semvec/pypi-packages huggingface dataset:
naga-gwas 0.4.1.post2
Network Assisted Genomic Association
License: MIT

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