{"id":31582920,"url":"https://github.com/brj0/mepylome","last_synced_at":"2025-10-05T23:20:41.613Z","repository":{"id":241544878,"uuid":"754503592","full_name":"brj0/mepylome","owner":"brj0","description":" Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files","archived":false,"fork":false,"pushed_at":"2025-09-23T05:34:59.000Z","size":15081,"stargazers_count":9,"open_issues_count":1,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-09-23T07:19:54.879Z","etag":null,"topics":["cnv","conumee","epigenetics","illumina","methylation","methylation-analysis","methylation-extractor","methylation-microarrays","methylation-plot","minfi","python","tumor-classification","umap"],"latest_commit_sha":null,"homepage":"https://mepylome.readthedocs.io","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/brj0.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-02-08T07:34:27.000Z","updated_at":"2025-09-23T05:34:12.000Z","dependencies_parsed_at":"2024-06-28T18:28:45.682Z","dependency_job_id":"3b519a7a-29da-4f6c-80b9-0e90e8df9bce","html_url":"https://github.com/brj0/mepylome","commit_stats":null,"previous_names":["brj0/mepylome"],"tags_count":17,"template":false,"template_full_name":null,"purl":"pkg:github/brj0/mepylome","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brj0%2Fmepylome","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brj0%2Fmepylome/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brj0%2Fmepylome/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brj0%2Fmepylome/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brj0","download_url":"https://codeload.github.com/brj0/mepylome/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brj0%2Fmepylome/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278532576,"owners_count":26002390,"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","status":"online","status_checked_at":"2025-10-05T02:00:06.059Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["cnv","conumee","epigenetics","illumina","methylation","methylation-analysis","methylation-extractor","methylation-microarrays","methylation-plot","minfi","python","tumor-classification","umap"],"created_at":"2025-10-05T23:20:40.244Z","updated_at":"2025-10-05T23:20:41.605Z","avatar_url":"https://github.com/brj0.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg alt=\"Mepylome Logo\" src=\"https://raw.githubusercontent.com/brj0/mepylome/main/mepylome/data/assets/mepylome.svg\" width=\"300\"\u003e\n\n\n[![PyPI version](https://badge.fury.io/py/mepylome.svg)](https://badge.fury.io/py/mepylome)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/mepylome.svg)\n[![Documentation Status](https://readthedocs.org/projects/mepylome/badge/?version=latest)](https://mepylome.readthedocs.io/en/latest/?badge=latest)\n[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/brj0/mepylome/blob/main/examples/tutorial.ipynb)\n\n-----------------\n\n\n# Mepylome: Methylation Array Analysis Toolkit\n\nMepylome is an efficient Python toolkit tailored for parsing, processing, and\nanalyzing methylation array IDAT files. Serving as a versatile library,\nMepylome supports a wide range of methylation analysis tasks. It also includes\nan interactive GUI that enables users to generate UMAP plots and CNV plots\n(Copy Number Variation) directly from collections of IDAT files.\n\n\n## Features\n\n- Parsing of IDAT files\n- Extraction of methylation signals\n- Calculation of Copy Number Variations (CNV) with visualization using\n  [plotly](https://github.com/plotly/plotly.py).\n- Support for the following Illumina array types: 450k, EPIC, EPICv2, MSA48\n- Significantly faster compared to [minfi](https://github.com/hansenlab/minfi)\n  and [conumee2](https://github.com/hovestadtlab/conumee2).\n- Methylation analysis tool with a graphical browser interface for UMAP\n  analysis, CNV plots and supervised classification\n  - Can be run from the command line with minimal setup or customized through a\n    Python script\n- CN-summary plots\n\n\n## Documentation\n\nThe mepylome documentation, including installation instructions, tutorial and API, is available at \u003chttps://mepylome.readthedocs.io/\u003e\n\n\n## Usage\n\n### Methylation extraction and copy number variation plots\n\n```python\nfrom pathlib import Path\n\nfrom mepylome import CNV, MethylData\n\n# Sample\nanalysis_dir = Path(\"/path/to/idat/directory\")\nsample_file = analysis_dir / \"200925700125_R07C01\"\n\n# CNV neutral reference files\nreference_dir = Path(\"/path/to/reference/directory\")\n\n# Get methylation data\nsample_methyl = MethylData(file=sample_file)\nreference_methyl = MethylData(file=reference_dir)\n\n# Beta value\nbetas = sample_methyl.betas\n\n# Print overview of processed data\nprint(sample_methyl)\n\n# CNV anylsis\ncnv = CNV.set_all(sample_methyl, reference_methyl)\n\n# Visualize CNV in the browser\ncnv.plot()\n```\n\n### Methylation analysis: Command-line interface and GUI\n\n\u003cimg alt=\"Mepylome Logo\" src=\"https://raw.githubusercontent.com/brj0/mepylome/main/docs/images/screenshot.png\"\u003e\n\n#### Basic usage:\n\nMepylome provides a command-line interface for launching a GUI and performing\nmethylation analysis. Ensure you have an analysis directory, a CNV reference\ndirectory, and an annotation file (located within the analysis directory). Use\nthe following command to initiate the analysis:\n\n```sh\nmepylome --analysis_dir /path/to/idats --reference_dir /path/to/ref\n```\n\nIf you want to perform a **quick test**, use:\n\n```sh\nmepylome --tutorial\n```\n\nThis command downloads sample IDAT files and provides a demonstration of the\npackage's functionality.\n\nYou can try the tutorial directly in **Google Colab**-without downloading or\ninstalling anything-by clicking the link below. Please note that GUI support is\nlimited in Colab.\n\n[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/brj0/mepylome/blob/main/examples/tutorial.ipynb)\n\n\nSee \u003chttps://mepylome.readthedocs.io/\u003e for details.\n\n\n## C++ parser\n\nMepylome also includes a C++ parser. See \u003chttps://mepylome.readthedocs.io/\u003e for\ndetails.\n\n\n## Contributing\n\nContributions are welcome! If you have any bug reports, feature requests, or suggestions, please open an issue or submit a pull request.\n\n\n## License\n\nThis project is licensed under the [MIT license](LICENSE).\n\n\n## Acknowledgements\n\nMepylome is strongly influenced by [minfi](https://github.com/hansenlab/minfi) and [conumee2](https://github.com/hovestadtlab/conumee2). Some functionalities, such as the manifest handler and parser, are adapted from [methylprep](https://github.com/FoxoTech/methylprep).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrj0%2Fmepylome","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrj0%2Fmepylome","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrj0%2Fmepylome/lists"}