Libraries and scripts for the IMPROVE project.
Clone the IMPROVE library
repository to a directory of your preference (outside of your drug response prediction (DRP) model's directory).
git clone https://github.com/JDACS4C-IMPROVE/IMPROVE
cd IMPROVE
git checkout develop
Download the cross-study analysis (CSA) benchmark data into your model's directory. For example:
./scripts/get-benchmarks $DESTINATION/csa_data/raw_data
The directory structure should look like this after the above steps have been completed:
IMPROVE
DRP_model
└── csa_data
Specify the full path to the IMPROVE library
with $PYTHONPATH and the path to the CSA data with $IMPROVE_DATA_DIR.
cd DRP_model
export PYTHONPATH=$PYTHONPATH:/your/path/to/IMPROVE
export IMPROVE_DATA_DIR="./csa_data/"
For a detailed guide on how to use the IMPROVE library
using an example model, LightGBM, see https://jdacs4c-improve.github.io/docs/content/unified_interface.html.
Two repositories demonstrating the use of the IMPROVE library
for drug response prediction: