Package: RestoreNet
Title: Random-Effects Stochastic Reaction Networks
Version: 1.0.1
Authors@R: 
    c(person(given = "Luca", 
            family = "Del Core", 
            email = "l.del.core@rug.nl", 
            role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-1672-6995")),
    person(given = "Marco", 
            family = "Grzegorczyk", 
            email = "m.a.grzegorczyk@rug.nl", 
            role = c("aut", "ths"),
            comment = c(ORCID = "0000-0002-2604-9270")),
    person(given = "Ernst", 
            family = "Wit", 
            email = "ernst.jan.camiel.wit@usi.ch", 
            role = c("aut", "ths"),
            comment = c(ORCID = "0000-0002-3671-9610")))
Description: A random-effects stochastic model that allows quick
        detection of clonal dominance events from clonal tracking data
        collected in gene therapy studies. Starting from the Ito-type
        equation describing the dynamics of cells duplication, death
        and differentiation at clonal level, we first considered its
        local linear approximation as the base model. The parameters of
        the base model, which are inferred using a maximum likelihood
        approach, are assumed to be shared across the clones. Although
        this assumption makes inference easier, in some cases it can be
        too restrictive and does not take into account possible
        scenarios of clonal dominance. Therefore we extended the base
        model by introducing random effects for the clones. In this
        extended formulation the dynamic parameters are estimated using
        a tailor-made expectation maximization algorithm. Further
        details on the methods can be found in L. Del Core et al.,
        (2022) <doi:10.1101/2022.05.31.494100>.
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.2.3.9000
Imports: Matrix, xtable, scales, stringr, ggplot2, scatterpie,
        RColorBrewer
Depends: R (>= 2.10)
LazyData: true
Suggests: R.rsp
VignetteBuilder: R.rsp
NeedsCompilation: no
Packaged: 2026-10-06 09:59:53 UTC; root
Author: Luca Del Core [aut, cre, cph]
        (<https://orcid.org/0000-0002-1672-6995>), Marco Grzegorczyk
        [aut, ths] (<https://orcid.org/0000-0002-2604-9270>), Ernst Wit
        [aut, ths] (<https://orcid.org/0000-0002-3671-9610>)
Maintainer: Luca Del Core <l.del.core@rug.nl>
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev make
        libicu-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
Built: R 4.6.0; ; 2026-10-06 10:02:08 UTC; unix
