Work

RTF: an R package for modelling time course data

Year: 2024

Type: article

Abstract: 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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btae597

Authors: Eva Brombacher, Clemens Kreutz

Institutions: University of Freiburg, University Medical Center Freiburg

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $4,188

Funders: Deutsche Forschungsgemeinschaft, Albert-Ludwigs-Universität Freiburg