{"id":13751415,"url":"https://github.com/scverse/scvi-tools","last_synced_at":"2025-12-14T22:59:52.869Z","repository":{"id":37259660,"uuid":"102567256","full_name":"scverse/scvi-tools","owner":"scverse","description":"Deep probabilistic analysis of single-cell and spatial omics data","archived":false,"fork":false,"pushed_at":"2025-05-12T11:28:03.000Z","size":155630,"stargazers_count":1370,"open_issues_count":47,"forks_count":388,"subscribers_count":25,"default_branch":"main","last_synced_at":"2025-05-12T11:44:08.979Z","etag":null,"topics":["cite-seq","deep-generative-model","deep-learning","human-cell-atlas","scrna-seq","scverse","single-cell-genomics","single-cell-rna-seq","variational-autoencoder","variational-bayes"],"latest_commit_sha":null,"homepage":"http://scvi-tools.org/","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":null,"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":"2017-09-06T05:39:48.000Z","updated_at":"2025-05-10T14:11:04.000Z","dependencies_parsed_at":"2023-07-17T08:41:10.842Z","dependency_job_id":"f0118cc0-0546-455b-80f5-a4461f8fe868","html_url":"https://github.com/scverse/scvi-tools","commit_stats":{"total_commits":3299,"total_committers":74,"mean_commits":44.58108108108108,"dds":0.4880266747499242,"last_synced_commit":"34122012193f0623d58c4bc8669699ab5446e2e2"},"previous_names":["yoseflab/scvi","yoseflab/scvi-tools"],"tags_count":121,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscvi-tools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscvi-tools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscvi-tools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscvi-tools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/scvi-tools/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253923522,"owners_count":21984921,"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","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":["cite-seq","deep-generative-model","deep-learning","human-cell-atlas","scrna-seq","scverse","single-cell-genomics","single-cell-rna-seq","variational-autoencoder","variational-bayes"],"created_at":"2024-08-03T09:00:44.483Z","updated_at":"2025-12-14T22:59:52.856Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":["🔬 Domain-Specific Applications","Python","其他_生物医药","Software packages","Ranked by starred repositories","Machine Learning Tasks and Models","Biomedical Research \u0026 Drug Discovery"],"sub_categories":["🧬 Biology \u0026 Medicine","网络服务_其他","Multi-assay data integration","Foundation Models"],"readme":"\u003ca href=\"https://scvi-tools.org/\"\u003e\n  \u003cimg\n    src=\"https://github.com/scverse/scvi-tools/blob/main/docs/_static/scvi-tools-horizontal.svg?raw=true\"\n    width=\"400\"\n    alt=\"scvi-tools\"\n  \u003e\n\u003c/a\u003e\n\n[![Stars][gh-stars-badge]][gh-stars-link]\n[![PyPI][pypi-badge]][pypi-link]\n[![PyPIDownloads][pepy-badge]][pepy-link]\n[![CondaDownloads][conda-badge]][conda-link]\n[![Docs][docs-badge]][docs-link]\n[![Build][build-badge]][build-link]\n[![Coverage][coverage-badge]][coverage-link]\n\n[scvi-tools] (single-cell variational inference tools) is a package for probabilistic modeling and\nanalysis of single-cell omics data, built on top of [PyTorch] and [AnnData].\n\n# Analysis of single-cell omics data\n\nscvi-tools is composed of models that perform many analysis tasks across single-cell, multi, and\nspatial omics data:\n\n- Dimensionality reduction\n- Data integration\n- Automated annotation\n- Factor analysis\n- Doublet detection\n- Spatial deconvolution\n- and more!\n\nIn the [user guide], we provide an overview of each model. All model implementations have a\nhigh-level API that interacts with [Scanpy] and includes standard save/load functions, GPU\nacceleration, etc.\n\n# Rapid development of novel probabilistic models\n\nscvi-tools contains the building blocks to develop and deploy novel probabilistic models. These\nbuilding blocks are powered by popular probabilistic and machine learning frameworks such as\n[PyTorch Lightning] and [Pyro]. For an overview of how the scvi-tools package is structured, you\nmay refer to the [codebase overview] page.\n\nWe recommend checking out the [skeleton repository] as a starting point for developing and\ndeploying new models with scvi-tools.\n\n# Basic installation\n\nFor conda,\n\n```bash\nconda install scvi-tools -c conda-forge\n```\n\nand for pip,\n\n```bash\npip install scvi-tools\n```\n\nPlease be sure to install a version of [PyTorch] that is compatible with your GPU (if applicable).\n\n# Resources\n\n- Tutorials, API reference, and installation guides are available in the [documentation].\n- For discussion of usage, check out our [forum].\n- Please use the [issues] to submit bug reports.\n- If you'd like to contribute, check out our [contributing guide].\n- If you find a model useful for your research, please consider citing the corresponding\n    publication.\n\n# Reference\n\nIf you use `scvi-tools` in your work, please cite\n\n\u003e **A Python library for probabilistic analysis of single-cell omics data**\n\u003e\n\u003e Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong,\n\u003e Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran,\n\u003e Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling Xu, Tal Ashuach, Mariano Gabitto,\n\u003e Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov,\n\u003e Carlos Talavera-López, Lior Pachter, Fabian J. Theis, Aaron Streets, Michael I. Jordan,\n\u003e Jeffrey Regier \u0026 Nir Yosef\n\u003e\n\u003e _Nature Biotechnology_ 2022 Feb 07. doi: [10.1038/s41587-021-01206-w](https://doi.org/10.1038/s41587-021-01206-w).\n\nalong with the publication describing the model used.\n\nYou can cite the scverse publication as follows:\n\n\u003e **The scverse project provides a computational ecosystem for single-cell omics data analysis**\n\u003e\n\u003e Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor Sturm, Adam Gayoso,\n\u003e Ilia Kats, Mikaela Koutrouli, Scverse Community, Bonnie Berger, Dana Pe’er, Aviv Regev,\n\u003e Sarah A. Teichmann, Francesca Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle \u0026\n\u003e Fabian J. Theis\n\u003e\n\u003e _Nature Biotechnology_ 2023 Apr 10. doi: [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).\n\nscvi-tools is part of the scverse® project ([website](https://scverse.org),\n[governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).\n\nIf you like scverse® and want to support our mission, please consider making a tax-deductible\n[donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time,\nprofessional 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\n[anndata]: https://anndata.readthedocs.io/en/latest/\n[build-badge]: https://github.com/scverse/scvi-tools/actions/workflows/build.yml/badge.svg\n[build-link]: https://github.com/scverse/scvi-tools/actions/workflows/build.yml/\n[codebase overview]: https://docs.scvi-tools.org/en/stable/user_guide/background/codebase_overview.html\n[conda-badge]: https://img.shields.io/conda/dn/conda-forge/scvi-tools?logo=Anaconda\n[conda-link]: https://anaconda.org/conda-forge/scvi-tools\n[contributing guide]: https://docs.scvi-tools.org/en/stable/developer/code.html\n[coverage-badge]: https://codecov.io/gh/scverse/scvi-tools/branch/main/graph/badge.svg\n[coverage-link]: https://codecov.io/gh/scverse/scvi-tools\n[docs-badge]: https://readthedocs.org/projects/scvi/badge/?version=latest\n[docs-link]: https://scvi.readthedocs.io/en/stable/?badge=stable\n[documentation]: https://docs.scvi-tools.org/\n[forum]: https://discourse.scvi-tools.org\n[gh-stars-badge]: https://img.shields.io/github/stars/scverse/scvi-tools?style=flat\u0026logo=GitHub\u0026color=blue\n[gh-stars-link]: https://github.com/scverse/scvi-tools/stargazers\n[issues]: https://github.com/scverse/scvi-tools/issues\n[pepy-badge]: https://static.pepy.tech/badge/scvi-tools\n[pepy-link]: https://pepy.tech/project/scvi-tools\n[pypi-badge]: https://img.shields.io/pypi/v/scvi-tools.svg\n[pypi-link]: https://pypi.org/project/scvi-tools\n[pyro]: https://pyro.ai/\n[pytorch]: https://pytorch.org\n[pytorch lightning]: https://lightning.ai/docs/pytorch/stable/\n[scanpy]: http://scanpy.readthedocs.io/\n[scvi-tools]: https://scvi-tools.org/\n[skeleton repository]: https://github.com/scverse/simple-scvi\n[user guide]: https://docs.scvi-tools.org/en/stable/user_guide/index.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscvi-tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fscvi-tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscvi-tools/lists"}