Preview

pnet_prostate_paper-published_to_zenodo
- .gitignore
  
  129 Bytes
- LICENSE
  
  18.1 kB
- README.md
  
  8.9 kB
- _plots
  - figure3
    - sankey_full.html
      
      3.3 MB
  - logo.png
    
    96.8 kB
  - screenshot.png
    
    1.3 MB
- analysis
  - __init__.py
    
    0 Bytes
  - data_extraction_utils.py
    
    12.3 kB
  - data_stats
    - __init__.py
      
      0 Bytes
    - cn_mut_vis
      - __init__.py
        
        0 Bytes
      - run.py
        
        2.1 kB
    - mutation_counts
      - __init__.py
        
        0 Bytes
      - number_mutations.py
        
        2.2 kB
      - number_mutations_mets_primary.py
        
        1.9 kB
    - mutation_dist
      - __init__.py
        
        0 Bytes
      - run.py
        
        1.1 kB
  - extended_figures
    - __init__.py
      
      0 Bytes
    - figure_ed2_computational_performance.py
      
      11.2 kB
    - figure_ed3_pnet_vs_dense.py
      
      10.6 kB
    - figure_ed4_fusion.py
      
      15.6 kB
    - figure_ed5_cnv.py
      
      15.6 kB
    - figure_ed5_importance.py
      
      18.6 kB
    - figure_ed7_activation.py
      
      6.1 kB
  - figure_1
    - __init__.py
      
      0 Bytes
    - figure_1.py
      
      8.1 kB
    - figure_1_d_auc_prc.py
      
      5.9 kB
    - figure_1_e_confusion_matrix.py
      
      4.2 kB
  - figure_2
    - __init__.py
      
      0 Bytes
    - figure2_utils.py
      
      7.0 kB
    - figure_2.py
      
      21.1 kB
    - figure_2_a_pnet_vs_dense.py
      
      10.3 kB
    - figure_2_b_external_validation.py
      
      7.4 kB
    - figure_2_c_survival.py
      
      12.5 kB
    - setup.py
      
      309 Bytes
  - figure_3
    - __init__.py
      
      0 Bytes
    - figure3_b_gene_importance.py
      
      16.5 kB
    - figure3_bc_activation_importance.py
      
      9.8 kB
    - figure3_c_activation.py
      
      7.6 kB
    - figure_3_sankey.py
      
      29.9 kB
    - prepare_data.py
      
      5.2 kB
    - setup.py
      
      309 Bytes
  - figure_4
    - MDM4_TP53.py
      
      866 Bytes
    - __init__.py
      
      0 Bytes
    - figure_4.py
      
      16.1 kB
    - figure_4_a.py
      
      7.4 kB
    - figure_4_c_screen.py
      
      3.3 kB
    - figure_4_d.py
      
      2.5 kB
    - figure_4_d_MDM4_AR_TP53.py
      
      2.0 kB
    - figure_4_e_drug_MDM4.py
      
      2.3 kB
    - figure_4_e_drug_MDM4_revision.py
      
      2.3 kB
    - setup.py
      
      309 Bytes
  - prepare_data.py
    
    4.8 kB
  - run_it_all.py
    
    1.6 kB
  - sup
    - __init__.py
      
      0 Bytes
    - crossvalidation.py
      
      3.8 kB
    - layer_sizes.py
      
      1.3 kB
    - n_params.py
      
      656 Bytes
    - setup.py
      
      315 Bytes
  - vis_utils.py
    
    3.8 kB
- config_path.py
  
  552 Bytes
- data
  - __init__.py
    
    0 Bytes
  - data_access.py
    
    1.5 kB
  - data_access_test.py
    
    1.4 kB
  - gmt_reader.py
    
    1.7 kB
  - pathways
    - __init__.py
      
      0 Bytes
    - gmt_pathway.py
      
      1.4 kB
    - gmt_pathway_test.py
      
      322 Bytes
    - reactome.py
      
      5.2 kB
    - reactome_test.py
      
      1.6 kB
  - prostate_paper
    - __init__.py
      
      0 Bytes
    - data_reader.py
      
      15.9 kB
    - download_data.py
      
      1.5 kB
    - download_validation_data.py
      
      1.8 kB
    - prepare_data_final_P1000.py
      
      3.8 kB
    - prepare_validation_data.py
      
      4.1 kB
    - split_data.py
      
      2.8 kB
- deepexplain
  - __init__.py
    
    0 Bytes
  - tensorflow_.py
    
    21.6 kB
- environment.yml
  
  863 Bytes
- model
  - __init__.py
    
    0 Bytes
  - builders
    - __init__.py
      
      0 Bytes
    - builder_utils.py
      
      5.4 kB
    - builders_utils.py
      
      10.9 kB
    - prostate_models.py
      
      18.5 kB
  - callbacks_custom.py
    
    9.2 kB
  - coef_weights_utils.py
    
    20.9 kB
  - constraints_custom.py
    
    1.6 kB
  - layers_custom.py
    
    25.6 kB
  - model_factory.py
    
    3.7 kB
  - model_utils.py
    
    6.0 kB
  - nn.py
    
    14.9 kB
  - pathway_connection.py
    
    10.2 kB
- pipeline
  - LeaveOneOut_pipeline.py
    
    5.4 kB
  - __init__.py
    
    0 Bytes
  - crossvalidation_pipeline.py
    
    6.8 kB
  - one_split.py
    
    13.4 kB
  - pipe_utils.py
    
    6.3 kB
  - train_validate.py
    
    21.4 kB
- preprocessing
  - __init__.py
    
    0 Bytes
  - pre.py
    
    1.2 kB
- review
  - 11-LOOCV
    - eval_LOOCV.py
      
      3.6 kB
  - 17-mutual_genes
    - mpschr-mutex-b1898f6
      - MutEx_test.ipynb
        
        555.0 kB
      - README.md
        
        981 Bytes
      - calc_mutual.ipynb
        
        161.8 kB
      - mutex
        
        __init__.py
        
        1 Byte
        
        mutex.py
        
        6.1 kB
      - plot_upset.ipynb
        
        441.5 kB
      - setup.py
        
        504 Bytes
  - 1_common_samples_with_met500
    - Data S5 sample Identifiers.xlsx
      
      32.5 kB
    - calc_distance.ipynb
      
      219.8 kB
    - check_common_samples.ipynb
      
      14.1 kB
  - 2-1-stats
    - __init__.py
      
      0 Bytes
    - calc_stats.ipynb
      
      44.1 kB
  - 23-MAML3
    - MAML3.ipynb
      
      26.6 kB
    - __init__.py
      
      0 Bytes
  - 3-4
    - number of neurons in model.ipynb
      
      28.1 kB
  - 4-TMB_and_CNV_burden
    - TMB and CNV burden.ipynb
      
      117.5 kB
    - compare_cnv_burden.py
      
      5.2 kB
    - compare_contribution.py
      
      2.8 kB
    - save_feature_importance.py
      
      4.7 kB
  - 4-minor
    - compare dense AUC.ipynb
      
      80.4 kB
    - mutation distribution.ipynb
      
      23.4 kB
    - sub_visualization.ipynb
      
      18.5 kB
  - 5-fusion
    - __init__.py
      
      0 Bytes
    - compare_contribution.py
      
      2.7 kB
    - compare_fusion.py
      
      5.2 kB
    - compare_ranking.py
      
      3.0 kB
    - fusion_ranking.py
      
      2.4 kB
    - genes_with_fusion.py
      
      3.1 kB
    - save_fusions.ipynb
      
      34.2 kB
    - save_fusions_genes.ipynb
      
      46.6 kB
  - 7-oncogenes
    - annotate_genes.py
      
      2.4 kB
    - firstlayer.py
      
      7.3 kB
    - sankey.py
      
      24.2 kB
  - 8-ge
    - DGE_analysis.R
      
      2.4 kB
    - MDM4_DGE.R
      
      3.0 kB
    - filter_read_counts_by_coding_genes.ipynb
      
      19.9 kB
    - filter_read_counts_by_sample.py
      
      750 Bytes
    - prepare_gene_expression_matrix.ipynb
      
      30.5 kB
    - prepare_read_counts_matrix.ipynb
      
      65.3 kB
  - 9-hotspot
    - __init__.py
      
      0 Bytes
    - compare_auc.py
      
      5.1 kB
    - compare_contribution.py
      
      2.6 kB
    - compare_ranking.py
      
      2.4 kB
    - prepare_mut_hotspot.ipynb
      
      36.7 kB
  - 9-single_copy
    - __init__.py
      
      0 Bytes
    - compare_auc.py
      
      5.1 kB
    - run_stability.py
      
      2.0 kB
  - learning_rate
    - Book1.xlsx
      
      30.2 kB
    - Screen Shot 2021-03-25 at 4.31.47 AM.png
      
      197.5 kB
  - screens
    - CRISPR.ipynb
      
      103.4 kB
    - drugs.ipynb
      
      231.9 kB
- train
  - __init__.py
    
    0 Bytes
  - params
    - P1000
      - ML_params_search
        
        crossvalidation_ML_params_search_logistic.py
        
        1.5 kB
        
        crossvalidation_ML_params_search_svm.py
        
        1.5 kB
        
        onesplit_ML_params_search_adaboost.py
        
        1.4 kB
        
        onesplit_ML_params_search_randomforest.py
        
        1.4 kB
        
        onesplit_ML_params_search_svm.py
        
        1.5 kB
        
        onesplit_ML_params_search_svm_linear.py
        
        1.4 kB
        
        onesplit_ML_params_search_tree.py
        
        1.4 kB
        
        onsplit_ML_params_search_logistic.py
        
        1.5 kB
      - compare
        
        crossvalidation_ML_test.py
        
        2.2 kB
        
        onsplit_ML_test.py
        
        2.2 kB
      - dense
        
        onesplit_number_samples_dense_sameweights.py
        
        2.6 kB
        
        onsplit_dense.py
        
        3.3 kB
      - external_validation
        
        pnet_validation.py
        
        2.9 kB
      - number_samples
        
        crossvalidation_average_reg_10.py
        
        3.8 kB
        
        crossvalidation_average_reg_10_tanh.py
        
        3.5 kB
        
        crossvalidation_number_samples_dense_sameweights.py
        
        2.7 kB
      - pnet
        
        crossvalidation_average_reg_10_tanh.py
        
        3.3 kB
        
        onsplit_average_reg_10_tanh_large_testing.py
        
        3.2 kB
        
        onsplit_average_reg_10_tanh_large_testing_inner.py
        
        3.3 kB
      - review
        
        10custom_arch
        
        onsplit_kegg.py
        
        2.8 kB
        
        9hotspot
        
        onsplit_average_reg_10_tanh_large_testing_count.py
        
        3.2 kB
        
        onsplit_average_reg_10_tanh_large_testing_hotspot.py
        
        3.2 kB
        
        9single_copy
        
        crossvalidation_average_reg_10_tanh_single_copy.py
        
        3.5 kB
        
        onsplit_average_reg_10_tanh_large_testing_single_copy.py
        
        3.2 kB
        
        LOOCV_reg_10_tanh.py
        
        3.6 kB
        
        cnv_burden_training
        
        __init__.py
        
        0 Bytes
        
        onsplit_average_reg_10_tanh_large_testing_TMB.py
        
        3.4 kB
        
        onsplit_average_reg_10_tanh_large_testing_TMB2.py
        
        3.4 kB
        
        onsplit_average_reg_10_tanh_large_testing_TMB_cnv.py
        
        3.4 kB
        
        onsplit_average_reg_10_tanh_large_testing_account_zero.py
        
        3.3 kB
        
        onsplit_average_reg_10_tanh_large_testing_account_zero2.py
        
        3.3 kB
        
        onsplit_average_reg_10_tanh_large_testing_cnv_burden.py
        
        3.4 kB
        
        onsplit_average_reg_10_tanh_large_testing_cnv_burden2.py
        
        3.5 kB
        
        crossvalidation_average_reg_10_tanh_cancer_genes.py
        
        3.2 kB
        
        fusion
        
        onsplit_average_reg_10_tanh_large_testing_TMB.py
        
        3.3 kB
        
        onsplit_average_reg_10_tanh_large_testing_fusion.py
        
        3.2 kB
        
        onsplit_average_reg_10_tanh_large_testing_fusion_zero.py
        
        3.3 kB
        
        onsplit_average_reg_10_tanh_large_testing_inner_fusion_genes.py
        
        3.3 kB
        
        learning_rate
        
        onsplit_average_reg_10_tanh_large_testing_inner_LR.py
        
        3.0 kB
        
        onsplit_average_reg_10_tanh_large_testing_ge.py
        
        3.3 kB
  - run_me.py
    
    6.0 kB
- utils
  - __init__.py
    
    0 Bytes
  - evaluate.py
    
    4.3 kB
  - loading_utils.py
    
    2.1 kB
  - logs.py
    
    1.2 kB
  - plots.py
    
    5.3 kB
  - rnd.py
    
    242 Bytes
  - saving.py
    
    400 Bytes
  - stats_utils.py
    
    8.1 kB
  - stats_utils_delong_xu.py
    
    5.3 kB

pnet_prostate_paper-published_to_zenodo.zip