{"id":18590494,"url":"https://github.com/lbrecic/epygenetics","last_synced_at":"2026-01-29T12:37:15.472Z","repository":{"id":242410703,"uuid":"809475508","full_name":"lbrecic/epygenetics","owner":"lbrecic","description":null,"archived":false,"fork":false,"pushed_at":"2024-09-04T10:09:46.000Z","size":12275,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-12-26T19:28:57.888Z","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/lbrecic.png","metadata":{"files":{"readme":"README.md","changelog":null,"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,"publiccode":null,"codemeta":null}},"created_at":"2024-06-02T19:43:13.000Z","updated_at":"2024-09-04T09:18:00.000Z","dependencies_parsed_at":null,"dependency_job_id":"b3516cea-8ba6-47a9-bc78-ac22018956ce","html_url":"https://github.com/lbrecic/epygenetics","commit_stats":null,"previous_names":["lbrecic/epygenetics"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbrecic%2Fepygenetics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbrecic%2Fepygenetics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbrecic%2Fepygenetics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lbrecic%2Fepygenetics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lbrecic","download_url":"https://codeload.github.com/lbrecic/epygenetics/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239359307,"owners_count":19625626,"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":"2024-11-07T00:56:13.883Z","updated_at":"2025-11-02T02:30:26.076Z","avatar_url":"https://github.com/lbrecic.png","language":"Python","readme":"\n# epygenetics\n\n`epygenetics` is a Python library designed to facilitate the execution, analysis, and testing of various epigenetic clocks. The library is built following the latest PEP8 standards and provides a comprehensive toolset for researchers and data scientists working in the field of epigenetics.\n\n## Table of Contents\n\n- [Installation](#installation)\n- [Usage](#usage)\n  - [Execution](#execution)\n  - [Testing](#testing)\n- [Implemented Epigenetic Clocks](#implemented-epigenetic-clocks)\n- [Contributing](#contributing)\n- [License](#license)\n\n## Installation\n\nTo install the `epygenetics` library, clone the repository and install the necessary dependencies:\n\n```bash\ngit clone https://github.com/lbrecic/epygenetics.git\ncd epygenetics\npip install -r requirements.txt\n```\n\n## Usage\n\nThe `epygenetics` library provides three main entry points: execution, analysis, and testing. Each entry point can be executed via the command line using the following format:\n\n```bash\npython -m epygenetics.\u003cmethod_name\u003e --flags...\n```\n\n### Execution\n\nTo run an epigenetic clock, use the `execution` method. The following example demonstrates how to execute a specific clock:\n\n```bash\npython -m epygenetics.execution -c \u003cclock_name\u003e -d \u003cdnam_file\u003e [options]\n```\n\n#### Example:\n\n```bash\npython -m epygenetics.execution -c Horvath1 -d path/to/dnam_file.csv -p path/to/pheno_file.csv -i -f path/to/imputation_file.csv -m regular -v\n```\n\n**Flags:**\n\n- `-c, --clock`: **(Required)** Name of the clock to execute.\n- `-d, --dnam`: **(Required)** Path to DNA methylation betas file.\n- `-p, --pheno`: Path to the pheno file (optional).\n- `-i, --imputation`: Impute missing CpG values (optional).\n- `-f, --imputation-file`: Path to CpG imputation file (optional).\n- `-m, --imputation-method`: Imputation method to use (optional, default: \\`regular\\`).\n- `-l, --loader`: Loader type (default: \\`csv\\`)\n- `-v, --verbose`: Show traceback if an error occurs (optional).\n\n### Testing\n\nTo run the automated tests provided in the library, use the `testing` method. The following example demonstrates how to execute the tests:\n\n```bash\npython -m epygenetics.testing [options]\n```\n\n#### Example:\n\n```bash\npython -m epygenetics.testing -u\n```\n\n**Flags:**\n\n- `-u, --unit`: Run unit tests only.\n- `-c, --comparison`: Run comparison with the methylCIPHER package only.\n\n## Implemented Epigenetic Clocks\n\nThe following epigenetic clocks have been implemented in the `epygenetics` library:\n\n- HRS in CH PhenoAge (HRSInChPhenoAge)\n- Non PRC PhenoAge (non_prcPhenoAge)\n- PRC PhenoAge (prcPhenoAge)\n- PhenoAge (PhenoAge)\n- EpiTOC (EpiTOC)\n- HypoClock (hypoClock)\n- MiAge (MiAge) (Not fully implemented)\n- Bocklandt (Bocklandt)\n- Garagnani (Garagnani)\n- Hannum (Hannum)\n- Horvath Multi-Tissue (Horvath1)\n- Lin (Lin)\n- Vidal-Bralo (VidalBralo)\n- Weidner (Weidner)\n- Zhang (Zhang)\n- Bohlin (Bohlin)\n- Knight (Knight)\n- Lee Control (LeeControl)\n- Lee Robust (LeeRobust)\n- Lee Refined-Robust (LeeRefinedRobust)\n- Mayne (Mayne)\n- PEDBE (PEDBE)\n- DNA Methylation Cortical Clock (DNAmClockCortical)\n- Horvath Skin \u0026 Blood (Horvath2)\n- Alcohol McCartney (Alcohol_McCartney)\n- BMI McCartney (BMI_McCartney)\n- Smoking McCartney (Smoking_McCartney)\n\n## Contributing\n\nContributions to the `epygenetics` library are welcome. Please submit pull requests or open issues on the [GitHub repository](https://github.com/lbrecic/epygenetics).\n\nBefore contributing, please ensure that your code adheres to the PEP8 standards and passes all tests.\n\n## License\n\nThis project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flbrecic%2Fepygenetics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flbrecic%2Fepygenetics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flbrecic%2Fepygenetics/lists"}