cardamom 0.0.2

A package for inference and simulation of gene regulatory networks

CARDAMOM

CARDAMOM is an executable Gene Regulatory Network (GRN) inference method, adapted for timestamped scRNA-seq dataset. The algorithm consists in fitting the parameters of a mechanistic model of gene expression: the simulation of the model, once calibrated, allows to reproduce the dataset used for the inference. The method has been introduced in [1]. It has been benchmarked among other GRN inference tools and applied on a real dataset in [2].

[1] E. Ventre. “Reverse engineering of a mechanistic model of gene expression using metastability and temporal dynamics”. In: In Silico Biology 14 (2021), pp. 89–113.

[2] E. Ventre, U. Herbach et al. "One model fits all: combining inference and simulation of gene regulatory networks". In: BioRxiv (2022).