├── .gitattributes ├── R ├── 00_PANCAN_function.R ├── 01_PANCAN_data.R ├── 02_PANCAN_classify.R ├── 03_PANCAN_analysis_man.R ├── 04_PANCAN_hypermutation_analysis.R ├── 05_PANCAN_gastric_validate.R └── 06_PANCAN_figures_manuscript.R ├── README.md ├── _config.yml └── data ├── Census_allWed Jul 13 11_38_59 2016.csv ├── MS_table_10.1038_nm.4191.csv ├── cancer_list.csv ├── firehoseNMF2016_01_28 ├── ACC-TP.bestclus.txt ├── BLCA-TP.bestclus.txt ├── BRCA-TP.bestclus.txt ├── CESC-TP.bestclus.txt ├── CHOL-TP.bestclus.txt ├── COAD-TP.bestclus.txt ├── COADREAD-TP.bestclus.txt ├── DLBC-TP.bestclus.txt ├── ESCA-TP.bestclus.txt ├── GBM-TP.bestclus.txt ├── GBMLGG-TP.bestclus.txt ├── HNSC-TP.bestclus.txt ├── KICH-TP.bestclus.txt ├── KIPAN-TP.bestclus.txt ├── KIRC-TP.bestclus.txt ├── KIRP-TP.bestclus.txt ├── LAML-TB.bestclus.txt ├── LGG-TP.bestclus.txt ├── LIHC-TP.bestclus.txt ├── LUAD-TP.bestclus.txt ├── LUSC-TP.bestclus.txt ├── MESO-TP.bestclus.txt ├── OV-TP.bestclus.txt ├── PAAD-TP.bestclus.txt ├── PCPG-TP.bestclus.txt ├── PRAD-TP.bestclus.txt ├── READ-TP.bestclus.txt ├── SARC-TP.bestclus.txt ├── SKCM-TM.bestclus.txt ├── STAD-TP.bestclus.txt ├── STES-TP.bestclus.txt ├── TGCT-TP.bestclus.txt ├── THCA-TP.bestclus.txt ├── THYM-TP.bestclus.txt ├── UCEC-TP.bestclus.txt ├── UCS-TP.bestclus.txt ├── UVM-TP.bestclus.txt └── pancan_bestclus.txt └── gastric_validation_data ├── ng.2983-S2.xlsx ├── ng.2983-S2_clinic.csv └── ng.2983-S2_mutations.csv /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhiyhu/NMD-paper/HEAD/.gitattributes -------------------------------------------------------------------------------- /R/00_PANCAN_function.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zhiyhu/NMD-paper/HEAD/R/00_PANCAN_function.R -------------------------------------------------------------------------------- /R/01_PANCAN_data.R: 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