077239</a>&gt;, synonymous codon usage orderliness (SCUO) Wan et al (2004) &lt;<a href="https://doi.org/10.1186%2F1471-2148-4-19" target="_top">doi:10.1186/1471-2148-4-19</a>&gt; and, relative synonymous codon usage (RSCU) Sharp et al (1986) &lt;<a href="https://doi.org/10.1093%2Fnar%2F14.13.5125" target="_top">doi:10.1093/nar/14.13.5125</a>&gt;. 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().



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vhcub: Virus-Host Codon Usage Co-Adaptation Analysis

https://cran.r-project.org/web/packages/vhcub

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) &lt;<a href="https://doi.org/10.1093%2Foxfordjournals.molbev.a004201" target="_top">doi:10.1093/oxfordjournals.molbev.a004201</a>&gt;, codon adaptation index (CAI) Sharp and Li (1987) &lt;<a href="https://doi.org/10.1093%2Fnar%2F15.3.1281" target="_top">doi:10.1093/nar/15.3.1281</a>&gt;, relative codon deoptimization index (RCDI) Puigbò et al (2010) &lt;<a href="https://doi.org/10.1186%2F1756-0500-3-87" target="_top">doi:10.1186/1756-0500-3-87</a>&gt;, similarity index (SiD) Zhou et al (2013) &lt;<a href="https://doi.org/10.1371%2Fjournal.pone.0077239" target="_top">doi:10.1371/journal.pone.0077239</a>&gt;, synonymous codon usage orderliness (SCUO) Wan et al (2004) &lt;<a href="https://doi.org/10.1186%2F1471-2148-4-19" target="_top">doi:10.1186/1471-2148-4-19</a>&gt; and, relative synonymous codon usage (RSCU) Sharp et al (1986) &lt;<a href="https://doi.org/10.1093%2Fnar%2F14.13.5125" target="_top">doi:10.1093/nar/14.13.5125</a>&gt;. 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().



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https://cran.r-project.org/web/packages/vhcub

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) &lt;<a href="https://doi.org/10.1093%2Foxfordjournals.molbev.a004201" target="_top">doi:10.1093/oxfordjournals.molbev.a004201</a>&gt;, codon adaptation index (CAI) Sharp and Li (1987) &lt;<a href="https://doi.org/10.1093%2Fnar%2F15.3.1281" target="_top">doi:10.1093/nar/15.3.1281</a>&gt;, relative codon deoptimization index (RCDI) Puigbò et al (2010) &lt;<a href="https://doi.org/10.1186%2F1756-0500-3-87" target="_top">doi:10.1186/1756-0500-3-87</a>&gt;, similarity index (SiD) Zhou et al (2013) &lt;<a href="https://doi.org/10.1371%2Fjournal.pone.0077239" target="_top">doi:10.1371/journal.pone.0077239</a>&gt;, synonymous codon usage orderliness (SCUO) Wan et al (2004) &lt;<a href="https://doi.org/10.1186%2F1471-2148-4-19" target="_top">doi:10.1186/1471-2148-4-19</a>&gt; and, relative synonymous codon usage (RSCU) Sharp et al (1986) &lt;<a href="https://doi.org/10.1093%2Fnar%2F14.13.5125" target="_top">doi:10.1093/nar/14.13.5125</a>&gt;. 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().

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      Virus-Host Codon Usage Co-Adaptation Analysis [R package vhcub version 1.0.0]
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      Ali Mostafa Anwar

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      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) &lt;<a href="https://doi.org/10.1093%2Foxfordjournals.molbev.a004201" target="_top">doi:10.1093/oxfordjournals.molbev.a004201</a>&gt;, codon adaptation index (CAI) Sharp and Li (1987) &lt;<a href="https://doi.org/10.1093%2Fnar%2F15.3.1281" target="_top">doi:10.1093/nar/15.3.1281</a>&gt;, relative codon deoptimization index (RCDI) Puigbò et al (2010) &lt;<a href="https://doi.org/10.1186%2F1756-0500-3-87" target="_top">doi:10.1186/1756-0500-3-87</a>&gt;, similarity index (SiD) Zhou et al (2013) &lt;<a href="https://doi.org/10.1371%2Fjournal.pone.0077239" target="_top">doi:10.1371/journal.pone.0077239</a>&gt;, synonymous codon usage orderliness (SCUO) Wan et al (2004) &lt;<a href="https://doi.org/10.1186%2F1471-2148-4-19" target="_top">doi:10.1186/1471-2148-4-19</a>&gt; and, relative synonymous codon usage (RSCU) Sharp et al (1986) &lt;<a href="https://doi.org/10.1093%2Fnar%2F14.13.5125" target="_top">doi:10.1093/nar/14.13.5125</a>&gt;. 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().
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