RTF：一个用于建模时间序列数据的 R 包。

RTF: an R package for modelling time course data.

机构信息

Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center-University of Freiburg, 79104 Freiburg, Germany.

Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany.

出版信息

Bioinformatics. 2024 Oct 1;40(10). doi: 10.1093/bioinformatics/btae597.

DOI:10.1093/bioinformatics/btae597

PMID:39383522

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11879456/

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.

摘要

延迟瞬态函数 (RTF) 方法是一种补充方法，可用于对细胞信号转导过程中常见的动力学进行建模，而这些动力学通常用常微分方程 (ODE) 来描述。我们引入了一个 R 包，该包实现了 RTF 方法，该方法最初是在基于 MATLAB 的 Data2Dynamics 建模框架内实现的。该包有助于对时间和剂量依赖性进行建模，并且包括模型简化以最小化过度拟合的可能性。它可以应用于实验数据或 ODE 模型的轨迹，以描述它们的动力学。此外，它可以根据一组时变数据的拟合 RTF 参数生成低维表示，有助于识别实验扰动的关键目标。