Installation

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

PyPI

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+https://github.com/theislab/scvelo

or:

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.

Dependencies

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.