Metadata-Version: 2.1
Name: naga-gwas
Version: 0.4.1.post2
Summary: Network Assisted Genomic Association
Home-page: https://github.com/shfong/naga
Author: Samson Fong
Author-email: shfong@ucsd.edu
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Dist: ijson
Requires-Dist: requests
Requires-Dist: pytz (>=2011k)
Requires-Dist: cycler (>=0.10)
Requires-Dist: kiwisolver (>=1.0.1)
Requires-Dist: pyparsing (!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1)
Requires-Dist: pytz
Requires-Dist: networkx (==1.11)
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: pandas (>=0.23.0)
Requires-Dist: scipy
Requires-Dist: seaborn
Requires-Dist: ndex2
Requires-Dist: python-igraph
Requires-Dist: py2cytoscape
Requires-Dist: coverage
Requires-Dist: pytest
Requires-Dist: mygene
Requires-Dist: scikit-learn
Requires-Dist: sphinx

Network Assisted Genomic Analysis (NAGA)
========================================

Network Assisted Genomic Analysis(NAGA) re-prioritizes significant single
nucleotide polymorphisms (SNPs) to genes using network diffusion methods
including random walk and heat diffusion. 

A companion website and REST API can be found at http://nbgwas.ucsd.edu/.

Documentation
=============

A readthedocs page will be coming soon! In the mean time, you can view
the documentations by building the sphinx documentation in the docs
directory. Simply run the following in the docs folder

.. code:: bash

    make docs

and open the index.html in the docs/build/html directory.

Installation
============

It is recommended that NAGA be run under Anaconda_ with python-igraph_ manually installed using **conda**
and to create a new conda environment


To create a new **conda** environment and activate it:

.. code:: bash

   conda create -n nagaenv
   source activate nagaenv

If you would like to use **naga** in a Jupyter Notebook, you will need to add the Jupyter kernel. To do so: 

.. code:: bash 

   # Make sure to activate the environment first!
   conda install ipykernel # or pip install ipykernel
   python -m ipykernel install --user --name nagaenv --display-name "Python (Naga)"


To install python-igraph_ via **conda**:

.. code:: bash

   conda install -c conda-forge python-igraph


To install NAGA via pip:

.. code:: bash

    pip install naga-gwas


Tutorial
========

`notebooks/tutorial.ipynb <https://github.com/shfong/naga/blob/master/notebooks/tutorial.ipynb>`_ demonstrates how to use this package once it
is installed.

Citing NAGA
=============

Publication to come...

.. _Anaconda: https://anaconda.org
.. _python-igraph: https://anaconda.org/conda-forge/python-igraph


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

0.4.2.post2 (2019-01-30)
------------------------

* Added instructions to add Jupyter kernel

0.4.1.post1 (2019-01-24)
------------------------

* Added link to tutorial notebook in long description


0.4.1 (2019-01-09)
------------------

* First release on PyPI



