├── LICENSE ├── README.md ├── __init__.py ├── cadrres_sc ├── __init__.py ├── analysis │ └── __init__.py ├── evaluation.py ├── model.py ├── pp │ ├── __init__.py │ ├── bayesian_sigmoid_curve_fitting_CCLE.py.backup │ ├── bayesian_sigmoid_curve_fitting_GDSC.py.backup │ ├── gexp.py │ └── scgexp.py └── utility.py ├── data ├── GDSC │ ├── GDSC_tissue_info.csv │ └── gdsc_all_abs_ic50_bayesian_sigmoid_only9dosages.csv ├── essential_genes.txt └── patient │ ├── log2_fc_cluster_tpm.csv │ └── percent_patient_tpm_cluster.xlsx ├── environment.yml ├── example_result ├── cadrres-wo-sample-bias_output_dict.pickle ├── cadrres-wo-sample-bias_param_dict.pickle ├── cadrres-wo-sample-bias_test_pred.csv ├── hn_drug_cw_dw10_100000_test_pred.csv ├── pred_combi_kill_log2_median_ic50_hn.csv └── pred_drug_kill_hn_drug_cw_dw10_100000.csv ├── notebooks ├── model_training.ipynb ├── predicting_combinatorial_drugs_scrna-seq.ipynb └── prediction_pretrained_model.ipynb ├── preprocessed_data └── GDSC │ ├── drug_stat.csv │ └── hn_drug_stat.csv └── scripts ├── A00-1_preprocess_rnaseq_result.ipynb ├── A01-1_get_scrnaseq_tpm.ipynb ├── A01-2R_normalization_factors.ipynb ├── A02-2_itth_CIBERSORT_deconvolution.ipynb ├── A02-3_normalization.ipynb ├── A02-4_clustering_scanpy_louvain (2020-07-13).ipynb ├── A02-4_clustering_scanpy_louvain.ipynb ├── A02-5_itth_scores.ipynb ├── A03_generate_TCGA_sample_metadata.ipynb ├── B01_single_cell_cluster_info_and_exp.ipynb ├── B02_drug_statistics.ipynb ├── D01-1_cross_validation_obj_functions.ipynb ├── D01-1_cross_validation_obj_functions_indication_specific.ipynb ├── D01-2_cross_validation_scores.ipynb ├── D01-2_cross_validation_scores_indication_specific.ipynb ├── D02-1_hn_model_training.ipynb ├── D02-2_hn_model_prediction.ipynb ├── D02-3_ic50_to_percent_cell_death.ipynb ├── D02-3_ic50_to_percent_cell_death_ElasticNet_RWEN.ipynb ├── D02-3_ic50_to_percent_cell_death_bulk.ipynb ├── D02-3_ic50_to_percent_cell_death_bulk_ElasticNet_RWEN.ipynb ├── D02-3_ic50_to_percent_cell_death_cell.ipynb ├── D02-3_ic50_to_percent_cell_death_cell_ElasticNet_RWEN.ipynb ├── D02-4_drug_combination.ipynb ├── D02-4_drug_combination_ElasticNet_RWEN.ipynb ├── D02-4_drug_combination_bulk.ipynb ├── D02-4_drug_combination_bulk_ElasticNet_RWEN.ipynb ├── D02-4_drug_combination_cell.ipynb ├── D02-4_drug_combination_cell_ElasticNet_RWEN.ipynb ├── D02-5_experimental_validation.ipynb ├── D02-5_experimental_validation_ElasticNet_RWEN.ipynb ├── D02-5_experimental_validation_bulk.ipynb ├── D02-5_experimental_validation_bulk_ElasticNet_RWEN.ipynb ├── D02-5_experimental_validation_cell.ipynb ├── D02-5_experimental_validation_cell_ElasticNet_RWEN.ipynb ├── F01_main_supplementary.ipynb ├── F02_main_supplement.ipynb ├── F10_sup_patient_specific_prediction_CCLEvsGDSC.ipynb ├── F3_2D_visualization_pathway.ipynb ├── F_sup_calculate_expected_response.ipynb ├── F_sup_combine_curve_ic50.ipynb ├── Fig4_sup_133.svg ├── Fig4_sup_201.svg └── sample.pdf /LICENSE: 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