{"id":18501605,"url":"https://github.com/const-ae/pylemur","last_synced_at":"2025-04-09T18:33:08.782Z","repository":{"id":227070370,"uuid":"770354901","full_name":"const-ae/pyLemur","owner":"const-ae","description":"A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.","archived":false,"fork":false,"pushed_at":"2024-04-17T12:11:29.000Z","size":3169,"stargazers_count":8,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-04-17T18:16:41.977Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/const-ae.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"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}},"created_at":"2024-03-11T12:08:32.000Z","updated_at":"2024-04-23T12:49:30.238Z","dependencies_parsed_at":"2024-03-11T13:40:24.140Z","dependency_job_id":"52347562-32dd-4cbb-8016-1ed0ff48d8e6","html_url":"https://github.com/const-ae/pyLemur","commit_stats":null,"previous_names":["const-ae/pylemur"],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FpyLemur","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FpyLemur/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FpyLemur/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FpyLemur/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/const-ae","download_url":"https://codeload.github.com/const-ae/pyLemur/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248087885,"owners_count":21045605,"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":"2024-11-06T13:54:23.310Z","updated_at":"2025-04-09T18:33:08.764Z","avatar_url":"https://github.com/const-ae.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pyLemur\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/const-ae/pyLemur/test.yaml?branch=main\n[link-tests]: https://github.com/const-ae/pyLemur/actions/workflows/test.yaml\n[link-docs]: https://pyLemur.readthedocs.io\n[badge-docs]: http://readthedocs.org/projects/pylemur/badge\n\nThe Python implementation of the LEMUR method to analyze multi-condition single-cell data. For the more complete version in R, see [github.com/const-ae/lemur](https://github.com/const-ae/lemur). To learn more check-out the [function documentation](https://pylemur.readthedocs.io/page/api.html) and the [tutorial](https://pylemur.readthedocs.io/page/notebooks/Tutorial.html) at [pylemur.readthedocs.io](https://pylemur.readthedocs.io). To check-out the source code or submit an issue go to [github.com/const-ae/pyLemur](https://github.com/const-ae/pyLemur)\n\n## Citation\n\n\u003e Ahlmann-Eltze C, Huber W (2025).\n\u003e “Analysis of multi-condition single-cell data with latent embedding multivariate regression.” Nature Genetics (2025).\n\u003e [doi:10.1038/s41588-024-01996-0](https://doi.org/10.1038/s41588-024-01996-0).\n\n# Getting started\n\n## Installation\n\nYou need to have Python 3.10 or newer installed on your system.\nThere are several alternative options to install pyLemur:\n\nInstall the latest release of `pyLemur` from [PyPI](https://pypi.org/project/pyLemur/):\n\n```bash\npip install pyLemur\n```\n\nAlternatively, install the latest development version directly from Github:\n\n```bash\npip install git+https://github.com/const-ae/pyLemur.git@main\n```\n\n## Documentation\n\nFor more information on the functions see the [API docs](https://pyLemur.readthedocs.io/page/api.html) and the [tutorial](https://pylemur.readthedocs.io/page/notebooks/Tutorial.html).\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[scverse-discourse]: https://discourse.scverse.org/\n[issue-tracker]: https://github.com/const-ae/pyLemur/issues\n\n## Building\n\nInstall the package in editable mode:\n\n```\npip install \".[dev,doc,test]\"\n```\n\nBuild the documentation locally\n\n```\ncd docs\nmake html\nopen _build/html/index.html\n```\n\nRun the unit tests\n\n```\npytest\n```\n\nRun pre-commit hooks manually\n\n```\npre-commit run --all-files\n```\n\nor individually\n\n```\nruff check\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fpylemur","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fconst-ae%2Fpylemur","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fpylemur/lists"}