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RestoreNet  

Random-Effects Stochastic Reaction Networks
View on CRAN: Click here


Download and install RestoreNet package within the R console
Install from CRAN:
install.packages("RestoreNet")

Install from Github:
library("remotes")
install_github("cran/RestoreNet")

Install by package version:
library("remotes")
install_version("RestoreNet", "1.0.1")



Attach the package and use:
library("RestoreNet")
Maintained by
Luca Del Core
[Scholar Profile | Author Map]
First Published: 2022-09-20
Latest Update: 2024-02-15
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) .
How to cite:
Luca Del Core (2022). RestoreNet: Random-Effects Stochastic Reaction Networks. R package version 1.0.1, https://cran.r-project.org/web/packages/RestoreNet. Accessed 10 Apr. 2025.
Previous versions and publish date:
1.0 (2022-09-20 12:46)
Other packages that cited RestoreNet R package
View RestoreNet citation profile
Other R packages that RestoreNet depends, imports, suggests or enhances
Complete documentation for RestoreNet
Functions, R codes and Examples using the RestoreNet R package
Some associated functions: BhattDist . KLDiv . VEuy . Y_RM . compile.h . condAIC . dBu . dD2 . dmvNorm . fit.null . fit.re . get.M . get.V . get.W . get.boxplots . get.dx . get.gnl . get.nl . get.rescaled . get.scatterpie . get.sim.tl . ldet . nQ . ngQ . norm2 . nullModelFitting . ny_u . relErr . rmvNorm . rndEffModelFitting . rndEffModelStats . tr . 
Some associated R codes: data.R . functions.R . importPackages.R .  Full RestoreNet package functions and examples
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