Metadata-Version: 2.3
Name: scanvi-explainer
Version: 0.1.0
Summary: Exapliner of scANVI using SHAP
Project-URL: Homepage, https://github.com/brickmanlab/scanvi-explainer
Project-URL: Documentation, https://scanvi-explainer.readthedocs.io
Project-URL: Repository, https://github.com/brickmanlab/scanvi-explainer.git
Project-URL: Issues, https://github.com/brickmanlab/scanvi-explainer/issues
Project-URL: Changelog, https://github.com/brickmanlab/scanvi-explainer/blob/master/CHANGELOG.md
Author-email: Martin Proks <martin.proks@sund.ku.dk>, Nazmus M Salehin <naz.salehin@sund.ku.dk>
License: MIT License
        
        Copyright (c) [year] [fullname]
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Keywords: explainer,interpretability,scanvi,shap
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: ruff>=0.6.4
Requires-Dist: shap>=0.41.0
Provides-Extra: dev
Requires-Dist: huggingface-hub; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Provides-Extra: doc
Requires-Dist: myst-nb>=1.1; extra == 'doc'
Requires-Dist: setuptools; extra == 'doc'
Requires-Dist: sphinx; extra == 'doc'
Requires-Dist: sphinx-book-theme>=1; extra == 'doc'
Requires-Dist: sphinxcontrib-bibtex>=1; extra == 'doc'
Description-Content-Type: text/markdown

# scanvi-explainer

[![build][build-badge]][build-link]
[![Documentation Status][docs]][docs-link]

Interpretability extension for [scANVI] using [SHAP] package.

Please see our [example](docs/notebooks/Example.ipynb) notebook on how to run scANVI Explainer.

## Installation

```console
$ pip install scanvi-explainer
```

## Install from source

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

## Build documentation

```console
$ 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 <br>
> Martin Proks, Nazmus Salehin, Joshua M. Brickman <br>
> bioRxiv 2024.02.16.580649; doi: [10.1101/2024.02.16.580649]

```BibTeX
@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}
}
```

[docs]: https://readthedocs.org/projects/scanvi-explainer/badge/?version=latest
[docs-link]: https://scanvi-explainer.readthedocs.io/en/latest/?badge=latest
[build-badge]: https://github.com/brickmanlab/scanvi-explainer/actions/workflows/build.yml/badge.svg
[build-link]: https://github.com/brickmanlab/scanvi-explainer/actions/workflows/build.yml
[scANVI]: https://docs.scvi-tools.org/en/stable/api/reference/scvi.model.SCANVI.html#scvi.model.SCANVI
[SHAP]: https://github.com/shap/shap
[10.1101/2024.02.16.580649]: https://doi.org/10.1101/2024.02.16.580649
