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VERSO

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

Viral Evolution ReconStructiOn (VERSO)


Bioconductor version: Development (3.19)

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>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Introduction HTML R Script
Running VERSO HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BiomedicalInformatics, Sequencing, Software, SomaticMutation
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License file LICENSE
Depends R (>= 4.1.0)
Imports utils, data.tree, ape, parallel, Rfast, stats
System Requirements
URL https://github.com/BIMIB-DISCo/VERSO
Bug Reports https://github.com/BIMIB-DISCo/VERSO
See More
Suggests BiocGenerics, BiocStyle, testthat, knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package VERSO_1.13.0.tar.gz
Windows Binary VERSO_1.13.0.zip
macOS Binary (x86_64) VERSO_1.13.0.tgz
macOS Binary (arm64) VERSO_1.13.0.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