https://github.com/JonnyTran/OpenOmics
A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
https://github.com/JonnyTran/OpenOmics
data-integration data-manipulation genomics multi-omics python
Last synced: 2 months ago
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A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
- Host: GitHub
- URL: https://github.com/JonnyTran/OpenOmics
- Owner: JonnyTran
- License: mit
- Created: 2018-03-16T17:35:27.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2024-04-02T22:00:28.000Z (about 1 year ago)
- Last Synced: 2024-04-30T09:26:20.269Z (about 1 year ago)
- Topics: data-integration, data-manipulation, genomics, multi-omics, python
- Language: Python
- Homepage: https://openomics.readthedocs.io/en/latest/
- Size: 68.5 MB
- Stars: 29
- Watchers: 7
- Forks: 13
- Open Issues: 15
-
Metadata Files:
- Readme: README.md
- Contributing: docs/contributing.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://badge.fury.io/py/openomics)
[](https://openomics.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/JonnyTran/OpenOmics/actions/workflows/python-package.yml)
[](https://codecov.io/gh/JonnyTran/OpenOmics)
[](https://snyk.io/advisor/python/openomics)
[](https://github.com/pyOpenSci/software-review/issues/31)
[](https://joss.theoj.org/papers/aca43e3c2989a803b514faef72dd3294)
[](https://zenodo.org/badge/latestdoi/125549505)
**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](https://openomics.readthedocs.io/en/latest/)
| [Stable](https://openomics.readthedocs.io/en/stable/))
| [OpenOmics at a glance](https://openomics.readthedocs.io/en/latest/usage/getting-started.html)
## 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 , 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](https://github.com/pyOpenSci/cookiecutter-pyopensci) project template, based off [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage).