Metadata-Version: 1.1
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
Description: 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
        
        
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
