scVelo requires Python 3.6 or later. We recommend to use Miniconda.


Install scVelo from PyPI using:

pip install -U scvelo

-U is short for --upgrade. If you get a Permission denied error, use pip install -U scvelo --user instead.

Development Version

To work with the latest development version, install from GitHub using:

pip install git+


git clone
pip install -e scvelo

-e is short for --editable and links the package to the original cloned location such that pulled changes are also reflected in the environment.


Parts of scVelo (directed PAGA and Louvain modularity) require (optional):

pip install python-igraph louvain

Using fast neighbor search via hnswlib further requires (optional):

pip install pybind11 hnswlib

Jupyter Notebook

To run the tutorials in a notebook locally, please install:

pip install notebook

and run jupyter notebook in the terminal. If you get the error Not a directory: 'xdg-settings', use jupyter notebook --no-browser instead and open the url manually (or use this bugfix).

If you run into issues, do not hesitate to approach us or raise a GitHub issue.