Cytopath requires Python 3.9. We recommend using Miniconda and setting up a new conda environment.

conda create -y -n cytopath_env python==3.9
conda activate cytopath_env


Install cytopath from PyPI using pip

pip install cytopath


Direct dependencies of Cytopath will be installed automatically in the step above however, additional dependencies of scvelo will need to be installed manually.

conda install -c conda-forge python-igraph louvain

Jupyter notebook

To run the tutorials install jupyter notebooks.

conda install notebook