BioML-CM/Grandline

Graph convolutional neural network classification model for integrating biological network and gene expression

Grandline

Graph convolutional neural network classification model for integrating biological network and gene expression (Grandline). It is a framework based on graph convolutional neural network for predicting phenotype based on an integration of gene expression data and a protein-protein interaction network. It can also identify important subnetworks that are critical for phenotype prediction in each sample.

How to use Grandline

git lfs clone https://github.com/BioML-CM/Grandline
conda create -n grandline python=3.7
conda activate grandline
cd Grandline
pip install -r requirements.txt
nohup jupyter notebook --port 8888 &

Next, open tutorial.ipynb on your browser.

To install git lfs on Ubuntu

Alternatively, you may download the example dataset directly from github and add to data directory.

curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | sudo bash
sudo apt-get install git-lfs
git lfs install

For other operating systems: https://github.com/git-lfs/git-lfs/wiki/Installation