Metadata-Version: 2.1
Name: openomics
Version: 0.8.8
Summary: OpenOmics provides a bioinformatics API and web-app platform integrate and visualize the multiomics and clinical data.
Home-page: https://github.com/BioMeCIS-Lab/OpenOmics
Author: Jonny Tran
Author-email: nhat.tran@mavs.uta.edu
License: MIT license
Description: <p align="center">
          <img src="https://github.com/BioMeCIS-Lab/OpenOmics/raw/master/openomics_web/assets/openomics_logo.png" max-height="200">
        </p>
        
        [![PyPI version](https://badge.fury.io/py/openomics.svg)](https://badge.fury.io/py/openomics)
        [![Documentation Status](https://readthedocs.org/projects/openomics/badge/?version=latest)](https://openomics.readthedocs.io/en/latest/?badge=latest)
        [![DOI](https://zenodo.org/badge/125549505.svg)](https://zenodo.org/badge/latestdoi/125549505)
        [![OpenOmics](https://github.com/BioMeCIS-Lab/OpenOmics/actions/workflows/python-package.yml/badge.svg?branch=master)](https://github.com/BioMeCIS-Lab/OpenOmics/actions/workflows/python-package.yml)
        [![codecov](https://codecov.io/gh/BioMeCIS-Lab/OpenOmics/branch/master/graph/badge.svg?token=WAN3PJwM42)](https://codecov.io/gh/BioMeCIS-Lab/OpenOmics)
        
        This Python package provide a series of tools to integrate and query the genomics, transcriptomics, proteomics, and
        clinical data (aka multi-omics data). With 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 via pip:
        
        ```
        $ pip install openomics
        ```
        
        ## 
        
        ## Citations
        The journal paper for this scientific package is currently being reviewed. In the meanwhile, the current package version can be cited with:
        
            # BibTeX
            @software{nhat_jonny_tran_2021_4552831,
              author       = {Nhat Tran and
                              Jean Gao},
              title        = {{BioMeCIS-Lab/OpenOmics: Bug fixes from pyOpenSci
                               Reviewer 2}},
              month        = feb,
              year         = 2021,
              publisher    = {Zenodo},
              version      = {v0.8.5},
              doi          = {10.5281/zenodo.4552831},
              url          = {https://doi.org/10.5281/zenodo.4552831}
            }
        
        ## Credits
        
        This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [pyOpenSci/cookiecutter-pyopensci](https://github.com/pyOpenSci/cookiecutter-pyopensci) project template, based off [audreyr/cookiecutter-pypackage](https://github.com/audreyr/cookiecutter-pypackage).
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.6
Description-Content-Type: text/markdown
