QSutils-package {QSutils} | R Documentation

## Quasispecies Diversity

### Description

Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and explorationâ€”functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indicesâ€”functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulationâ€”functions useful for generating random viral quasispecies data.

### Details

The DESCRIPTION file:

Package: | QSutils
Type: | Package
Title: | Quasispecies Diversity
Version: | 1.12.0
Date: | 2018-04-06
Authors@R: | c(person("Mercedes", "Guerrero-Murillo", email="mergumu@gmail.com", role=c("cre", "aut"), comment = c(ORCID = "0000-0002-5556-2460")), person("Josep", "Gregori i Font", role=c ("aut"), comment = c(ORCID = "0000-0002-4253-8015")))
Depends: | R (>= 3.5), Biostrings, BiocGenerics,methods
Imports: | ape, stats, psych
Encoding: | UTF-8
Description: | Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.
License: | file LICENSE
biocViews: | Software, Genetics, DNASeq, GeneticVariability, Sequencing, Alignment, SequenceMatching, DataImport
VignetteBuilder: | knitr
Suggests: | BiocStyle, knitr, rmarkdown, ggplot2
NeedsCompilation: | no
Packaged: | 2018-05-28 14:56:11 UTC; mervhir
RoxygenNote: | 6.0.1
git_url: | https://git.bioconductor.org/packages/QSutils
git_branch: | RELEASE_3_14
git_last_commit: | 3942c07
git_last_commit_date: | 2021-10-26
Date/Publication: | 2021-10-26
Author: | Mercedes Guerrero-Murillo [cre, aut] (<https://orcid.org/0000-0002-5556-2460>), Josep Gregori i Font [aut] (<https://orcid.org/0000-0002-4253-8015>)
Maintainer: | Mercedes Guerrero-Murillo <mergumu@gmail.com>

### Author(s)

NA

Maintainer: NA

### References

Gregori J, Perales C, Rodriguez-Frias F, Esteban JI, Quer J, Domingo E. Viral quasispecies complexity measures. Virology. 2016 Jun;493:227-37. doi: 10.1016/j.virol.2016.03.017. Epub 2016 Apr 6. Review. PubMed PMID: 27060566.

Gregori J, Salicrú M, Domingo E, Sanchez A, Esteban JI, Rodríguez-Frías F, Quer J. Inference with viral quasispecies diversity indices: clonal and NGS approaches. Bioinformatics. 2014 Apr 15;30(8):1104-1111. Epub 2014 Jan 2. PubMed PMID: 24389655.

Gregori J, Esteban JI, Cubero M, Garcia-Cehic D, Perales C, Casillas R, Alvarez-Tejado M, Rodríguez-Frías F, Guardia J, Domingo E, Quer J. Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants. PLoS One. 2013 Dec 31;8(12):e83361. doi: 10.1371/journal.pone.0083361. eCollection 2013. PubMed PMID: 24391758; PubMed Central PMCID: PMC3877031.

Ramírez C, Gregori J, Buti M, Tabernero D, Camós S, Casillas R, Quer J, Esteban R, Homs M, Rodriguez-Frías F. A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model. Antiviral Res. 2013 May;98(2):273-83.doi: 10.1016/j.antiviral.2013.03.007. Epub 2013 Mar 20. PubMed PMID: 23523552.

[Package QSutils version 1.12.0 Index]