{"id":13612116,"url":"https://github.com/BIMSBbioinfo/maui","last_synced_at":"2025-04-13T11:31:35.819Z","repository":{"id":57440156,"uuid":"158563455","full_name":"BIMSBbioinfo/maui","owner":"BIMSBbioinfo","description":"Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit","archived":false,"fork":false,"pushed_at":"2023-07-06T21:33:24.000Z","size":3208,"stargazers_count":47,"open_issues_count":6,"forks_count":18,"subscribers_count":15,"default_branch":"master","last_synced_at":"2024-03-14T17:13:40.026Z","etag":null,"topics":["autoencoder","bioinformatics","cancer-genomics","deep-learning","latent-factor-model","multi-omics"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BIMSBbioinfo.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}},"created_at":"2018-11-21T14:49:57.000Z","updated_at":"2024-01-25T15:00:35.000Z","dependencies_parsed_at":"2024-01-14T04:52:25.909Z","dependency_job_id":"c28b8fa5-c86e-4993-a7ff-15225ee93734","html_url":"https://github.com/BIMSBbioinfo/maui","commit_stats":{"total_commits":117,"total_committers":4,"mean_commits":29.25,"dds":0.02564102564102566,"last_synced_commit":"7d329c736b681216093fd725b134a68e6e914c8e"},"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2Fmaui","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2Fmaui/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2Fmaui/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BIMSBbioinfo%2Fmaui/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BIMSBbioinfo","download_url":"https://codeload.github.com/BIMSBbioinfo/maui/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248705668,"owners_count":21148574,"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":["autoencoder","bioinformatics","cancer-genomics","deep-learning","latent-factor-model","multi-omics"],"created_at":"2024-08-01T20:00:22.702Z","updated_at":"2025-04-13T11:31:34.882Z","avatar_url":"https://github.com/BIMSBbioinfo.png","language":"Jupyter Notebook","readme":"\u003cdiv align=\"center\"\u003e\n\t\u003cimg src=\"hex-maui.png\" alt=\"maui\"\u003e\n\u003c/div\u003e\n\n# maui\n\n[![Downloads](https://pepy.tech/badge/maui-tools)](https://pepy.tech/project/maui-tools)  [![codecov](https://codecov.io/gh/bimsbbioinfo/maui/branch/master/graph/badge.svg)](https://codecov.io/gh/bimsbbioinfo/maui) [![Codacy Badge](https://api.codacy.com/project/badge/Grade/36c1f3f252b543139fd930ba5f674535)](https://www.codacy.com/app/jonathanronen/maui?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=BIMSBbioinfo/maui\u0026amp;utm_campaign=Badge_Grade) [![PyPI version](https://badge.fury.io/py/maui-tools.svg)](https://badge.fury.io/py/maui-tools) [![Documentation Status](https://readthedocs.org/projects/maui/badge/?version=latest)](https://maui.readthedocs.io/en/latest/?badge=latest) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)\n\n\n\n\u003c!-- [![Build Status](https://travis-ci.com/BIMSBbioinfo/maui.svg?branch=master)](https://travis-ci.com/BIMSBbioinfo/maui) --\u003e\n\n\nMulti-omics Autoencoder Integration (**maui**) is a python package for multi-omics data analysis. It is based on a bayesian latent factor model, with inference done using artificial neural networks. For details, check out our LSA paper: https://www.life-science-alliance.org/content/2/6/e201900517\n\n## Installation\n\nmaui works with Python 3.6 and TensorFlow 1.1 (does not yet support the yet unreleased TensorFlow 2.0). The easiest way to install is from pypi:\n\n\tpip install -U maui-tools\n\nThis will install all necessary dependencies including keras an tensorflow. The default tensorflow (cpu) will be installed. If tensorflow GPU is needed, please install it prior to installation of maui.\n\nThe development version may be installed by cloning this repo and running `python setup.py install`, or, using `pip` directly from github:\n\n\tpip install -e git+https://github.com/BIMSBbioinfo/maui.git#egg=maui\n\n\n#### Optional dependencies\n\nSurvival analysis functionality supplied by lifelines [1]. It may be installed directly from pip using `pip install lifelines`.\n\n## Usage\n\nSee [the vignette](vignette/maui_vignette.ipynb), and check out [the documentation](https://maui.readthedocs.io/en/latest/).\n\n\n## Citation\n\n\u003e  Evaluation of colorectal cancer subtypes and cell lines using deep learning. Jonathan Ronen, Sikander Hayat, Altuna Akalin. Life Science Alliance Dec 2019, 2 (6) e201900517; DOI: 10.26508/lsa.201900517\n\n## Contributing\n\nOpen an issue, send us a pull request, or shoot us an e-mail.\n\n## License\n\nmaui is released under the [GNU General Public License v3.0](LICENSE) or later.\n\n---------------------\n@jonathanronen, BIMSBbioinfo, 2018\n\n\n[1]: https://github.com/CamDavidsonPilon/lifelines\n","funding_links":[],"categories":["Software packages and methods"],"sub_categories":["Multi-omics autoencoders"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBIMSBbioinfo%2Fmaui","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FBIMSBbioinfo%2Fmaui","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBIMSBbioinfo%2Fmaui/lists"}