Metadata-Version: 2.1
Name: cardamom
Version: 0.0.2
Summary: A package for inference and simulation of gene regulatory networks
Author-email: Elias Ventre <eliasventre@hotmail.fr>
License-File: LICENSE
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown

# 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).
