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.
To contribute to scVelo,
cd into the cloned directory and
install the latest packages required for development together with the pre-commit hooks:
pip install -r requirements-dev.txt pre-commit install
- 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:
conda 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.