QSutils

DOI: 10.18129/B9.bioc.QSutils    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see QSutils.

Quasispecies Diversity

Bioconductor version: 3.9

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 and Josep Gregori i Font

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Alignment, DNASeq, DataImport, GeneticVariability, Genetics, SequenceMatching, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	file LICENSE
Depends	R (>= 3.5), Biostrings, BiocGenerics, methods
Imports	ape, stats, psych
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, ggplot2
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	QSutils_1.2.0.tar.gz
Windows Binary	QSutils_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	QSutils_1.2.0.tgz
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/
Package Downloads Report	Download Stats