{ "_id": "6a1c15881d7bb097a0a2f403", "Package": "ViralEntropR", "Title": "A Computational Pipeline for Entropy-Informed Detection of\nEmerging Viral Variants", "Version": "0.6.2", "Authors@R": "c(\nperson(\"Vadim\", \"Tyuryaev\", ,\"vadim.tyuryaev@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0008-1361-6265\")),\nperson(\"Jane\", \"Heffernan\", , \"jmheffer@yorku.ca\",\nrole = c(\"aut\")),\nperson(\"Hanna\", \"Jankowski\", , \"hkj@yorku.ca\",\nrole = c(\"aut\"))\n)", "Description": "Implements an entropy-informed pipeline for detecting\nemerging variants in viral amino acid sequence data, extending\nprior clustering-based approaches including hemagglutinin\nclustering methods (Li et al., 2015)\n. Provides a fully vectorized\nFASTA preprocessing toolkit covering header parsing, two-pass\ndate and country extraction, ambiguous-residue filtering, and\ninteger encoding under a 25-symbol amino acid alphabet.\nComputes per-site Shannon entropy across user-defined\ncumulative, sliding, or disjoint temporal partitions and\nclusters per-site entropy values using Gaussian mixture models\nvia 'mclust' (Scrucca et al., 2016) .\nQuantifies temporal distributional shifts between partitions\nusing the Hellinger distance (van der Vaart, 1998)\n, and detects temporal change\npoints non-parametrically using energy statistics (Matteson and\nJames, 2014) via 'ecp' or\nwild binary segmentation (Fryzlewicz, 2014)\n via 'HDcpDetect'. Per-site amino-acid\nfrequency tables and entropy trajectory plots characterize\nsequence composition and evolutionary dynamics across time. A\nconfigurable multi-variant simulation engine generates\nsynthetic sequence time series with known ground truth for\nbenchmarking detection pipelines. A curated dataset of\nSARS-CoV-2 Variants of Concern and Variants of Interest with\nassociated lineage and surveillance metadata is included, along\nwith a bundled National Center for Biotechnology Information\n(NCBI) Spike protein sample and vignettes demonstrating the\nfull workflow.", "License": "MIT + file LICENSE", "Language": "en-GB", "Date": "2026-05-07", "URL": "https://github.com/vadimtyuryaev/ViralEntropR,\nhttps://doi.org/10.5281/zenodo.19040165,\nhttps://vadimtyuryaev.github.io/ViralEntropR/", "BugReports": "https://github.com/vadimtyuryaev/ViralEntropR/issues", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr, R.rsp", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev\nlibuv1-dev libxml2-dev", "Repository": "https://vadimtyuryaev.r-universe.dev", "Date/Publication": "2026-05-31 07:23:55 UTC", 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