This repository contains scripts used to analyze an osteosarcoma dataset, based on patients master regulator signatures. The script is presented in the form of a jupyter notebook, which is run with an R kernel enabled.
The required packages are listed in the first cell notebook. All other files needed are in the SourceCode_files directory
TARGET_OS_Discovery_ClinicalData.csvThis file contains all of the patient metadata, like relapse status, metastatic disease status, and survival post treatment.TOS_TPM.txtRead counts measured in transcripts per million, which was downloaded directly from the TARGET Osteosarcoma study. This is the input for viper.ens2entrez.rdaThis has information for mapping genes labels from ensembl ids to entrez ids. This is necessary for downstream MR processing.viper_dset.csvA precomputed table of master regulator signatures for each patient. The process used to generate this file is described in detail in the report.