Key result
RTF R package models time and dose dependencies in cellular signaling to complement ordinary differential equations.
Why the study?
The retarded transient function (RTF) approach provides a complementary method to ODEs for modelling cellular signalling dynamics, requiring accessible implementation.
The RTF R package provides a new computational tool for modelling dynamics in cellular signalling processes, complementing ODE-based methods.
SUMMARY: The retarded transient function (RTF) approach serves as a complementary method to ordinary differential equations (ODEs) for modelling dynamics typically observed in cellular signalling processes. We introduce an R package that implements the RTF approach, originally implemented within the MATLAB-based Data2Dynamics modelling framework. This package facilitates the modelling of time and dose dependencies, and it includes the possibility of model reduction to minimize overfitting. It can be applied to experimental data or trajectories of ODE models to characterize their dynamics. Additionally, it can generate a low-dimensional representation based on the fitted RTF parameters of a set of time-resolved data, aiding in the identification of key targets of experimental perturbations. AVAILABILITY AND IMPLEMENTATION: The R package RTF is available at https://github.com/kreutz-lab/RTF.
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Brombacher et al. (2024) studied this question. RTF R package was evaluated. The RTF R package was introduced to model time and dose dependencies in cellular signalling processes, serving as a complementary method to ordinary differential equations.
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