QSutils

DOI: 10.18129/B9.bioc.QSutils    

Quasispecies Diversity

Bioconductor version: Release (3.8)

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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("QSutils", version = "3.8")

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 1.0.0
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_1.0.0.tar.gz
Windows Binary QSutils_1.0.0.zip
Mac OS X 10.11 (El Capitan) QSutils_1.0.0.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 http://bioconductor.org/packages/QSutils/
Package Downloads Report Download Stats

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