{"id":47273587,"url":"https://github.com/scverse/rapids-singlecell","last_synced_at":"2026-04-01T22:51:10.318Z","repository":{"id":45724026,"uuid":"364573913","full_name":"scverse/rapids-singlecell","owner":"scverse","description":"rapids-singlecell: GPU-accelerated framework for scRNA analysis","archived":false,"fork":false,"pushed_at":"2026-03-24T05:17:57.000Z","size":385661,"stargazers_count":341,"open_issues_count":22,"forks_count":43,"subscribers_count":7,"default_branch":"main","last_synced_at":"2026-03-29T15:19:29.030Z","etag":null,"topics":["anndata","bioinformatics","gpu","scverse","single-cell"],"latest_commit_sha":null,"homepage":"https://rapids-singlecell.readthedocs.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scverse.png","metadata":{"files":{"readme":"README.md","changelog":null,"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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-05-05T12:46:51.000Z","updated_at":"2026-03-29T15:09:01.000Z","dependencies_parsed_at":"2024-03-25T10:28:09.387Z","dependency_job_id":"a82dfb36-fd36-42fb-b807-fe734d1fab70","html_url":"https://github.com/scverse/rapids-singlecell","commit_stats":null,"previous_names":["scverse/rapids-singlecell","scverse/rapids_singlecell"],"tags_count":65,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/rapids-singlecell","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Frapids-singlecell","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Frapids-singlecell/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Frapids-singlecell/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Frapids-singlecell/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/rapids-singlecell/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Frapids-singlecell/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31292703,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-01T21:15:39.731Z","status":"ssl_error","status_checked_at":"2026-04-01T21:15:34.046Z","response_time":53,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["anndata","bioinformatics","gpu","scverse","single-cell"],"created_at":"2026-03-15T15:00:25.783Z","updated_at":"2026-04-01T22:51:10.296Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":["Python"],"sub_categories":[],"readme":"[![Stars](https://img.shields.io/github/stars/scverse/rapids_singlecell?style=flat\u0026logo=GitHub\u0026color=blue)](https://github.com/scverse/rapids_singlecell/stargazers)\n[![PyPI](https://img.shields.io/pypi/v/rapids-singlecell?logo=PyPI)](https://pypi.org/project/rapids-singlecell)\n[![Downloads](https://static.pepy.tech/badge/rapids-singlecell)](https://pepy.tech/project/rapids-singlecell)\n[![Documentation Status](https://readthedocs.org/projects/rapids-singlecell/badge/?version=latest)](https://rapids-singlecell.readthedocs.io/en/latest/?badge=latest)\n[![CI-Pass](https://github.com/scverse/rapids_singlecell/actions/workflows/test-gpu.yml/badge.svg)](https://github.com/scverse/rapids_singlecell/actions/workflows/test-gpu.yml)\n[![codecov](https://codecov.io/gh/scverse/rapids-singlecell/graph/badge.svg?token=PFHJEQD94X)](https://codecov.io/gh/scverse/rapids-singlecell)\n[![Chat](https://img.shields.io/badge/zulip-join_chat-%2367b08f.svg)](https://scverse.zulipchat.com)\n\n\n# rapids-singlecell: GPU-Accelerated Single-Cell Analysis within scverse®\n\nrapids-singlecell provides GPU-accelerated single-cell analysis with an AnnData-first API.\nIt is largely compatible with Scanpy and includes selected functionality from Squidpy, decoupler, and pertpy.\nComputations use CuPy and NVIDIA RAPIDS for performance on large datasets.\n\n- **GPU acceleration**: Common single-cell workflows on `AnnData` run on the GPU.\n- **Ecosystem compatibility**: Works with Scanpy APIs; includes pieces from Squidpy, decoupler, and pertpy.\n- **Simple installation**: Available via Conda and PyPI.\n\n## Documentation\n\nFor more information please have a look through the [documentation](https://rapids-singlecell.readthedocs.io/en/latest/)\n\n## Citation\n\nIf you use this tool, please cite: [![arXiv](https://img.shields.io/badge/arXiv-2603.02402-b31b1b.svg)](https://doi.org/10.48550/arXiv.2603.02402)\n\nPlease cite the relevant tools if used: [decoupler](https://doi.org/10.1093/bioadv/vbac016) for decoupler functions, [squidpy](https://doi.org/10.1038/s41592-021-01358-2) for spatial analysis, and [pertpy](https://doi.org/10.1038/s41592-024-02233-6) for perturbation analysis.\n\n[//]: # (numfocus-fiscal-sponsor-attribution)\n\nrapids-singlecell 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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Frapids-singlecell","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Frapids-singlecell","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Frapids-singlecell/lists"}