Metadata-Version: 2.1
Name: openomics
Version: 0.8.5
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
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
Requires-Dist: biopython
Requires-Dist: large-image
Requires-Dist: bokeh
Requires-Dist: dask[complete]
Requires-Dist: networkx (>=2.1)
Requires-Dist: numpy (>=1.16.5)
Requires-Dist: pandas
Requires-Dist: matplotlib
Requires-Dist: scipy
Requires-Dist: astropy
Requires-Dist: h5py
Requires-Dist: requests
Requires-Dist: setuptools
Requires-Dist: typing
Requires-Dist: bioservices
Requires-Dist: itsdangerous
Requires-Dist: dash
Requires-Dist: dash-daq
Requires-Dist: dash-bootstrap-components
Requires-Dist: gunicorn
Requires-Dist: six
Requires-Dist: validators
Requires-Dist: sqlalchemy
Requires-Dist: filetype
Requires-Dist: gtfparse
Requires-Dist: scikit-allel
Requires-Dist: rarfile
Requires-Dist: goatools
Requires-Dist: obonet

=========
OpenOmics
=========

.. image:: https://github.com/BioMeCIS-Lab/OpenOmics/raw/master/openomics_web/assets/openomics_logo.png

.. image:: https://img.shields.io/pypi/v/OpenOmics.svg
        :target: https://pypi.python.org/pypi/OpenOmics

.. image:: https://img.shields.io/travis/BioMeCIS-Lab/OpenOmics.svg
        :target: https://travis-ci.org/BioMeCIS-Lab/OpenOmics

.. image:: https://codecov.io/gh/BioMeCIS-Lab/OpenOmics/branch/master/graph/badge.svg
        :target: https://codecov.io/gh/BioMeCIS-Lab/OpenOmics

.. image:: https://readthedocs.org/projects/openomics/badge/?version=latest
        :target: https://openomics.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status

.. image:: https://pyup.io/repos/github/BioMeCIS-Lab/OpenOmics/shield.svg
     :target: https://pyup.io/repos/github/BioMeCIS-Lab/OpenOmics/
     :alt: Updates


OpenOmics provides a bioinformatics API and web-app platform integrate, analyze, and visualize the multi-omics and clinical data.


* Free software: MIT license
* Documentation: https://openomics.readthedocs.io.


Features
--------

* Provides a bioinformatics workflow to generate integrative results from multi-omics data.
* Facilitates integration of various bio-databases, multi-omics expression, genomics, and clinical data.
* Highly flexible to different data types and missing data.
* Provides researchers with means to consistently store and explore their experimental datasets.
* Enables scalable performance with parallel computing, while easily configurable to deploy on both single machine and a cluster.
* Usable by both developers and scientists with its intuitive Python API and web-app dashboard interface (WIP).

Credits
-------

This package was created with Cookiecutter_ and the `pyOpenSci/cookiecutter-pyopensci`_ project template, based off `audreyr/cookiecutter-pypackage`_.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`pyOpenSci/cookiecutter-pyopensci`: https://github.com/pyOpenSci/cookiecutter-pyopensci
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.8.5 (Pending)
_______________
* Build web-app dashboard interface for importing user multiomics data files


0.8.4 (2020-01-07)
------------------
* Replace Pandas Dataframe with Dask DataFrame for parallel processings


0.7.2 (2019-09-01)
------------------

* Added compatibility for Python 2.7
* Refactored ClinicalData
* Built working documentations with Sphinx on readthedocs
* Added pytests for MultiOmicsData
* First successful build on Travis CI on Python 3.4-3.7, 2.7


0.6.0 (2019-08-31)
------------------

* First release on PyPI.


