└─ data/:
| └─ Supplementary File 1.xlsx: supplementary files and machine learning training datasets
| └─ TCGA_138_zscored.xlsx: TCGA expression data with z-scored normalization
| └─ TCGA_clinical.xlsx: TCGA clinical data
| └─ TCGA_testing.csv: machine learning test TCGA dataset
| └─ pairs40_featureCounts.csv: 40 paired RNA-seq data in Fig. 3c
└─ scripts/:
| └─ TMZ_scripts.ipynb: analysis code and scripts to reproduce figures
| └─ TMZep.py: machine learning model
| └─ bioNet.py: finding genes related to target
| └─ cnape.ipynb: predicting CNA using RNA-seq data
| └─ norm.r: normalization of RNA-seq data
| └─ preprocess_tcga.r: merge TCGA CNA data and RNA data