{"id":29303528,"url":"https://github.com/scverse/snapatac2","last_synced_at":"2025-07-07T01:08:55.802Z","repository":{"id":38836883,"uuid":"434794072","full_name":"scverse/SnapATAC2","owner":"scverse","description":"Single-cell epigenomics analysis tools","archived":false,"fork":false,"pushed_at":"2025-06-30T14:08:49.000Z","size":25037,"stargazers_count":264,"open_issues_count":55,"forks_count":34,"subscribers_count":9,"default_branch":"main","last_synced_at":"2025-07-01T05:03:46.785Z","etag":null,"topics":["single-cell-genomics"],"latest_commit_sha":null,"homepage":"https://scverse.org/SnapATAC2","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/scverse.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":"CODE_OF_CONDUCT.md","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":"2021-12-04T03:09:16.000Z","updated_at":"2025-06-30T13:47:50.000Z","dependencies_parsed_at":"2023-09-26T05:13:36.188Z","dependency_job_id":"15dba9ea-d184-41b3-9bd3-48253dcf6f12","html_url":"https://github.com/scverse/SnapATAC2","commit_stats":null,"previous_names":["scverse/snapatac2","kaizhang/snapatac2"],"tags_count":27,"template":false,"template_full_name":null,"purl":"pkg:github/scverse/SnapATAC2","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2FSnapATAC2","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2FSnapATAC2/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2FSnapATAC2/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2FSnapATAC2/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/SnapATAC2/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2FSnapATAC2/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263996092,"owners_count":23541402,"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":["single-cell-genomics"],"created_at":"2025-07-07T01:08:54.897Z","updated_at":"2025-07-07T01:08:55.770Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"SnapATAC2: A Python/Rust package for single-cell epigenomics analysis\n=====================================================================\n\n![PyPI](https://img.shields.io/pypi/v/snapatac2)\n![PyPI - Downloads](https://img.shields.io/pypi/dm/snapatac2)\n![Continuous integration](https://github.com/scverse/SnapATAC2/workflows/test-python-package/badge.svg)\n![GitHub Repo stars](https://img.shields.io/github/stars/scverse/SnapATAC2?style=social)\n\n\u003e [!TIP]\n\u003e Got raw fastq files? Check out our new single-cell preprocessing package [precellar](https://github.com/regulatory-genomics/precellar)!\n\nSnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis framework, featuring:\n\n- Scale to more than 10 million cells.\n- Blazingly fast preprocessing tools for BAM to fragment files conversion and count matrix generation.\n- Matrix-free spectral embedding algorithm that is applicable to a wide range of single-cell omics data, including single-cell ATAC-seq, single-cell RNA-seq, single-cell Hi-C, and single-cell methylation.\n- Efficient and scalable co-embedding algorithm for single-cell multi-omics data integration.\n- End-to-end analysis pipeline for single-cell ATAC-seq data, including preprocessing, dimension reduction, clustering, data integration, peak calling, differential analysis, motif analysis, regulatory network analysis.\n- Seamless integration with other single-cell analysis packages such as Scanpy.\n- Implementation of fully backed AnnData.\n\n[//]: # (numfocus-fiscal-sponsor-attribution)\n\nSnapATAC2 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\nDocumentation\n-------------\n\n- **Full Documentation**: https://scverse.org/SnapATAC2/\n- **Installation instructions**: https://scverse.org/SnapATAC2/install.html\n- **Tutorial/Demo**: https://scverse.org/SnapATAC2/tutorials/index.html\n\nHow to cite\n-----------\n\nZhang, K., Zemke, N. R., Armand, E. J. \u0026 Ren, B. (2024).\nA fast, scalable and versatile tool for analysis of single-cell omics data.\nNature Methods, 1–11. https://doi.org/10.1038/s41592-023-02139-9\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fsnapatac2","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fsnapatac2","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fsnapatac2/lists"}