{ "_id": "6a1ed73fb401979e7340ed49", "Package": "VERSO", "Version": "1.23.0", "Date": "2026-03-09", "Title": "Viral Evolution ReconStructiOn (VERSO)", "Authors@R": "c(person(\"Daniele\", \"Ramazzotti\", role=c(\"aut\"),email=\"daniele.ramazzotti@unimib.it\",\ncomment = c(ORCID = \"0000-0002-6087-2666\")),\nperson(\"Fabrizio\",\"Angaroni\",role=c(\"aut\"),email=\"fabrizio.angaroni@unimib.it\"),\nperson(\"Davide\",\"Maspero\",role=c(\"cre\",\"aut\"),email=\"d.maspero@campus.unimib.it\"),\nperson(\"Alex\",\"Graudenzi\",role=c(\"aut\"),email=\"alex.graudenzi@unimib.it\"),\nperson(\"Luca\", \"De Sano\", role=c(\"aut\"), email=\"luca.desano@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9618-3774\")))", "Name": "VERSO: an R package for the inference of viral evolution models", "Description": "Mutations that rapidly accumulate in viral genomes during\na pandemic can be used to track the evolution of the virus and,\naccordingly, unravel the viral infection network. To this\nextent, sequencing samples of the virus can be employed to\nestimate models from genomic epidemiology and may serve, for\ninstance, to estimate the proportion of undetected infected\npeople by uncovering cryptic transmissions, as well as to\npredict likely trends in the number of infected, hospitalized,\ndead and recovered people. VERSO is an algorithmic framework\nthat processes variants profiles from viral samples to produce\nphylogenetic models of viral evolution. The approach solves a\nBoolean Matrix Factorization problem with phylogenetic\nconstraints, by maximizing a log-likelihood function. VERSO\nincludes two separate and subsequent steps; in this package we\nprovide 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": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:15 UTC", "RemoteUrl": "https://github.com/bioc/VERSO", "RemoteRef": "HEAD", "RemoteSha": "99a5fe8335cd404c29bdd3592b800dd3e74d2dae", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-20 10:07:59 UTC", "User": "root" }, "Author": "Daniele Ramazzotti [aut] (ORCID:\n),\nFabrizio Angaroni [aut],\nDavide Maspero [cre, aut],\nAlex Graudenzi [aut],\nLuca De Sano [aut] (ORCID: )", "Maintainer": "Davide Maspero ", "MD5sum": "8939d319d26508949be9d389b2b85968", "_user": "bioc", "_type": 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