cellflow-tools 0.0.9

Modeling complex perturbations with flow matching at single-cell resolution

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.