{"id":29303552,"url":"https://github.com/scverse/simple-scvi","last_synced_at":"2026-03-02T21:08:30.271Z","repository":{"id":104815068,"uuid":"590187667","full_name":"scverse/simple-scvi","owner":"scverse","description":"Simple scVI implementation","archived":false,"fork":false,"pushed_at":"2025-06-23T17:38:10.000Z","size":85,"stargazers_count":11,"open_issues_count":3,"forks_count":4,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-07-07T01:09:03.318Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scverse.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"docs/contributing.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-01-17T20:56:41.000Z","updated_at":"2025-06-17T08:54:15.000Z","dependencies_parsed_at":"2023-12-25T20:10:29.268Z","dependency_job_id":"41fdaa46-8913-4f07-af47-27347350d186","html_url":"https://github.com/scverse/simple-scvi","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/simple-scvi","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fsimple-scvi","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fsimple-scvi/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fsimple-scvi/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fsimple-scvi/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/simple-scvi/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fsimple-scvi/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266447658,"owners_count":23929994,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-22T02:00:09.085Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-07-07T01:09:00.997Z","updated_at":"2026-03-02T21:08:25.221Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# simple-scvi\n\n[![Tests][badge-tests]][link-tests]\n[![Documentation][badge-docs]][link-docs]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/simple-scvi/test.yaml?branch=main\n[link-tests]: https://github.com/scverse/simple-scvi/actions/workflows/test.yml\n[badge-docs]: https://img.shields.io/readthedocs/simple-scvi\n\nExternal 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.\n\nThis package was initialized using the [cookicutter-scverse](https://github.com/scverse/cookiecutter-scverse) template. We advise all external projects to use the cookicutter template.\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular, the\n\n-   [API documentation][link-api].\n\n## Installation\n\nYou need to have Python 3.8 or newer installed on your system. If you don't have\nPython installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).\n\nThere are several alternative options to install simple-scvi:\n\n\u003c!--\n1) Install the latest release of `simple-scvi` from `PyPI \u003chttps://pypi.org/project/simple-scvi/\u003e`_:\n\n```bash\npip install simple-scvi\n```\n--\u003e\n\n1. Install the latest development version:\n\n```bash\npip install git+https://github.com/adamgayoso/simple-scvi.git@main\n```\n\n## Release notes\n\nSee the [changelog][changelog].\n\n## Contact\n\nFor questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].\nIf you found a bug, please use the [issue tracker][issue-tracker].\n\n## Citation\n\n```\n@article{gayoso2022python,\n  title={A Python library for probabilistic analysis of single-cell omics data},\n  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},\n  journal={Nature biotechnology},\n  volume={40},\n  number={2},\n  pages={163--166},\n  year={2022},\n  publisher={Nature Publishing Group US New York}\n}\n```\n\n[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/adamgayoso/simple-scvi/issues\n[changelog]: https://simple-scvi.readthedocs.io/latest/changelog.html\n[link-docs]: https://simple-scvi.readthedocs.io\n[link-api]: https://simple-scvi.readthedocs.io/latest/api.html\n\n[//]: # (numfocus-fiscal-sponsor-attribution)\n\nsimple-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/).\nIf 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.\n\n\u003cdiv align=\"center\"\u003e\n\u003ca href=\"https://numfocus.org/project/scverse\"\u003e\n  \u003cimg\n    src=\"https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png\"\n    width=\"200\"\n  \u003e\n\u003c/a\u003e\n\u003c/div\u003e\n\nCopyright (c) 2025, Yosef Lab, Weizmann Institute of Science\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fsimple-scvi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fsimple-scvi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fsimple-scvi/lists"}