DOI: 10.18129/B9.bioc.QSutils    

This is the development version of QSutils; for the stable release version, see QSutils.

Quasispecies Diversity

Bioconductor version: Development (3.15)

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 <mergumu at gmail.com>, Josep Gregori i Font <mergumu at gmail.com>

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

Citation (from within R, enter citation("QSutils")):


To install this package, start R (version "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


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biocViews Alignment, DNASeq, DataImport, GeneticVariability, Genetics, SequenceMatching, Sequencing, Software
Version 1.13.0
In Bioconductor since BioC 3.8 (R-3.5) (3 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
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Source Repository git clone https://git.bioconductor.org/packages/QSutils
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QSutils
Package Short Url https://bioconductor.org/packages/QSutils/
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