CellFlow - Modeling Complex Perturbations with Flow Matching

CellFlow is a framework for predicting single-cell phenotypes induced by complex perturbations. It is quite flexible and enables researchers to systematically explore how cells respond to a wide range of experimental interventions, including drug treatments, genetic modifications, cytokine stimulation, morphogen pathway modulation or even entire organoid protocols.

Check out the preprint for details!

Example Applications

Modeling the effect of single and combinatorial drug treatments
Predicting the phenotypic response to genetic perturbations
Modeling the development of perturbed organisms
Cell fate engineering
Optimizing protocols for growing organoids
... and more; check out the documentation for more information.

Installation

Install CellFlow by running::

pip install cellflow-tools

In order to install CellFlow in editable mode, run::

git clone https://github.com/theislab/cellflow
cd cellflow
pip install -e .

For further instructions how to install jax, please refer to https://github.com/google/jax.

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