Network Assisted Genomic Association
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/.
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
and open the index.html in the docs/build/html directory.
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
notebooks/tutorial.ipynb demonstrates how to use this package once it is installed.
Publication to come…
Added instructions to add Jupyter kernel
Added link to tutorial notebook in long description
First release on PyPI
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