Package: VERSO 1.17.0

Davide Maspero

VERSO: Viral Evolution ReconStructiOn (VERSO)

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.

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

VERSO_1.17.0.tar.gz
VERSO_1.17.0.zip(r-4.5)VERSO_1.17.0.zip(r-4.4)VERSO_1.17.0.zip(r-4.3)
VERSO_1.17.0.tgz(r-4.4-any)VERSO_1.17.0.tgz(r-4.3-any)
VERSO_1.17.0.tar.gz(r-4.5-noble)VERSO_1.17.0.tar.gz(r-4.4-noble)
VERSO_1.17.0.tgz(r-4.4-emscripten)VERSO_1.17.0.tgz(r-4.3-emscripten)
VERSO.pdf |VERSO.html
VERSO/json (API)
NEWS

# Install 'VERSO' in R:
install.packages('VERSO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bimib-disco/verso/issues

Datasets:
  • inference - Results obtained running VERSO on the provided input dataset.
  • variants - Mutation data obtained by variant calling from raw data of a selected set of SARS-CoV-2 samples available from NCBI BioProject PRJNA610428.

On BioConductor:VERSO-1.17.0(bioc 3.21)VERSO-1.16.0(bioc 3.20)

biomedicalinformaticssequencingsomaticmutation

6.05 score 7 stars 144 downloads 2 mentions 2 exports 13 dependencies

Last updated 2 months agofrom:bd1b576417. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winOKDec 18 2024
R-4.5-linuxOKDec 18 2024
R-4.4-winOKDec 18 2024
R-4.4-macOKDec 18 2024
R-4.3-winOKDec 18 2024
R-4.3-macOKDec 18 2024

Exports:VERSOwrite.newick.tree

Dependencies:apedata.treedigestlatticenlmeR6RcppRcppArmadilloRcppGSLRcppParallelRcppZigguratRfaststringi

Introduction

Rendered fromv1_introduction.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2023-04-16
Started: 2023-04-16

Running VERSO

Rendered fromv2_running_VERSO.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2023-04-16
Started: 2023-04-16