{"id":26355769,"url":"https://github.com/jonnytran/openomics","last_synced_at":"2025-03-16T13:17:47.822Z","repository":{"id":46963504,"uuid":"125549505","full_name":"JonnyTran/OpenOmics","owner":"JonnyTran","description":"A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.","archived":false,"fork":false,"pushed_at":"2024-04-02T22:00:28.000Z","size":71843,"stargazers_count":29,"open_issues_count":15,"forks_count":13,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-04-30T09:26:20.269Z","etag":null,"topics":["data-integration","data-manipulation","genomics","multi-omics","python"],"latest_commit_sha":null,"homepage":"https://openomics.readthedocs.io/en/latest/","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/JonnyTran.png","metadata":{"files":{"readme":"README.md","changelog":null,"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}},"created_at":"2018-03-16T17:35:27.000Z","updated_at":"2024-04-27T04:27:29.000Z","dependencies_parsed_at":"2024-04-04T23:49:24.581Z","dependency_job_id":null,"html_url":"https://github.com/JonnyTran/OpenOmics","commit_stats":{"total_commits":2001,"total_committers":14,"mean_commits":"142.92857142857142","dds":0.4892553723138431,"last_synced_commit":"6cc61d0d311d324906b71c0fb7124c7dbd576986"},"previous_names":["biomecis-lab/openomics"],"tags_count":27,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JonnyTran%2FOpenOmics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JonnyTran%2FOpenOmics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JonnyTran%2FOpenOmics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JonnyTran%2FOpenOmics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JonnyTran","download_url":"https://codeload.github.com/JonnyTran/OpenOmics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243871910,"owners_count":20361380,"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":["data-integration","data-manipulation","genomics","multi-omics","python"],"created_at":"2025-03-16T13:17:46.560Z","updated_at":"2025-03-16T13:17:47.817Z","avatar_url":"https://github.com/JonnyTran.png","language":"Python","readme":"\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://openomics.readthedocs.io/en/latest/\" target=\"_blank\" rel=\"noopener noreferrer\"\u003e\n        \u003cimg src=\"https://github.com/JonnyTran/OpenOmics/raw/master/openomics_web/assets/openomics_logo.png\" max-height=\"200\"\u003e\n    \u003c/a\u003e\n\u003c/p\u003e\n\n[![PyPI version](https://badge.fury.io/py/openomics.svg)](https://badge.fury.io/py/openomics)\n[![Documentation Status](https://readthedocs.org/projects/openomics/badge/?version=latest)](https://openomics.readthedocs.io/en/latest/?badge=latest)\n[![OpenOmics](https://github.com/JonnyTran/OpenOmics/actions/workflows/python-package.yml/badge.svg?branch=master)](https://github.com/JonnyTran/OpenOmics/actions/workflows/python-package.yml)\n[![codecov](https://codecov.io/gh/JonnyTran/OpenOmics/branch/master/graph/badge.svg?token=6N1UZ27MPH)](https://codecov.io/gh/JonnyTran/OpenOmics)\n[![openomics](https://snyk.io/advisor/python/openomics/badge.svg)](https://snyk.io/advisor/python/openomics)\n\n[![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/31)\n[![status](https://joss.theoj.org/papers/aca43e3c2989a803b514faef72dd3294/status.svg)](https://joss.theoj.org/papers/aca43e3c2989a803b514faef72dd3294)\n[![DOI](https://zenodo.org/badge/125549505.svg)](https://zenodo.org/badge/latestdoi/125549505)\n\n**OpenOmics is currently under active development and we may break API compatibility in the future.**\n\nThis Python package provide a series of tools to integrate and explore the genomics, transcriptomics, proteomics, and\nclinical data (aka multi-omics data). With interfaces to popular annotation databases and scalable data-frame\nmanipulation tools, OpenOmics facilitates the common\ndata wrangling tasks when preparing data for RNA-seq bioinformatics analysis.\n\nDocumentation ([Latest](https://openomics.readthedocs.io/en/latest/)\n| [Stable](https://openomics.readthedocs.io/en/stable/))\n| [OpenOmics at a glance](https://openomics.readthedocs.io/en/latest/usage/getting-started.html)\n\n## Features\nOpenOmics assist in integration of heterogeneous multi-omics bioinformatics data. The library provides a Python API as well as an interactive Dash web interface.\nIt features support for:\n- Genomics, Transcriptomics, Proteomics, and Clinical data.\n- Harmonization with 20+ popular annotation, interaction, disease-association databases.\n\nOpenOmics also has an efficient data pipeline that bridges the popular data manipulation Pandas library and Dask distributed processing to address the following use cases:\n\n- Providing a standard pipeline for dataset indexing, table joining and querying, which are transparent and customizable\n  for end-users.\n- Providing Efficient disk storage for large multi-omics dataset with Parquet data structures.\n- Integrating various data types including interactions and sequence data, then exporting to NetworkX graphs or data generators for down-stream machine learning.\n- Accessible by both developers and scientists with a Python API that works seamlessly with an external Galaxy tool interface or the built-in Dash web interface (WIP).\n\n\n## Installation:\n### PyPI\n```console\npip install openomics\n```\n\n### Conda\n```sh\nconda install openomics -c jonnytran # Work in progress\n```\n\n### From source\n```sh\ngit clone https://github.com/JonnyTran/OpenOmics/\ncd OpenOmics\npip install -e .\n```\n\n##\n\n## Citations\nThe journal paper for this scientific package was reviewed by JOSS at \u003chttps://joss.theoj.org/papers/10.21105/joss.03249#\u003e, and can be cited with:\n\n    # BibTeX\n    @article{Tran2021,\n      doi = {10.21105/joss.03249},\n      url = {https://doi.org/10.21105/joss.03249},\n      year = {2021},\n      publisher = {The Open Journal},\n      volume = {6},\n      number = {61},\n      pages = {3249},\n      author = {Nhat C. Tran and Jean X. Gao},\n      title = {OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases.},\n      journal = {Journal of Open Source Software}\n    }\n\n\n\n## Credits\n\nThank you for extremely helpful feedback and guidance from the pyOpenSci reviewers. This package was created with the [pyOpenSci/cookiecutter-pyopensci](https://github.com/pyOpenSci/cookiecutter-pyopensci) project template, based off [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage).\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjonnytran%2Fopenomics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjonnytran%2Fopenomics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjonnytran%2Fopenomics/lists"}