/simdrugs

Python notebooks for analyses and simulating drug response on patient-specific pathway signatures

Primary LanguageJupyter NotebookApache License 2.0Apache-2.0

Simulating drug response by calibrating patient-specific pathway signatures

This repository contains the source code and the data necessary to reproduce the results presented in the paper.

Repository structure

  • Scripts and notebooks -> scripts_and_notebooks
  • Data and trained models -> data

Data availability

Due to the restriction on the access to the TCGA data, we are not at the liberty to share the data. If an individual wishes to replicate the results, they could apply for access the TCGA data at their access portal (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga). Alternatively, you can download the ssGSEA scores at this link https://drive.google.com/drive/folders/1faP7-IzfzFDv4sJjnl00AKRmqw2l0UMB?usp=sharing Simply paste the downloaded files in the data folder and run the notebooks/scripts.