CardamomOT
==========

.. py:module:: CardamomOT

.. autoapi-nested-parse::

   CardamomOT
   =====================================================================================

   A gene regulatory network inference method adapted to time-course scRNA-seq datasets.

   The algorithm consists of calibrating the parameters of a mechanistic model of gene
   expression. The calibrated model can then be simulated to reproduce the dataset used
   for inference. The simulation part is based on the Harissa package.

   Key Features
   ------------
   - Mechanistic inference of gene regulatory networks from scRNA-seq data
   - Supports time-course and trajectory data
   - Integration with mechanistic simulation models
   - Network visualization and analysis tools

   .. rubric:: References

   1. Ventre E, et al. (2021).
   2. Ventre E, et al. (2023).
   3. Maugé Y. and Ventre E. (2026). CardamomOT: a mechanistic optimal transport-based framework for gene regulatory network inference, trajectory reconstruction and generative modeling. doi: 10.64898/2026.03.31.715390

   Author
   ------
   Elias Ventre
   Yann Mauge

   License
   -------
   MIT License



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/CardamomOT/config/index
   /autoapi/CardamomOT/inference/index
   /autoapi/CardamomOT/model/index
   /autoapi/CardamomOT/tools/index