{"id":13751919,"url":"https://github.com/scverse/scirpy","last_synced_at":"2025-07-07T01:09:20.972Z","repository":{"id":37483787,"uuid":"232568640","full_name":"scverse/scirpy","owner":"scverse","description":"A scanpy extension to analyse single-cell TCR and BCR data.","archived":false,"fork":false,"pushed_at":"2025-05-05T17:34:30.000Z","size":175634,"stargazers_count":230,"open_issues_count":43,"forks_count":37,"subscribers_count":10,"default_branch":"main","last_synced_at":"2025-05-05T18:50:01.148Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://scirpy.scverse.org/en/latest/","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":"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":"2020-01-08T13:23:52.000Z","updated_at":"2025-04-14T19:54:19.000Z","dependencies_parsed_at":"2024-02-22T21:27:29.497Z","dependency_job_id":"005db86b-5920-4796-b724-dda6acfe2842","html_url":"https://github.com/scverse/scirpy","commit_stats":{"total_commits":904,"total_committers":14,"mean_commits":64.57142857142857,"dds":"0.20575221238938057","last_synced_commit":"02955d72382ca9371e40bc1f94d4c44046f7ca35"},"previous_names":["icbi-lab/scirpy"],"tags_count":41,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscirpy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscirpy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscirpy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/scverse%2Fscirpy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/scverse","download_url":"https://codeload.github.com/scverse/scirpy/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253303204,"owners_count":21886906,"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":[],"created_at":"2024-08-03T09:00:57.036Z","updated_at":"2025-07-07T01:09:20.966Z","avatar_url":"https://github.com/scverse.png","language":"Python","funding_links":[],"categories":["单细胞与空间组学","🔬 VDJ Analysis","Ranked by starred repositories"],"sub_categories":["其他新抗原工具","Single-Cell"],"readme":"# Scirpy: single-cell immune receptor analysis in Python\n\n[![Tests][badge-tests]][link-tests]\n[![Documentation][badge-docs]][link-docs]\n[![PyPI][badge-pypi]][link-pypi]\n[![bioconda][badge-bioconda]][link-bioconda]\n[![airr][badge-airr]][link-airr]\n[![Powered by NumFOCUS][badge-numfocus]][link-numfocus]\n\nScirpy is a package to analyse T cell receptor (TCR) or B cell receptor (BCR)\nrepertoires from single-cell RNA sequencing (scRNA-seq) data in Python.\nIt seamlessly integrates with [scanpy][] and [mudata][] and provides various modules for data import, analysis and visualization.\n\n[//]: # \"numfocus-fiscal-sponsor-attribution\"\n\nscirpy 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\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/scverse/scirpy/test.yaml?branch=main\n[link-tests]: https://github.com/scverse/scirpy/actions/workflows/test.yml\n[badge-docs]: https://img.shields.io/readthedocs/scirpy\n[badge-pypi]: https://img.shields.io/pypi/v/scirpy?logo=PyPI\n[link-pypi]: https://pypi.org/project/scirpy/\n[link-bioconda]: http://bioconda.github.io/recipes/scirpy/README.html\n[badge-bioconda]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat\n[badge-airr]: https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1\u0026message=compliant\u0026color=008AFF\u0026labelColor=000000\u0026style=flat\n[link-airr]: https://docs.airr-community.org/en/stable/swtools/airr_swtools_standard.html\n[scverse]: https://scverse.org\n[scanpy]: https://scanpy.readthedocs.io/\n[mudata]: https://github.com/scverse/mudata\n[badge-numfocus]: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat\u0026colorA=E1523D\u0026colorB=007D8A\n[link-numfocus]: http://numfocus.org\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular, the\n\n- [Tutorial][link-tutorial], and the\n- [API documentation][link-api].\n\n## Installation\n\nYou need to have Python 3.10 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 scirpy:\n\n1. Install the latest release of `scirpy` from [PyPI](https://pypi.org/project/scirpy/):\n\n    ```bash\n    pip install scirpy\n    ```\n\n2. Get it from [Bioconda][link-bioconda]:\n\n    First **setup conda channels [as described here](https://bioconda.github.io/#usage)**. Then install scirpy:\n\n    ```bash\n    conda install scirpy\n    ```\n\n3. Install the latest development version:\n\n    ```bash\n    pip install git+https://github.com/scverse/scirpy.git@main\n    ```\n\n4. Run it in a container using [Docker][] or [Podman][]:\n\n    ```bash\n    docker pull quay.io/biocontainers/scirpy:\u003ctag\u003e\n    ```\n\nwhere `tag` is one of [these tags](https://quay.io/repository/biocontainers/scirpy?tab=tags).\n\n## Release notes\n\nSee the [changelog][changelog].\n\n## Support and Contact\n\nWe are happy to assist with problems when using scirpy.\n\n- If you need help with scirpy or have questions regarding single-cell immune-cell receptor analysis in general, please join us in the [scverse discourse][scverse-discourse].\n- For bug report or feature requests, please use the [issue tracker][issue-tracker].\n\nWe try to respond within two working days, however fixing bugs or implementing new features\ncan take substantially longer, depending on the availability of our developers.\n\n## Citation\n\nIf you use `scirpy` in your work, please cite the `scirpy`\npublication as follows:\n\n\u003e **Scirpy: A Scanpy extension for analyzing single-cell T-cell\n\u003e receptor sequencing data**\n\u003e\n\u003e Gregor Sturm, Tamas Szabo, Georgios Fotakis, Marlene Haider, Dietmar\n\u003e Rieder, Zlatko Trajanoski, Francesca Finotello\n\u003e\n\u003e _Bioinformatics_ 2020 Sep 15. doi:\n\u003e [10.1093/bioinformatics/btaa611](https://doi.org/10.1093/bioinformatics/btaa611).\n\nYou can cite the scverse publication as follows:\n\n\u003e **The scverse project provides a computational ecosystem for\n\u003e single-cell omics data analysis**\n\u003e\n\u003e Isaac Virshup, Danila Bredikhin, Lukas Heumos, Giovanni Palla, Gregor\n\u003e Sturm, Adam Gayoso, Ilia Kats, Mikaela Koutrouli, Scverse Community,\n\u003e Bonnie Berger, Dana Pe’er, Aviv Regev, Sarah A. Teichmann, Francesca\n\u003e Finotello, F. Alexander Wolf, Nir Yosef, Oliver Stegle \u0026 Fabian J.\n\u003e Theis\n\u003e\n\u003e _Nat Biotechnol._ 2023 Apr 10. doi:\n\u003e [10.1038/s41587-023-01733-8](https://doi.org/10.1038/s41587-023-01733-8).\n\n[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/scverse/scirpy/issues\n[changelog]: https://scirpy.readthedocs.io/latest/changelog.html\n[link-docs]: https://scirpy.readthedocs.io\n[link-api]: https://scirpy.readthedocs.io/latest/api.html\n[link-tutorial]: https://scirpy.scverse.org/en/latest/tutorials.html\n[Docker]: https://www.docker.com/\n[Podman]: https://podman.io/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscirpy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fscverse%2Fscirpy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fscverse%2Fscirpy/lists"}