| Name | scanvi-explainer JSON |
| Version |
0.3.1
JSON |
| download |
| home_page | None |
| Summary | Exapliner of scANVI using SHAP |
| upload_time | 2024-09-27 22:20:01 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| 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. |
| keywords |
explainer
interpretability
scanvi
shap
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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
Raw data
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"description": "# scanvi-explainer\n\n[![build][build-badge]][build-link]\n[![Documentation Status][docs]][docs-link]\n\nInterpretability extension for [scANVI] using [SHAP] package.\n\nPlease see our [example](docs/notebooks/Example.ipynb) notebook on how to run scANVI Explainer.\n\n## Installation\n\n```console\n$ pip install scanvi-explainer\n```\n\n## Install from source\n\n```console\n$ git clone https://github.com/brickmanlab/scanvi-explainer.git && cd scanvi-explainer\n$ uv sync\n```\n\n## Build documentation\n\n```console\n$ sphinx-build -M html docs docs/_build\n```\n\n## Citation\n\nPlease consider citing scANVI Explainer if you use in your research.\n\n> Deep Learning Based Models for Preimplantation Mouse and Human Development <br>\n> Martin Proks, Nazmus Salehin, Joshua M. Brickman <br>\n> bioRxiv 2024.02.16.580649; doi: [10.1101/2024.02.16.580649]\n\n```BibTeX\n@article{Proks2024.02.16.580649,\n\tauthor = {Proks, Martin and Salehin, Nazmus and Brickman, Joshua M.},\n\ttitle = {Deep Learning Based Models for Preimplantation Mouse and Human Development},\n\telocation-id = {2024.02.16.580649},\n\tyear = {2024},\n\tdoi = {10.1101/2024.02.16.580649},\n\tpublisher = {Cold Spring Harbor Laboratory},\n\tURL = {https://www.biorxiv.org/content/early/2024/02/16/2024.02.16.580649},\n\teprint = {https://www.biorxiv.org/content/early/2024/02/16/2024.02.16.580649.full.pdf},\n\tjournal = {bioRxiv}\n}\n```\n\n[docs]: https://readthedocs.org/projects/scanvi-explainer/badge/?version=latest\n[docs-link]: https://scanvi-explainer.readthedocs.io/en/latest/?badge=latest\n[build-badge]: https://github.com/brickmanlab/scanvi-explainer/actions/workflows/build.yml/badge.svg\n[build-link]: https://github.com/brickmanlab/scanvi-explainer/actions/workflows/build.yml\n[scANVI]: https://docs.scvi-tools.org/en/stable/api/reference/scvi.model.SCANVI.html#scvi.model.SCANVI\n[SHAP]: https://github.com/shap/shap\n[10.1101/2024.02.16.580649]: https://doi.org/10.1101/2024.02.16.580649\n",
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