README.md

Example Notebooks

The notebooks contained in this directory demonstrate the Vitessce Python package functionality.

Setup

Some of the example notebooks rely on external single-cell data analysis packages. An environment containing these additional packages can be installed with conda or pip.

cd docs/notebooks
conda env create -f environment.yml
conda activate vitessce-python-notebooks
pip install -e "../..[dev]"

Run

jupyter lab

Troubleshooting

If you previously had the vitessce Python package v1 installed, you may need to uninstall the previous lab extension due to conflicts between the v1 and v2 widget JS code.

jupyter labextension uninstall vitessce-jupyter