├── .gitignore ├── LICENSE ├── LICENSE.docx ├── Makefile ├── README.md ├── Software_package_info.txt ├── app ├── LICENSE_jax ├── LICENSE_slapdash ├── README.md ├── __init__.py ├── images │ └── chart.png ├── run_flask.py ├── setup.py └── tcga_viz_app │ ├── __init__.py │ ├── app.py │ ├── callbacks.py │ ├── components.py │ ├── custom_dash.py │ ├── data.py │ ├── data │ ├── BRCA_contingency_table.csv │ ├── HNSC_contingency_table.csv │ ├── KIRC_contingency_table.csv │ ├── KIRP_contingency_table.csv │ ├── LGG_contingency_table.csv │ ├── LUAD_contingency_table.csv │ ├── LUSC_contingency_table.csv │ ├── OV_contingency_table.csv │ ├── PRAD_contingency_table.csv │ ├── SKCM_contingency_table.csv │ ├── STAD_contingency_table.csv │ ├── cancer_data.csv │ ├── full_dr.csv │ ├── primary_cv_contingency.csv │ ├── primary_ext_contingency.csv │ └── sample_dr.csv │ ├── exceptions.py │ ├── layouts.py │ ├── page_about.py │ ├── page_classifier.py │ ├── page_dr.py │ ├── page_hm.py │ ├── pages.py │ ├── plotting.py │ ├── router.py │ ├── server.py │ ├── settings.py │ ├── static │ ├── LICENSE.txt │ ├── about_page.md │ ├── bootstrap.min.css │ ├── custom.css │ ├── favicon.ico │ ├── font-awesome │ │ ├── css │ │ │ ├── font-awesome.css │ │ │ └── font-awesome.min.css │ │ └── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ └── fontawesome-webfont.woff2 │ └── slapdash.css │ ├── utils.py │ └── wsgi.py ├── data ├── external │ ├── .gitkeep │ └── gse18549_sample_anns.csv ├── img │ ├── Female_shadow_anatomy_without_labels.png │ ├── Heart_and_lung.png │ ├── Human_body_silhouette.png │ ├── Human_body_silhouette.svg │ ├── Internal_organs.png │ ├── Internal_organs.svg │ ├── Intestine_1.gif │ ├── Liver_(transparent).png │ ├── Silhouette_of_a_mouse.jpg │ ├── cancer_data.csv │ ├── cancer_names.csv │ ├── cohort_sizes.csv │ ├── metastasis_schematic_simple_v2.tiff │ ├── pdx_schematic_2.tiff │ └── umap_2d.csv ├── interim │ └── .gitkeep ├── processed │ └── .gitkeep └── raw │ ├── .gitkeep │ ├── brca_cases_basal.txt │ ├── cases_BRAF.txt │ ├── cases_ERG.txt │ ├── cases_ETV1.txt │ ├── cases_ETV4.txt │ ├── cases_FLI1.txt │ ├── cases_FOXA1.txt │ ├── cases_IDH1.txt │ ├── cases_LGr1.txt │ ├── cases_LGr2.txt │ ├── cases_LGr3.txt │ ├── cases_LGr4.txt │ ├── cases_NF1.txt │ ├── cases_RAS.txt │ ├── cases_SPOP.txt │ ├── cases_Triple_WT.txt │ ├── cases_atypical.txt │ ├── cases_bronchioid.txt │ ├── cases_cin.txt │ ├── cases_cnhigh.txt │ ├── cases_cnlow.txt │ ├── cases_ebv.txt │ ├── cases_expression_cluster1.txt │ ├── cases_expression_cluster2.txt │ ├── cases_expression_cluster3.txt │ ├── cases_expression_cluster4.txt │ ├── cases_gs.txt │ ├── cases_her2.txt │ ├── cases_luma.txt │ ├── cases_lumb.txt │ ├── cases_m1.txt │ ├── cases_m2.txt │ ├── cases_m3.txt │ ├── cases_m4.txt │ ├── cases_mRNA_cluster_1.txt │ ├── cases_mRNA_cluster_2.txt │ ├── cases_mRNA_cluster_3.txt │ ├── cases_magnoid.txt │ ├── cases_neural.txt │ ├── cases_pole.txt │ ├── cases_primitive.txt │ ├── cases_proneural.txt │ ├── cases_secretory.txt │ ├── cases_squamoid.txt │ ├── data_clinical_sample.txt │ ├── gbm_cases_classical.txt │ ├── gbm_cases_mesenchymal.txt │ ├── glioma_gdc_manifest.2018-01-31T19_50_13.151970.txt │ ├── hnsc_cases_basal.txt │ ├── hnsc_cases_classical.txt │ ├── hnsc_cases_mesenchymal.txt │ ├── hnsc_data_clinical_sample.txt │ ├── kirc_data_clinical_sample.txt │ ├── kirp_cases_all.txt │ ├── lusc_cases_basal.txt │ ├── lusc_cases_classical.txt │ ├── prad_data_clinical_sample.txt │ ├── sample_type_codes.csv │ ├── stad_cases_msi.txt │ └── ucec_cases_msi.txt ├── environment.yml ├── models ├── .gitkeep ├── primary_type │ └── .gitkeep ├── primary_type_ext_val │ └── .gitkeep ├── subtype │ └── .gitkeep └── subtype_ext_val │ └── .gitkeep ├── notebooks ├── .gitkeep ├── interactive_dataviz.ipynb └── paper_figures_v2.ipynb ├── references └── .gitkeep ├── src ├── __init__.py ├── data │ ├── .gitkeep │ ├── cohort.txt │ ├── combine_datasets.R │ ├── convert_eset_to_feather.R │ ├── convert_to_eset.R │ ├── download.R │ ├── generate_dataframe_prelim_subtypes_with_TCGA_data.R │ └── subtype_scripts │ │ ├── TCGA_ids_and_subtype_GBM.R │ │ ├── TCGA_ids_and_subtype_glioma.R │ │ ├── TCGA_ids_and_subtype_hnsc.R │ │ ├── TCGA_ids_and_subtype_kirc.R │ │ ├── TCGA_ids_and_subtype_kirp.R │ │ ├── TCGA_ids_and_subtype_luad.R │ │ ├── TCGA_ids_and_subtype_lusc.R │ │ ├── TCGA_ids_and_subtype_ovarian_cancer.R │ │ ├── TCGA_ids_and_subtype_prad.R │ │ ├── TCGA_ids_and_subtype_skcm.R │ │ ├── TCGA_ids_and_subtype_stad.R │ │ ├── TCGA_ids_and_subtype_ucec.R │ │ └── TCGA_ids_and_subtypes_brca.R ├── features │ ├── .gitkeep │ ├── ConvertCvToMetrics.R │ ├── ExtractSubtypeFeatures.R │ ├── GenerateCSVs.R │ └── build_features.py ├── primary_type │ ├── ConvolutionalNeuralNetworks │ │ ├── ExternalTest.py │ │ ├── GroupRunCNN.sh │ │ ├── TaloScan.py │ │ └── runCNN.sh │ ├── Helpers │ │ ├── Config.py │ │ ├── DataRna.py │ │ └── Model.py │ ├── InceptionNet │ │ ├── ExternalTest.py │ │ ├── GroupRunInceptionNet.sh │ │ ├── TaloScan.py │ │ └── runInceptionNet.sh │ └── ResNet │ │ ├── Config.py │ │ ├── DataRna.py │ │ ├── ExternalTest.py │ │ ├── GroupRunResNet.sh │ │ ├── TaloScan.py │ │ └── runResNet.sh ├── subtype │ └── models │ │ ├── .gitkeep │ │ ├── .gitkeep_1 │ │ ├── R │ │ ├── RF │ │ │ ├── minimal_features.R │ │ │ ├── minimal_features_1.R │ │ │ ├── minimal_features_validation.R │ │ │ ├── minimal_features_validation_1.R │ │ │ ├── predict_breast_tumor_subtype_RF.R │ │ │ ├── predict_breast_tumor_subtype_RF_1.R │ │ │ ├── predict_ovarian_tumor_subtype_RF.R │ │ │ ├── predict_ovarian_tumor_subtype_RF_1.R │ │ │ ├── predict_tumor_subtype_RF.R │ │ │ ├── predict_tumor_subtype_RF_1.R │ │ │ ├── predict_tumor_type_RF.R │ │ │ ├── predict_tumor_type_RF_1.R │ │ │ ├── predict_tumor_type_validation.R │ │ │ └── predict_tumor_type_validation_1.R │ │ ├── auxilary_functions.R │ │ ├── auxilary_functions_1.R │ │ └── 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