Package: VERSO
Version: 1.22.0
Date: 2026-03-09
Title: Viral Evolution ReconStructiOn (VERSO)
Authors@R: c(person("Daniele", "Ramazzotti", role=c("aut"),email="daniele.ramazzotti@unimib.it",
                comment = c(ORCID = "0000-0002-6087-2666")),
    person("Fabrizio","Angaroni",role=c("aut"),email="fabrizio.angaroni@unimib.it"),
    person("Davide","Maspero",role=c("cre","aut"),email="d.maspero@campus.unimib.it"),
    person("Alex","Graudenzi",role=c("aut"),email="alex.graudenzi@unimib.it"),
    person("Luca", "De Sano", role=c("aut"), email="luca.desano@gmail.com",
                comment = c(ORCID = "0000-0002-9618-3774")))
Depends: R (>= 4.1.0)
Imports: utils, data.tree, ape, parallel, Rfast, stats
Suggests: BiocGenerics, BiocStyle, testthat, knitr
Name: VERSO: an R package for the inference of viral evolution models
Description: 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.
Encoding: UTF-8
License: file LICENSE
URL: https://github.com/BIMIB-DISCo/VERSO
BugReports: https://github.com/BIMIB-DISCo/VERSO
biocViews: BiomedicalInformatics, Sequencing, SomaticMutation
RoxygenNote: 7.3.3
VignetteBuilder: knitr
Config/pak/sysreqs: make libicu-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 12:54:15 UTC
RemoteUrl: https://github.com/bioc/VERSO
RemoteRef: RELEASE_3_23
RemoteSha: 68c974c5925c5f32d57386a4e39d38d33fa54cba
NeedsCompilation: no
Packaged: 2026-07-03 23:58:52 UTC; root
Author: Daniele Ramazzotti [aut] (ORCID:
    <https://orcid.org/0000-0002-6087-2666>),
  Fabrizio Angaroni [aut],
  Davide Maspero [cre, aut],
  Alex Graudenzi [aut],
  Luca De Sano [aut] (ORCID: <https://orcid.org/0000-0002-9618-3774>)
Maintainer: Davide Maspero <d.maspero@campus.unimib.it>