{ "_id": "6a26991824555f66ed51dc56", "Package": "RestoreNet", "Title": "Random-Effects Stochastic Reaction Networks", "Version": "1.0.1", "Authors@R": "c(person(given = \"Luca\",\nfamily = \"Del Core\",\nemail = \"l.del.core@rug.nl\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-1672-6995\")),\nperson(given = \"Marco\",\nfamily = \"Grzegorczyk\",\nemail = \"m.a.grzegorczyk@rug.nl\",\nrole = c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0002-2604-9270\")),\nperson(given = \"Ernst\",\nfamily = \"Wit\",\nemail = \"ernst.jan.camiel.wit@usi.ch\",\nrole = c(\"aut\", \"ths\"),\ncomment = c(ORCID = \"0000-0002-3671-9610\")))", "Description": "A random-effects stochastic model that allows quick\ndetection of clonal dominance events from clonal tracking data\ncollected in gene therapy studies. Starting from the Ito-type\nequation describing the dynamics of cells duplication, death\nand differentiation at clonal level, we first considered its\nlocal linear approximation as the base model. The parameters of\nthe base model, which are inferred using a maximum likelihood\napproach, are assumed to be shared across the clones. Although\nthis assumption makes inference easier, in some cases it can be\ntoo restrictive and does not take into account possible\nscenarios of clonal dominance. Therefore we extended the base\nmodel by introducing random effects for the clones. In this\nextended formulation the dynamic parameters are estimated using\na tailor-made expectation maximization algorithm. Further\ndetails on the methods can be found in L. Del Core et al.,\n(2022) .", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.2.3.9000", "LazyData": "true", "VignetteBuilder": "R.rsp", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-08 10:23:40 UTC", "User": "root" }, "Author": "Luca Del Core [aut, cre, cph]\n(), Marco Grzegorczyk\n[aut, ths] (), Ernst Wit\n[aut, ths] ()", "Maintainer": "Luca Del Core ", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev make\nlibicu-dev libuv1-dev", "Repository": "https://delcore-luca.r-universe.dev", "Date/Publication": "2024-02-16 02:30:12 UTC", "RemoteUrl": "https://github.com/cran/RestoreNet", "RemoteRef": "HEAD", "RemoteSha": "cf0167c84e61acd6c253890525b511ec9b2f46b9", "MD5sum": "1bd485ce575bf2c5a7372dbec07da3fc", "_user": "delcore-luca", "_type": "src", "_file": "RestoreNet_1.0.1.tar.gz", "_fileid": "229f405cd3269cecf9ad5bfa391468e522173a99d3d22aad34d4138b5fc215d1", "_filesize": 617059, "_sha256": 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