https://github.com/scverse/simple-scvi
Simple scVI implementation
https://github.com/scverse/simple-scvi
Last synced: 3 months ago
JSON representation
Simple scVI implementation
- Host: GitHub
- URL: https://github.com/scverse/simple-scvi
- Owner: scverse
- License: bsd-3-clause
- Created: 2023-01-17T20:56:41.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-06-23T17:38:10.000Z (12 months ago)
- Last Synced: 2025-07-07T01:09:03.318Z (11 months ago)
- Language: Python
- Homepage:
- Size: 83 KB
- Stars: 11
- Watchers: 3
- Forks: 4
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# simple-scvi
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/simple-scvi/test.yaml?branch=main
[link-tests]: https://github.com/scverse/simple-scvi/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/simple-scvi
External and simple implementation of scVI. This repository shows a minimal implementation of the [scVI](https://www.nature.com/articles/s41592-018-0229-2) model using [scvi-tools](https://scvi-tools.org) in an externally deployed package.
This package was initialized using the [cookicutter-scverse](https://github.com/scverse/cookiecutter-scverse) template. We advise all external projects to use the cookicutter template.
## Getting started
Please refer to the [documentation][link-docs]. In particular, the
- [API documentation][link-api].
## Installation
You need to have Python 3.8 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
There are several alternative options to install simple-scvi:
1. Install the latest development version:
```bash
pip install git+https://github.com/adamgayoso/simple-scvi.git@main
```
## Release notes
See the [changelog][changelog].
## Contact
For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].
## Citation
```
@article{gayoso2022python,
title={A Python library for probabilistic analysis of single-cell omics data},
author={Gayoso, Adam and Lopez, Romain and Xing, Galen and Boyeau, Pierre and Valiollah Pour Amiri, Valeh and Hong, Justin and Wu, Katherine and Jayasuriya, Michael and Mehlman, Edouard and Langevin, Maxime and others},
journal={Nature biotechnology},
volume={40},
number={2},
pages={163--166},
year={2022},
publisher={Nature Publishing Group US New York}
}
```
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/adamgayoso/simple-scvi/issues
[changelog]: https://simple-scvi.readthedocs.io/latest/changelog.html
[link-docs]: https://simple-scvi.readthedocs.io
[link-api]: https://simple-scvi.readthedocs.io/latest/api.html
[//]: # (numfocus-fiscal-sponsor-attribution)
simple-scvi is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
Copyright (c) 2025, Yosef Lab, Weizmann Institute of Science