Package: vhcub 1.0.0

Ali Mostafa Anwar

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().

Authors:Ali Mostafa Anwar [aut, cre], Mohamed Soudy [aut]

vhcub_1.0.0.tar.gz
vhcub_1.0.0.zip(r-4.7)vhcub_1.0.0.zip(r-4.6)vhcub_1.0.0.zip(r-4.5)
vhcub_1.0.0.tgz(r-4.6-any)vhcub_1.0.0.tgz(r-4.5-any)
vhcub_1.0.0.tar.gz(r-4.7-any)vhcub_1.0.0.tar.gz(r-4.6-any)
vhcub_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
vhcub/json (API)

# Install 'vhcub' in R:

install.packages('vhcub', repos = c('https://aliyoussef96.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aliyoussef96/vhcub/issues

On CRAN:

3.40 score 5 stars 169 downloads 1 mentions 13 exports 48 dependencies

Last updated from:49f58dab1d. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	185
source / vignettes	OK	201
linux-release-x86_64	WARNING	177
macos-release-arm64	WARNING	165
macos-oldrel-arm64	WARNING	294
windows-devel	WARNING	136
windows-release	WARNING	130
windows-oldrel	WARNING	123
wasm-release	OK	117

Exports:CAI.values dinuc.base dinuc.codon dinuc.syncodon ENc.GC3plot ENc.values fasta.read GC.content PR2.plot RCDI.values RSCU.values SCUO.values SiD.value

Dependencies:ade4 Biobase BiocGenerics Biostrings cli coRdon cpp11 crayon data.table dplyr farver generics ggplot2 glue gtable IRanges isoband labeling lattice lifecycle magrittr MASS nlme pillar pixmap pkgconfig purrr R6 RColorBrewer Rcpp RcppArmadillo rlang S4Vectors S7 scales segmented Seqinfo seqinr sp stringi stringr tibble tidyselect utf8 vctrs viridisLite withr XVector

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Codon Adaptation Index (CAI)	CAI.values
Statistical dinucleotide over- and underrepresentation (base model).	dinuc.base
Statistical dinucleotide over- and underrepresentation (codon model).	dinuc.codon
Statistical dinucleotide over- and underrepresentation (syncodon model).	dinuc.syncodon
ENc-GC3 scatterplot.	ENc.GC3plot
Effective Number of Codons (ENc).	ENc.values
Read fasta formate and convert it to data frame	fasta.read
GC content	GC.content
Parity rule 2 (PR2) plot	PR2.plot
Relative Codon Deoptimization Index (RCDI)	RCDI.values
Relative Synonymous Codon Usage (RSCU)	RSCU.values
Synonymous codon usage eorderliness (SCUO)	SCUO.values
Similarity Index (SiD)	SiD.value
vhcub: A package to analysis the co-adaptation of codon usage between a virus and its host.	vhcub-package vhcub