QSutils-package: Quasispecies Diversity
In VHIRHepatiques/QSutils: Quasispecies Diversity
QSutils-package 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 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.
Details
The DESCRIPTION file:
This package was not yet installed at build time.
Author(s)
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>
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.
VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.
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| QSutils-package | 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 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.
Details
The DESCRIPTION file:
This package was not yet installed at build time.
Author(s)
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>
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.
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