OpenOmics
OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)
Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: joss.theoj.org, zenodo.org -
✓Committers with academic emails
3 of 14 committers (21.4%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.5%) to scientific vocabulary
Keywords
Keywords from Contributors
Scientific Fields
Repository
A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
Basic Info
- Host: GitHub
- Owner: JonnyTran
- License: mit
- Language: Python
- Default Branch: master
- Homepage: https://openomics.readthedocs.io/en/latest/
- Size: 68.5 MB
Statistics
- Stars: 33
- Watchers: 4
- Forks: 11
- Open Issues: 23
- Releases: 4
Topics
Metadata Files
README.md
OpenOmics is currently under active development and we may break API compatibility in the future.
This Python package provide a series of tools to integrate and explore the genomics, transcriptomics, proteomics, and clinical data (aka multi-omics data). With interfaces to popular annotation databases and scalable data-frame manipulation tools, OpenOmics facilitates the common data wrangling tasks when preparing data for RNA-seq bioinformatics analysis.
Documentation (Latest | Stable) | OpenOmics at a glance
Features
OpenOmics assist in integration of heterogeneous multi-omics bioinformatics data. The library provides a Python API as well as an interactive Dash web interface. It features support for: - Genomics, Transcriptomics, Proteomics, and Clinical data. - Harmonization with 20+ popular annotation, interaction, disease-association databases.
OpenOmics also has an efficient data pipeline that bridges the popular data manipulation Pandas library and Dask distributed processing to address the following use cases:
- Providing a standard pipeline for dataset indexing, table joining and querying, which are transparent and customizable for end-users.
- Providing Efficient disk storage for large multi-omics dataset with Parquet data structures.
- Integrating various data types including interactions and sequence data, then exporting to NetworkX graphs or data generators for down-stream machine learning.
- 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).
Installation:
PyPI
console
pip install openomics
Conda
sh
conda install openomics -c jonnytran # Work in progress
From source
sh
git clone https://github.com/JonnyTran/OpenOmics/
cd OpenOmics
pip install -e .
Citations
The journal paper for this scientific package was reviewed by JOSS at https://joss.theoj.org/papers/10.21105/joss.03249#, and can be cited with:
# BibTeX
@article{Tran2021,
doi = {10.21105/joss.03249},
url = {https://doi.org/10.21105/joss.03249},
year = {2021},
publisher = {The Open Journal},
volume = {6},
number = {61},
pages = {3249},
author = {Nhat C. Tran and Jean X. Gao},
title = {OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases.},
journal = {Journal of Open Source Software}
}
Credits
Thank you for extremely helpful feedback and guidance from the pyOpenSci reviewers. This package was created with the pyOpenSci/cookiecutter-pyopensci project template, based off audreyr/cookiecutter-pypackage.
Owner
- Name: Nhat (Jonny) Tran
- Login: JonnyTran
- Kind: user
- Website: jonny.bio
- Twitter: Jonny_Wireless
- Repositories: 41
- Profile: https://github.com/JonnyTran
Graph neural networks, bioinformatics, and ML engineering for all things NLP, RNA/protein sequence learning, and knowledge graphs. Work GH: @JTran-IDM
Citation (CITATION.cff)
--- cff-version: 1.2.0 message: "Please cite our paper if you use this code in your own work." title: "OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. [Computer software]" authors: - family-names: "Tran" given-names: "Nhat C." - family-names: "Gao" given-names: "Jean X." date-released: 2021-05-06 license: cc-by-4.0 url: "https://joss.theoj.org/papers/10.21105/joss.03249#"
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 4 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jonny Tran | n****n@m****u | 1,022 |
| JonnyTran | J****n@g****m | 704 |
| JonnyTran | j****n@g****m | 123 |
| JonnyTran | D****9 | 77 |
| pyup-bot | g****t@p****o | 22 |
| Nhat (Jonny) Tran | 4****n | 18 |
| deepsource-autofix[bot] | 6****] | 12 |
| sdhutchins | s****s@u****u | 10 |
| snyk-bot | s****t@s****o | 6 |
| Shaurita Hutchins | m****s@g****m | 2 |
| t-silvers | s****s@m****e | 2 |
| Arfon Smith | a****n | 2 |
| Steve Moss | g****l@g****m | 1 |
| DeepSource Bot | b****t@d****o | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 16
- Total pull requests: 115
- Average time to close issues: 6 days
- Average time to close pull requests: 8 days
- Total issue authors: 8
- Total pull request authors: 8
- Average comments per issue: 2.81
- Average comments per pull request: 0.06
- Merged pull requests: 26
- Bot issues: 0
- Bot pull requests: 51
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- JonnyTran (6)
- ksielemann (3)
- sdhutchins (1)
- pyup-bot (1)
- jamesbraza (1)
- Rana-Sabrii (1)
- piyushm27 (1)
- gawbul (1)
Pull Request Authors
- deepsource-autofix[bot] (51)
- JonnyTran (38)
- pyup-bot (27)
- sdhutchins (2)
- gawbul (2)
- snyk-bot (2)
- arfon (1)
- t-silvers (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- astropy *
- biopython *
- bioservices *
- bokeh *
- dash *
- dash-bootstrap-components *
- dash-daq *
- dask *
- filetype *
- goatools *
- gtfparse *
- gunicorn *
- h5py *
- itsdangerous *
- matplotlib *
- networkx *
- numpy *
- obonet *
- pandas *
- rarfile *
- scipy *
- six *
- sqlalchemy *
- typing *
- validators *
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v1 composite
- Sphinx *
- bumpversion *
- coverage *
- flake8 *
- furo *
- graphviz *
- myst-parser *
- pip *
- pytest >=7.0.0
- pytest-cov *
- pytest-runner *
- ruamel.yaml *
- sphinx-autobuild *
- sphinx-automodapi *
- sphinx-copybutton *
- sphinx-inline-tabs *
- sphinx_autodoc_typehints *
- tornado >=6.3.3
- tox *
- tqdm *
- twine *
- watchdog *
- wheel *