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

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:

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:

# 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:

conda install -c conda-forge python-igraph

To install NAGA via pip:

pip install naga-gwas

Tutorial

notebooks/tutorial.ipynb demonstrates how to use this package once it is installed.

Citing NAGA

Carlin, Daniel E., Samson H. Fong, Yue Qin, Tongqiu Jia, Justin K. Huang, Bokan Bao, Chao Zhang, and Trey Ideker. "A Fast and Flexible Framework for Network-Assisted Genomic Association." iScience 16 (2019): 155.