{"id":31805721,"url":"https://github.com/theislab/mapqc","last_synced_at":"2025-10-11T02:57:43.937Z","repository":{"id":282946306,"uuid":"944409099","full_name":"theislab/mapqc","owner":"theislab","description":"MapQC - a metric for the evaluation of single-cell query-to-reference mappings","archived":false,"fork":false,"pushed_at":"2025-10-06T20:12:22.000Z","size":33371,"stargazers_count":9,"open_issues_count":2,"forks_count":1,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-10-06T22:18:35.403Z","etag":null,"topics":["atlas","integration","mapping","query-to-reference-mapping","single-cell","transcriptomics"],"latest_commit_sha":null,"homepage":"https://mapqc.readthedocs.io/en/latest/","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/theislab.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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2025-03-07T09:47:27.000Z","updated_at":"2025-08-08T08:02:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"8a596a2c-2bf2-4a11-8c4c-a39deaa5595a","html_url":"https://github.com/theislab/mapqc","commit_stats":null,"previous_names":["theislab/mapqc"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/mapqc","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmapqc","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmapqc/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmapqc/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmapqc/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/mapqc/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmapqc/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278692996,"owners_count":26029414,"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":"2025-10-06T02:00:05.630Z","response_time":65,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","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":["atlas","integration","mapping","query-to-reference-mapping","single-cell","transcriptomics"],"created_at":"2025-10-11T02:57:40.026Z","updated_at":"2025-10-11T02:57:43.930Z","avatar_url":"https://github.com/theislab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mapQC\n\n[![Tests][badge-tests]][tests]\n[![Documentation][badge-docs]][documentation]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/mapqc/test.yaml?branch=main\n[badge-docs]: https://img.shields.io/readthedocs/mapqc\n\nA metric for the evaluation of single-cell query-to-reference mappings\n\n## Getting started\n\nPlease refer to the [documentation](https://mapqc.readthedocs.io/), in particular, the [API documentation](https://mapqc.readthedocs.io/en/latest/api/index.html) for detailed package documentation. For reproduction of the results in the paper, check out the [mapQC reproducibility repository](https://github.com/theislab/mapqc_reproducibility). \u003cbr\u003e\u003cbr\u003e\nBelow a few notes on how and when to use mapQC:\n\n### What does mapQC do?\n\nMapQC evaluates the quality of a query-to-reference mapping, and outputs a cell-level mapQC score for every query cell. MapQC scores higher than 2 indicate a large distance of the query cell to the reference. Given a healthy/control reference, we expect query controls to have low mapQC scores, and query case/disease cells to have higher mapQC scores in the case of case-specific cellular phenotypes. You can thus use mapQC scores to assess, in a quantitative manner, if your mapping was successful.\n\n![Overview of mapQC workflow](https://raw.githubusercontent.com/theislab/mapqc/main/docs/_static/images/mapQC_concept_figure.png)\n\u003cp style=\"margin-top: 0;\"\u003e\u003csmall\u003e\u003ci\u003eOverview of mapQC's workflow\u003c/i\u003e\u003c/small\u003e\u003c/p\u003e\n\n### What are the data requirements for using mapQC?\n\nIn short, you need one AnnData object, including:\n- A large scale reference, including only its healthy/control cells.\n- A mapped query dataset, with healthy/control cells (must-have) and case/perturbed cells (if you have them).\n- Metadata (query/reference status, study, sample, and optionally clustering and cell type annotations)\n- A mapping-derived embedding including both the reference and the query\n\nIn the [quick-start tutorial notebook](./docs/notebooks/mapqc_quickstart.ipynb) we provide a more extensive description of the exact data requirements.\n\n\n## Installation\n\nYou need to have Python 3.10 or newer installed on your system.\n\nThere are several alternative options to install mapQC:\n\n1) Install the latest release of `mapqc` from [PyPI][]:\n\n```bash\npip install mapqc\n```\n\n1. Install the latest development version:\n\n```bash\npip install git+https://github.com/theislab/mapqc.git@main\n```\n\n## Release notes\n\nSee the [changelog][].\n\n## Contact\n\nI am happy to hear any comments, suggestions, or even bugs that you run into. I would like to make this package run as smoothly as possible! So for any of these, submit an issue on the mapQC GitHub page and I will be glad to help.\n\n## Citation\n\n[Sikkema et al.](https://www.biorxiv.org/content/10.1101/2025.05.23.655749v1), bioRxiv 2025.\n\n[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge\n[scverse discourse]: https://discourse.scverse.org/\n[issue tracker]: https://github.com/theislab/mapqc/issues\n[tests]: https://github.com/theislab/mapqc/actions/workflows/test.yml\n[documentation]: https://mapqc.readthedocs.io\n[changelog]: https://mapqc.readthedocs.io/en/latest/changelog.html\n[api documentation]: https://mapqc.readthedocs.io/en/latest/api.html\n[pypi]: https://pypi.org/project/mapqc\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmapqc","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fmapqc","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmapqc/lists"}