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]

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vhcub.pdf |vhcub.html✨
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:

13 exports 4 stars 1.39 score 61 dependencies 1 mentions 131 downloads

Last updated 9 months agofrom:c6031198a2. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 27 2024
R-4.5-win	WARNING	Aug 27 2024
R-4.5-linux	WARNING	Aug 28 2024
R-4.4-win	WARNING	Aug 28 2024
R-4.4-mac	WARNING	Aug 27 2024
R-4.3-win	WARNING	Aug 27 2024
R-4.3-mac	WARNING	Aug 27 2024

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 askpass Biobase BiocGenerics Biostrings cli colorspace coRdon crayon curl data.table dplyr fansi farver generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable httr IRanges isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime munsell nlme openssl pillar pixmap pkgconfig purrr R6 RColorBrewer Rcpp RcppArmadillo rlang S4Vectors scales segmented seqinr sp stringi stringr sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

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