├── .RsessionInfo.txt ├── .gitattributes ├── .gitignore ├── 1-ReadData ├── download_dataset.sh ├── readData_head_neck.R └── readData_melanoma.R ├── 2-Imputation └── impute_tpm.R ├── 3-Normalization └── normalization.R ├── 4-Clustering ├── inter_tumor_distance.R └── metabolic_landscape.R ├── 5-PathwayActivity ├── TCGA_pathway_activity.R └── scRNA_pathway_activity.R ├── 6-PathwayHeterogeneity ├── GeneSignature-of-Low_OXPHOS_Glycolysis_Hypoxia.R ├── OXPHOS_Glycolysis_Hypoxia_Correlation_plot-CCLE.R ├── OXPHOS_Glycolysis_Hypoxia_Correlation_plot.R ├── intra_malignant_heterogeneity.R ├── intra_non-malignant_heterogeneity.R.R └── runGSEA_preRank.R ├── 7-MetabolicFeatures ├── non-malignant_subtype.R └── runGSEA.R ├── Data ├── KEGG_metabolism.gmt ├── TCGA │ ├── HNSC │ │ ├── gdc_manifest_20180330_170153.txt │ │ └── gdc_sample_sheet.2018-03-30.tsv │ ├── download_TCGA.md │ └── generate_matrix.py ├── gene_length.txt ├── h.all.v6.1.symbols.gmt └── nonMetabolic_KEGG.gmt ├── LICENSE ├── README.md ├── 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