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
If you get a
Permission denied error, use
pip install -U scvelo --user instead.
To work with the latest development version, install from GitHub using:
pip install git+https://github.com/theislab/scvelo
git clone https://github.com/theislab/scvelo 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.
- anndata - annotated data object.
- scanpy - toolkit for single-cell analysis.
- numpy, scipy, pandas, scikit-learn, matplotlib.
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
To run the tutorials in a notebook locally, please install:
pip install notebook
jupyter notebook in the terminal. If you get the error
Not a directory: 'xdg-settings',
jupyter notebook --no-browser instead and open the url manually (or use this
If you run into issues, do not hesitate to approach us or raise a GitHub issue.