https://github.com/theislab/cellflow

Modeling complex perturbations with CellFlow
https://github.com/theislab/cellflow

Last synced: 10 months ago
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Modeling complex perturbations with CellFlow

• Host: GitHub
• URL: https://github.com/theislab/cellflow
• Owner: theislab
• License: other
• Created: 2024-07-11T15:13:27.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2025-09-29T19:20:12.000Z (10 months ago)
• Last Synced: 2025-09-30T07:27:57.433Z (10 months ago)
• Language: Python
• Homepage: https://cellflow.readthedocs.io/
• Size: 12.3 MB
• Stars: 86
• Watchers: 0
• Forks: 16
• Open Issues: 64
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: docs/contributing.rst
  • License: LICENSE

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README

          


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CellFlow - Modeling Complex Perturbations with Flow Matching 

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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](https://www.biorxiv.org/content/10.1101/2025.04.11.648220v1.abstract) 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](https://cellflow.readthedocs.io) 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.