DOI: 10.18129/B9.bioc.QSutils  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see QSutils.

Quasispecies Diversity

Bioconductor version: 3.16

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.

Author: Mercedes Guerrero-Murillo [cre, aut] , Josep Gregori i Font [aut]

Maintainer: Mercedes Guerrero-Murillo <mergumu at gmail.com>

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HTML R Script QSUtils-Alignment
HTML R Script QSutils-Diversity
HTML R Script QSutils-Simulation
PDF   Reference Manual
Text   NEWS


biocViews Alignment, DNASeq, DataImport, GeneticVariability, Genetics, SequenceMatching, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 3.8 (R-3.5) (4.5 years)
License file LICENSE
Depends R (>= 3.5), Biostrings, BiocGenerics, methods
Imports ape, stats, psych
Suggests BiocStyle, knitr, rmarkdown, ggplot2
Depends On Me
Imports Me
Suggests Me
Links To Me
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Source Package QSutils_1.16.0.tar.gz
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