{"id":35091368,"url":"https://github.com/lucas-diedrich/bpca","last_synced_at":"2026-01-18T02:48:29.919Z","repository":{"id":330597712,"uuid":"1120543639","full_name":"lucas-diedrich/bpca","owner":"lucas-diedrich","description":"Bayesian Principal Component Analysis in Python","archived":false,"fork":false,"pushed_at":"2025-12-27T14:13:20.000Z","size":511,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-12-28T04:57:56.644Z","etag":null,"topics":["bayesian-inference","omics","pca"],"latest_commit_sha":null,"homepage":"https://bpca.readthedocs.io/en/latest/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lucas-diedrich.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":"CITATION.cff","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":"2025-12-21T12:53:21.000Z","updated_at":"2025-12-27T14:13:00.000Z","dependencies_parsed_at":"2025-12-28T05:00:45.124Z","dependency_job_id":null,"html_url":"https://github.com/lucas-diedrich/bpca","commit_stats":null,"previous_names":["lucas-diedrich/bpca"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/lucas-diedrich/bpca","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucas-diedrich%2Fbpca","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucas-diedrich%2Fbpca/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucas-diedrich%2Fbpca/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucas-diedrich%2Fbpca/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lucas-diedrich","download_url":"https://codeload.github.com/lucas-diedrich/bpca/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucas-diedrich%2Fbpca/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28400397,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-13T14:36:09.778Z","status":"ssl_error","status_checked_at":"2026-01-13T14:35:19.697Z","response_time":56,"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":["bayesian-inference","omics","pca"],"created_at":"2025-12-27T14:38:51.144Z","updated_at":"2026-01-16T22:59:57.600Z","avatar_url":"https://github.com/lucas-diedrich.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# bpca\n\n[![Tests][badge-tests]][tests]\n[![Integration Tests][badge-integration-tests]][integration-tests]\n[![codecov](https://codecov.io/gh/lucas-diedrich/bpca/graph/badge.svg?token=SIA7YSWCET)](https://codecov.io/gh/lucas-diedrich/bpca)\n[![Documentation][badge-docs]][documentation]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/lucas-diedrich/bpca/test.yaml?branch=main\n[badge-integration-tests]: https://github.com/lucas-diedrich/bpca/actions/workflows/integration-test.yaml/badge.svg\n[badge-docs]: https://img.shields.io/readthedocs/bpca\n\nBayesian Principal Component Analysis\n\n## Getting started\nBPCA follows the standard scikit-learn syntax\n\n```python\nfrom bpca import BPCA\nfrom sklearn.datasets import load_iris\n\niris_dataset = load_iris()\nX = iris_dataset[\"data\"]\n\n# Fit + Extract information\nbpca = BPCA(n_components=2)\nusage = bpca.fit_transform(X)\nloadings = bpca.components_\nexplained_variance_ratio = bpca.explained_variance_ratio_\n```\n\nPlease refer to the [documentation][], in particular, the [API documentation][].\n\n\n## Installation\n\nYou need to have Python 3.11 or newer installed on your system.\n\n\n1. Install the latest release of `bpca` from [PyPI][]:\n\n```bash\npip install bpca\n```\n\n\n2. Or Install the latest development version:\n\n```bash\npip install git+https://github.com/lucas-diedrich/bpca.git@main\n```\n\n## Release notes\n\nSee the [Release Notes][].\n\n## Contact\n\nFor questions and help requests, you can reach out in the [scverse discourse][].\nIf you found a bug, please use the [issue tracker][].\n\n## Citation\n\nThis package implements the algorithm proposed by Oba, 2003 and is built on the reference implementation by Stacklies et al, 2008 **Please cite the original authors**\n\n\u003e Oba, S. et al. A Bayesian missing value estimation method for gene expression profile data. Bioinformatics 19, 2088 - 2096 (2003).\n\n\u003e Stacklies, W., Redestig, H., Scholz, M., Walther, D. \u0026 Selbig, J. pcaMethods—a bioconductor package providing PCA methods for incomplete data. Bioinformatics 23, 1164 - 1167 (2007).\n\nGenerative model proposed by Bishop, 1998:\n\u003e Bishop, C. Bayesian PCA. in Advances in Neural Information Processing Systems vol. 11 (MIT Press, 1998).\n\nIf you find this implementation useful, consider giving it a star on GitHub and [cite this implementation](https://github.com/lucas-diedrich/bpca/blob/main/CITATION.cff)\n\n\u003e Diedrich, L. bpca [Computer software]. https://github.com/lucas-diedrich/bpca.git\n\n[uv]: https://github.com/astral-sh/uv\n[scverse discourse]: https://discourse.scverse.org/\n[issue tracker]: https://github.com/lucas-diedrich/bpca/issues\n[tests]: https://github.com/lucas-diedrich/bpca/actions/workflows/test.yaml\n[integration-tests]: https://github.com/lucas-diedrich/bpca/actions/workflows/integration-test.yaml\n[documentation]: https://bpca.readthedocs.io\n[Release Notes]: https://github.com/lucas-diedrich/bpca/releases\n[api documentation]: https://bpca.readthedocs.io/en/latest/api.html\n[pypi]: https://pypi.org/project/bpca\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucas-diedrich%2Fbpca","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flucas-diedrich%2Fbpca","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucas-diedrich%2Fbpca/lists"}