/deep-drug-repurposing

Primary LanguagePython

Drug Repurposing

Installation

pip install -r requirements.txt

Predict drug candidates for covid

  • Download the data here and set the data directories in config.json.

  • Use python predict_drug.py -c config.json to generate a drug list and store in a output file assigned in config.json.

It is recommended to put all settings in a config file, i.e. config.json.

Use the biological graph object (msi)

from predict_drug import run_predict
msi = run_predict()

# retrieve the nodes in graph
msi.graph.nodes

# check the connections of a node
msi.graph['DB04865']

Train the hierarchical GCN (protein and pathway level)

python tran_dual_gcn.py

Currently we are using networkx. Click and find more interfaces from the documents.