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QSutils

Quasispecies Diversity


Bioconductor version: Release (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("QSutils")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("QSutils")
QSUtils-Alignment HTML R Script
QSutils-Diversity HTML R Script
QSutils-Simulation HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, DNASeq, DataImport, GeneticVariability, Genetics, SequenceMatching, Sequencing, Software
Version 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL-2
Depends R (>= 3.5), Biostrings, pwalign, BiocGenerics, methods
Imports ape, stats, psych
System Requirements
URL
See More
Suggests BiocStyle, knitr, rmarkdown, ggplot2
Linking To
Enhances
Depends On Me
Imports Me longreadvqs
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package QSutils_1.22.0.tar.gz
Windows Binary QSutils_1.22.0.zip
macOS Binary (x86_64) QSutils_1.22.0.tgz
macOS Binary (arm64) QSutils_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/QSutils
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QSutils
Bioc Package Browser https://code.bioconductor.org/browse/QSutils/
Package Short Url https://bioconductor.org/packages/QSutils/
Package Downloads Report Download Stats