{"id":17366479,"url":"https://github.com/theislab/graphcompass","last_synced_at":"2026-03-05T13:03:10.238Z","repository":{"id":219170070,"uuid":"747365407","full_name":"theislab/graphcompass","owner":"theislab","description":"GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems","archived":false,"fork":false,"pushed_at":"2025-07-11T14:20:21.000Z","size":2995,"stargazers_count":38,"open_issues_count":4,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-01-15T00:52:45.506Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-01-23T19:33:42.000Z","updated_at":"2025-10-30T04:41:22.000Z","dependencies_parsed_at":"2024-01-25T21:24:37.898Z","dependency_job_id":"e79e3228-9c55-4029-b664-614c0aa743fd","html_url":"https://github.com/theislab/graphcompass","commit_stats":null,"previous_names":["theislab/graphcompass"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/graphcompass","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgraphcompass","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgraphcompass/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgraphcompass/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgraphcompass/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/graphcompass/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fgraphcompass/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30127218,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-05T12:40:50.676Z","status":"ssl_error","status_checked_at":"2026-03-05T12:39:32.209Z","response_time":93,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":[],"created_at":"2024-10-15T22:00:54.334Z","updated_at":"2026-03-05T13:03:10.207Z","avatar_url":"https://github.com/theislab.png","language":"Jupyter Notebook","funding_links":[],"categories":["Jupyter Notebook"],"sub_categories":[],"readme":"![GraphCompass](graphcompass_logo.jpg)\nGraphCompass (**Graph** **Comp**arison Tools for Differential **A**nalyses in **S**patial **S**ystems) is a Python-based framework that brings together a robust suite of graph analysis and visualization methods, specifically tailored for the differential analysis of cell spatial organization using spatial omics data.\n\nIt is developed on top on [`Squidpy`](https://github.com/scverse/squidpy/) and [`AnnData`](https://github.com/scverse/anndata).\n\n## Features\nGraphCompass provides differential analysis methods to study spatial organization across conditions at three levels of abstraction: \n1. Cell-type-specific subgraphs:\n\n   i. Portrait method,\n\n   ii. Diffusion method.\n3. Cellular neighborhoods:\n\n   i. GLMs for neighborhood enrichment analysis.\n4. Entire graphs:\n\n   i. Wasserstein WL kernel,\n\n   ii. Filtration curves.\n\nTutorials for the different methods can be found in the `notebooks` folder. \n\n\n## Requirements\nYou will find all the necessary dependencies in the `pyproject.toml` file. Dependencies are automatically installed when you install GraphCompass.\n\n## Installation\nYou can install _GraphCompass_ via [pip] from [PyPI](https://pypi.org/project/graphcompass/).\n ```console\n$ pip install graphcompass\n```\n\nor\nyou can install _GraphCompass_ by cloning the repository and running:\n```console\n$ pip install -e .\n```\n\n \n\n## Citation\n\nMayar Ali, Merel Kuijs, Soroor Hediyeh-zadeh, Tim Treis, Karin Hrovatin, Giovanni Palla, Anna C Schaar, Fabian J Theis, GraphCompass: spatial metrics for differential analyses of cell organization across conditions, *Bioinformatics*, Volume 40, Issue Supplement\\_1, July 2024, Pages i548–i557, https://doi.org/10.1093/bioinformatics/btae242\n\n\n## Contributing\n\n**[COMING SOON]** Contributions are very welcome.\nTo learn more, see the [Contributor Guide].\n\n## License\n\nDistributed under the terms of the [MIT license][license],\n_GraphCompass_ is free and open source software.\n\n## Issues\n\nIf you encounter any problems,\nplease [file an issue] along with a detailed description.\n\n## Credits\n\nThis project was generated from [@cjolowicz]'s [Hypermodern Python Cookiecutter] template.\n\n[@cjolowicz]: https://github.com/cjolowicz\n[pypi]: https://pypi.org/\n[hypermodern python cookiecutter]: https://github.com/cjolowicz/cookiecutter-hypermodern-python\n[file an issue]: https://github.com/theislab/graphcompass/issues\n[pip]: https://pip.pypa.io/\n\n\u003c!-- github-only --\u003e\n\n[license]: https://github.com/theislab/graphcompass/blob/main/LICENSE\n[COMING SOON] [contributor guide]: https://github.com/theislab/graphcompass/blob/main/CONTRIBUTING.md\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fgraphcompass","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fgraphcompass","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fgraphcompass/lists"}