{"id":37072956,"url":"https://github.com/lueckenlab/patpy","last_synced_at":"2026-01-14T08:33:56.714Z","repository":{"id":260236133,"uuid":"637826449","full_name":"lueckenlab/patpy","owner":"lueckenlab","description":"Toolbox for single-cell data analysis on sample level","archived":false,"fork":false,"pushed_at":"2025-12-15T18:14:00.000Z","size":42340,"stargazers_count":8,"open_issues_count":26,"forks_count":5,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-12-19T01:19:02.650Z","etag":null,"topics":["compbio","single-cell-rna-seq"],"latest_commit_sha":null,"homepage":"","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/lueckenlab.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":"2023-05-08T13:44:56.000Z","updated_at":"2025-11-05T15:24:12.000Z","dependencies_parsed_at":null,"dependency_job_id":"6bddf95b-e097-4c3f-a920-e3f4194770ab","html_url":"https://github.com/lueckenlab/patpy","commit_stats":null,"previous_names":["lueckenlab/patpy"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/lueckenlab/patpy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lueckenlab%2Fpatpy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lueckenlab%2Fpatpy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lueckenlab%2Fpatpy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lueckenlab%2Fpatpy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lueckenlab","download_url":"https://codeload.github.com/lueckenlab/patpy/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lueckenlab%2Fpatpy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28414355,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-14T08:31:27.429Z","status":"ssl_error","status_checked_at":"2026-01-14T08:31:19.098Z","response_time":107,"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":["compbio","single-cell-rna-seq"],"created_at":"2026-01-14T08:33:56.206Z","updated_at":"2026-01-14T08:33:56.701Z","avatar_url":"https://github.com/lueckenlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# patpy – sample-level analysis framework for single-cell data\n\n\u003cimg src=\"./docs/_static/patpy_logo.png\" width=\"100px\"\u003e\n\npatpy is a toolbox for single-cell data analysis on sample level.\n\nIt provides:\n- 👨‍⚕️ Interface to sample representation methods (otherwise known as patient representation)\n- 📈 Analysis functions to get the most of your data\n- 📊 Metrics for sample representation evaluation\n\n![overview](./docs/_static/patpy_pipeline.png)\n\n# ⚠️ Warning: Development in Progress ⚠️\n\n\u003e **This repository is currently under active development**\n\u003e Features and functionalities may change unexpectedly, and some aspects of the project are not yet complete.\n\n---\n\n**Please proceed with caution** and feel free to contribute, but be aware that:\n\n-   The codebase is still evolving.\n-   Documentation may be incomplete.\n-   Some features may be unstable or subject to change.\n\nIf you have any questions or face bugs, feel free to open an [issue](https://github.com/lueckenlab/patpy/issues).\n\nThank you for your patience and interest. Stay tuned for updates!\n\n---\n\n[![Tests][badge-tests]][link-tests]\n[![Documentation][badge-docs]][link-docs]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/lueckenlab/patpy/test.yaml?branch=main\n[link-tests]: https://github.com/lueckenlab/patpy/actions/workflows/test.yml\n[badge-docs]: https://img.shields.io/readthedocs/patpy\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular, the\n\n-   [API documentation][link-api].\n\n## Installation\n\nYou need to have Python 3.9 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 patpy:\n\n\n1. Install the latest release of `patpy` from [`PyPI`](https://pypi.org/project/patpy/):\n\n```bash\npip install patpy\n```\n\n2. Install the latest development version:\n\n```bash\npip install git+https://github.com/lueckenlab/patpy.git@main\n```\n\nTo install specific dependencies for some sample representation tools, use the following command:\n\n```bash\npip install patpy[pilot]\n```\n\nAll the available dependency groups: `diffusionemd`, `mrvi`, `pilot`, `scpoli`, `wassersteintsne`.\n\n## Release notes\n\nSee the [changelog][changelog].\n\n## Contact\n\nFor questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].\nIf you found a bug, please use the [issue tracker][issue-tracker].\n\n## Building docs\n\n1. Install [sphinx](https://www.sphinx-doc.org/en/master/usage/installation.html)\n\nYou may need add path to `sphinx-doc` to the `$PATH`\n\n2. Install other `doc` section dependencies from the [pyproject.toml](https://github.com/lueckenlab/patpy/blob/main/pyproject.toml)\n\n3. Build the documentation pages:\n\n```bash\ncd docs\nmake html\n```\n\n4. Open `docs/_build/html/index.html`\n\n## Citation\n\nPreprint is coming soon. So far, you can refer to this repository as following:\n\n### APA\n\nShitov, V. (2024). patpy – sample-level analysis framework for single-cell data (Version 0.10.0) [Computer software]. https://github.com/lueckenlab/patpy/\n\n### BibTeX\n\n```bibtex\n@misc{shitov_patpy_2024,\n  author = {Shitov, Vladimir},\n  title = {patpy – sample-level analysis framework for single-cell data},\n  year = {2024},\n  url = {https://github.com/lueckenlab/patpy/},\n  note = {Version 0.11.3}\n}\n```\n\n[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/lueckenlab/patpy/issues\n[changelog]: https://patpy.readthedocs.io/en/latest/changelog.html\n[link-docs]: https://patpy.readthedocs.io\n[link-api]: https://patpy.readthedocs.io/en/latest/api/index.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flueckenlab%2Fpatpy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flueckenlab%2Fpatpy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flueckenlab%2Fpatpy/lists"}