scanvi-explainer

Interpretability extension for scANVI using SHAP package.

Please see our example notebook on how to run scANVI Explainer.

Installation

$ pip install scanvi-explainer

Install from source

$ git clone https://github.com/brickmanlab/scanvi-explainer.git && cd scanvi-explainer
$ uv sync

Build documentation

$ sphinx-build -M html docs docs/_build

Citation

Please consider citing scANVI Explainer if you use in your research.

Deep Learning Based Models for Preimplantation Mouse and Human Development
Martin Proks, Nazmus Salehin, Joshua M. Brickman
bioRxiv 2024.02.16.580649; doi: 10.1101/2024.02.16.580649

@article{Proks2024.02.16.580649,
	author = {Proks, Martin and Salehin, Nazmus and Brickman, Joshua M.},
	title = {Deep Learning Based Models for Preimplantation Mouse and Human Development},
	elocation-id = {2024.02.16.580649},
	year = {2024},
	doi = {10.1101/2024.02.16.580649},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2024/02/16/2024.02.16.580649},
	eprint = {https://www.biorxiv.org/content/early/2024/02/16/2024.02.16.580649.full.pdf},
	journal = {bioRxiv}
}