Installation

cellrank requires Python version >= 3.8 to run. We recommend using Mamba to manage Python environments. If you encounter any problems, feel free to open an issue.

Conda

CellRank can also be installed via conda-forge as:

conda install -c conda-forge cellrank

This installation method is preferred because it also contains PETSc and SLEPc, libraries for large-scale linear algebra problems CellRank relies on (e.g., when computing macrostates or fate probabilities).

PyPI

CellRank is also available on PyPI:

pip install cellrank

Development Version

To stay up-to-date with the newest version, run:

pip install git+https://github.com/theislab/cellrank.git@main