Installation

Environment

We recommend using a fresh Conda environment for VoyagerPy. To create a new environment with the name voyagerpy and Python 3.8, run

$ conda create -n voyagerpy python=3.8

To activate the environment, run

$ conda activate voyagerpy

Since VoyagerPy is currently only published to PyPI, we recommend installing VoyagerPy and its dependencies with pip.

Install from PyPI

To install VoyagerPy from PyPI run:

$ pip install voyagerpy

We use Scanpy in the tutorials. Since VoyagerPy shares many dependencies with Scanpy, we recommend installing Scanpy as well with pip. To install Scanpy, run

$ pip install "scanpy[leiden]"

Development version

You can also install VoyagerPy from GitHub by running

$ pip install git+https://github.com/pmelsted/voyagerpy.git