VERSO

DOI: 10.18129/B9.bioc.VERSO  

Viral Evolution ReconStructiOn (VERSO)

Bioconductor version: Release (3.16)

Mutations that rapidly accumulate in viral genomes during a pandemic can be used to track the evolution of the virus and, accordingly, unravel the viral infection network. To this extent, sequencing samples of the virus can be employed to estimate models from genomic epidemiology and may serve, for instance, to estimate the proportion of undetected infected people by uncovering cryptic transmissions, as well as to predict likely trends in the number of infected, hospitalized, dead and recovered people. VERSO is an algorithmic framework that processes variants profiles from viral samples to produce phylogenetic models of viral evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a log-likelihood function. VERSO includes two separate and subsequent steps; in this package we provide an R implementation of VERSO STEP 1.

Author: Daniele Ramazzotti [aut] , Fabrizio Angaroni [aut], Davide Maspero [cre, aut], Alex Graudenzi [aut], Luca De Sano [aut]

Maintainer: Davide Maspero <d.maspero at campus.unimib.it>

Installation

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

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

BiocManager::install("VERSO")

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("VERSO")

 

PDF	R Script	VERSO
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiomedicalInformatics, Sequencing, Software, SomaticMutation
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	file LICENSE
Depends	R (>= 4.1.0)
Imports	ape, parallel, Rfast, stats
LinkingTo
Suggests	BiocGenerics, BiocStyle, testthat, knitr
SystemRequirements
Enhances
URL	https://github.com/BIMIB-DISCo/VERSO
BugReports	https://github.com/BIMIB-DISCo/VERSO
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	VERSO_1.8.0.tar.gz
Windows Binary	VERSO_1.8.0.zip
macOS Binary (x86_64)	VERSO_1.8.0.tgz
macOS Binary (arm64)	VERSO_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/VERSO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/VERSO
Bioc Package Browser	https://code.bioconductor.org/browse/VERSO/
Package Short Url	https://bioconductor.org/packages/VERSO/
Package Downloads Report	Download Stats