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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Metadata
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Release files for cellflow-tools 0.0.9
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