Installation¶

cellrank requires Python ≥ 3.12. If you encounter any problems, feel free to open an issue.

pip / uv (recommended)¶

Install CellRank from PyPI:

pip install cellrank

Or, using uv, a fast, modern pip replacement:

uv pip install cellrank

Optional extras¶

CellRank provides optional dependency groups for common workflows:

pip install "cellrank[moscot]"  # moscot for optimal transport (RealTimeKernel)
pip install "cellrank[plot]"    # additional plotting dependencies

conda / mamba / pixi¶

CellRank is available on conda-forge. This installation method is recommended if you need PETSc and SLEPc, libraries for large-scale linear algebra that CellRank uses when computing macrostates or fate probabilities on large datasets:

mamba install -c conda-forge cellrank

Or, using pixi, a fast, modern conda replacement:

pixi add cellrank

To also install PETSc and SLEPc (conda-only packages):

mamba install -c conda-forge cellrank petsc4py slepc4py

Note

Windows users: PETSc and SLEPc are not built for Windows on conda-forge (only Linux and macOS). Because the conda-forge cellrank package depends on pygpcca, which in turn requires petsc, mamba install -c conda-forge cellrank cannot be solved on Windows and fails with an error such as petsc [...] does not exist (perhaps a missing channel).

On Windows, install CellRank with pip install cellrank instead. PETSc and SLEPc are optional — without them CellRank falls back to a slower SciPy-based eigensolver for computing macrostates and fate probabilities, which is fine for small to medium datasets. To use PETSc and SLEPc on Windows, run CellRank inside WSL and install via conda there.

Development version¶

To install the latest development version from GitHub:

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

See Contributing guide for setting up a full development environment.