https://github.com/brickmanlab/scanvi-explainer
scANVI Explainer
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
-
✓DOI references
Found 5 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary
Keywords
Repository
scANVI Explainer
Basic Info
- Host: GitHub
- Owner: brickmanlab
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://scanvi-explainer.readthedocs.io
- Size: 2.64 MB
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
scanvi-explainer
Interpretability extension for scANVI using SHAP package.
Please see our example 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
Martin Proks, Nazmus Salehin, Joshua M. Brickman
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}
}
Owner
- Name: Brickman group
- Login: brickmanlab
- Kind: organization
- Location: Copenhagen
- Website: https://danstem.ku.dk/research1/brickman/
- Repositories: 3
- Profile: https://github.com/brickmanlab
Professor Joshua Brickman at Center for Stem Cell Medicine (reNEW), University of Copenhagen
GitHub Events
Total
- Watch event: 3
Last Year
- Watch event: 3
Packages
- Total packages: 1
-
Total downloads:
- pypi 16 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
pypi.org: scanvi-explainer
Exapliner of scANVI using SHAP
- Homepage: https://github.com/brickmanlab/scanvi-explainer
- Documentation: https://scanvi-explainer.readthedocs.io
- 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.
-
Latest release: 0.3.1
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout main composite
- astral-sh/setup-uv v2 composite
- actions/checkout main composite
- actions/download-artifact v4 composite
- actions/upload-artifact v4 composite
- astral-sh/setup-uv v2 composite
- pypa/gh-action-pypi-publish release/v1 composite
- ruff >=0.6.4
- shap >=0.41.0