VERSO
Viral Evolution ReconStructiOn (VERSO)
Bioconductor version: Release (3.20)
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("VERSO")):
Installation
To install this package, start R (version "4.4") 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")| Introduction | HTML | R Script |
| Running VERSO | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BiomedicalInformatics, Sequencing, Software, SomaticMutation |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | VERSO_1.16.0.zip |
| macOS Binary (x86_64) | VERSO_1.16.0.tgz |
| macOS Binary (arm64) | VERSO_1.16.0.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 |