├── .gitignore ├── BNclusteringExample ├── BNclustering.pdf ├── clusterfns.R ├── generatebinaryBN.R └── knitrfiles │ └── BNclustering.Rmd ├── BNclusteringUpdate ├── clusterfns.R ├── generatebinaryBN.R └── knitrfiles │ ├── BNclustering.Rmd │ └── BNclustering.pdf ├── LICENSE ├── README.md ├── code ├── BBMMclusterEM_0.1.0.tgz ├── KM-plot.R ├── alternative_clustering_methods.R ├── multivariate_cox.R └── permutation-test-string.R ├── data ├── annotation-matrix.txt ├── binary-mutation-matrix.txt ├── networks │ ├── blca-network.txt │ ├── brca-network.txt │ ├── cesc-network.txt │ ├── cluster-A-network.txt │ ├── cluster-B-network.txt │ ├── cluster-C-network.txt │ ├── cluster-D-network.txt │ ├── cluster-E-network.txt │ ├── cluster-F-network.txt │ ├── cluster-G-network.txt │ ├── cluster-H-network.txt │ ├── cluster-I-network.txt │ ├── cluster-J-network.txt │ ├── cluster-K-network.txt │ ├── cluster-L-network.txt │ ├── cluster-M-network.txt │ ├── cluster-N-network.txt │ ├── cluster-O-network.txt │ ├── cluster-P-network.txt │ ├── cluster-Q-network.txt │ ├── cluster-R-network.txt │ ├── cluster-S-network.txt │ ├── cluster-T-network.txt │ ├── cluster-U-network.txt │ ├── cluster-V-network.txt │ ├── coadread-network.txt │ ├── esca-network.txt │ ├── gbm-network.txt │ ├── hnsc-network.txt │ ├── kirc-network.txt │ ├── kirp-network.txt │ ├── laml-network.txt │ ├── lgg-network.txt │ ├── lihc-network.txt │ ├── luad-network.txt │ ├── lusc-network.txt │ ├── ov-network.txt │ ├── paad-network.txt │ ├── pcpg-network.txt │ ├── prad-network.txt │ ├── sarc-network.txt │ ├── stad-network.txt │ ├── thca-network.txt │ └── ucec-network.txt ├── string-network.txt ├── tcga-clinical-information.txt ├── tcga_clinical_Cell2018.csv └── tcga_clinical_processing.R └── figures ├── TP53-frequency-supervised.cys ├── TP53-frequency-unsupervised.cys ├── brca-network.cys ├── paad-network.cys ├── supervised20network.cys └── unsupervised20network.cys /.gitignore: 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