├── .dockerignore ├── .gitattributes ├── .github └── workflows │ ├── lint.yaml │ └── pytest.yaml ├── .gitignore ├── Dockerfile ├── LICENSE ├── LICENSE_bundled ├── README.md ├── entrypoint.sh ├── environment ├── README.md ├── environment.yml └── scripts │ ├── environment_base.yml │ ├── install_other_packages.sh │ ├── install_r_packages.r │ └── setup_data.py ├── libs └── ccc │ ├── __init__.py │ ├── coef │ ├── __init__.py │ └── impl.py │ ├── conf.py │ ├── corr.py │ ├── giant.py │ ├── log.py │ ├── log_config.yaml │ ├── methods.py │ ├── numpy │ └── __init__.py │ ├── plots.py │ ├── pytorch │ ├── __init__.py │ └── core.py │ ├── scipy │ ├── __init__.py │ └── stats.py │ ├── settings.py │ ├── sklearn │ ├── __init__.py │ └── metrics.py │ └── utils │ ├── __init__.py │ └── utility_functions.py ├── misc └── logo │ ├── ccc.png │ └── ccc.svg ├── nbs ├── .jupytext ├── 05_preprocessing │ ├── 00-gtex_v8-split_by_tissue.ipynb │ ├── 05-gtex_v8-select_top_genes.ipynb │ ├── 07-gtex_v8-metadata.ipynb │ ├── 10-understudied_genes.ipynb │ └── py │ │ ├── 00-gtex_v8-split_by_tissue.py │ │ ├── 05-gtex_v8-select_top_genes.py │ │ ├── 07-gtex_v8-metadata.py │ │ └── 10-understudied_genes.py ├── 10_compute_correlations │ └── 05_gtex_v8 │ │ ├── 05_01-gtex-var_pc_log2-pearson.ipynb │ │ ├── 06_01-gtex-var_pc_log2-spearman.ipynb │ │ ├── 07_01-gtex-var_pc_log2-ccc.ipynb │ │ ├── 08_01-gtex-var_pc_log2-mic_e-parallel.ipynb │ │ ├── 50-combine_all.ipynb │ │ └── py │ │ ├── 05_01-gtex-var_pc_log2-pearson.py │ │ ├── 06_01-gtex-var_pc_log2-spearman.py │ │ ├── 07_01-gtex-var_pc_log2-ccc.py │ │ ├── 08_01-gtex-var_pc_log2-mic_e-parallel.py │ │ └── 50-combine_all.py ├── 15_intersections │ ├── 03-gtex_whole_blood-intersections.ipynb │ └── py │ │ └── 03-gtex_whole_blood-intersections.py ├── 20_comparison_others │ ├── 50-combine_all.ipynb │ ├── 55-gtex_whole_blood-intersections-mic.ipynb │ ├── 60-time_test-1_cpu_core.ipynb │ ├── 61-time_test-3_cpu_cores.ipynb │ ├── 62-time_test-6_cpu_cores.ipynb │ └── py │ │ ├── 50-combine_all.py │ │ ├── 55-gtex_whole_blood-intersections-mic.py │ │ ├── 60-time_test-1_cpu_core.py │ │ ├── 61-time_test-3_cpu_cores.py │ │ └── 62-time_test-6_cpu_cores.py ├── 25_pvalue │ ├── 00-ccc_pvalue_dist-generate-data_matrix.ipynb │ ├── 01-ccc_pvalue_dist-generate-gene_pairs.ipynb │ ├── 05-ccc_pvalue_dist-plot.ipynb │ ├── 10-sample_gene_pair_categories.ipynb │ ├── 15-compute_pvalues_from_samples.ipynb │ ├── 17-adjust_pvalues_fdr.ipynb │ └── py │ │ ├── 00-ccc_pvalue_dist-generate-data_matrix.py │ │ ├── 01-ccc_pvalue_dist-generate-gene_pairs.py │ │ ├── 05-ccc_pvalue_dist-plot.py │ │ ├── 10-sample_gene_pair_categories.py │ │ ├── 15-compute_pvalues_from_samples.py │ │ └── 17-adjust_pvalues_fdr.py ├── 99_manuscript │ ├── coefs_comp │ │ ├── 05-analyze_significant_pairs.ipynb │ │ ├── 08_00-gtex_whole_blood-general_plots.ipynb │ │ ├── 08_05-gtex_whole_blood-intersections_plots.ipynb │ │ ├── 08_09-gtex_whole_blood-gene_pairs00-compute.ipynb │ │ ├── 08_10-gtex_whole_blood-gene_pairs00-plot.ipynb │ │ ├── 08_15-gtex_whole_blood-gene_pairs01-compute.ipynb │ │ ├── 08_16-gtex_whole_blood-gene_pairs01-plot.ipynb │ │ ├── 15_00-gtex_whole_blood-general_plots-mic.ipynb │ │ ├── 20_00-gtex_whole_blood-UTY_KDM6A.ipynb │ │ └── py │ │ │ ├── 05-analyze_significant_pairs.py │ │ │ ├── 08_00-gtex_whole_blood-general_plots.py │ │ │ ├── 08_05-gtex_whole_blood-intersections_plots.py │ │ │ ├── 08_09-gtex_whole_blood-gene_pairs00-compute.py │ │ │ ├── 08_10-gtex_whole_blood-gene_pairs00-plot.py │ │ │ ├── 08_15-gtex_whole_blood-gene_pairs01-compute.py │ │ │ ├── 08_16-gtex_whole_blood-gene_pairs01-plot.py │ │ │ ├── 15_00-gtex_whole_blood-general_plots-mic.py │ │ │ └── 20_00-gtex_whole_blood-UTY_KDM6A.py │ ├── giant │ │ ├── 03_00-giant-get_gene_info.ipynb │ │ ├── 03_05-giant-predict_tissue.ipynb │ │ ├── 03_10-giant-gene_interactions_table.ipynb │ │ ├── 03_10-giant-summarize_tissue_predictions.ipynb │ │ └── py │ │ │ ├── 03_00-giant-get_gene_info.py │ │ │ ├── 03_05-giant-predict_tissue.py │ │ │ ├── 03_10-giant-gene_interactions_table.py │ │ │ └── 03_10-giant-summarize_tissue_predictions.py │ ├── intro │ │ ├── 05-relationships_analysis.ipynb │ │ └── py │ │ │ └── 05-relationships_analysis.py │ ├── k_max │ │ ├── 01-k_max-runs.ipynb │ │ ├── 03-k_max-plots.ipynb │ │ └── py │ │ │ ├── 01-k_max-runs.py │ │ │ └── 03-k_max-plots.py │ ├── misc │ │ ├── 01-data_with_substructures.ipynb │ │ └── py │ │ │ └── 01-data_with_substructures.py │ ├── supplementary_files │ │ ├── 00-supplementary_file1.ipynb │ │ ├── 01-supplementary_file2.ipynb │ │ ├── 01-supplementary_file3.ipynb │ │ └── py │ │ │ ├── 00-supplementary_file1.py │ │ │ ├── 01-supplementary_file2.py │ │ │ └── 01-supplementary_file3.py │ └── time_test │ │ ├── 07-time_test-plot.ipynb │ │ └── py │ │ └── 07-time_test-plot.py ├── others │ └── 05_clustermatch_profiling │ │ ├── 05_cm_optimized │ │ ├── 04-cm_ari_numba.txt │ │ ├── 04-cm_ari_sklearn.txt │ │ ├── 04-compare_numba_ari.ipynb │ │ ├── 05-cm_precompute_parts_false.txt │ │ ├── 05-cm_precompute_parts_true.txt │ │ ├── 05-compare_precomputing_of_parts.ipynb │ │ ├── 06-cm_many_genes.txt │ │ ├── 06-many_genes.ipynb │ │ ├── 07-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 07-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 07-many_samples.ipynb │ │ └── py │ │ │ ├── 04-compare_numba_ari.py │ │ │ ├── 05-compare_precomputing_of_parts.py │ │ │ ├── 06-many_genes.py │ │ │ └── 07-many_samples.py │ │ ├── 06_cm_optimized │ │ ├── 04-cm_ari_numba.txt │ │ ├── 04-compare_numba_ari.ipynb │ │ ├── 06-cm_many_genes.txt │ │ ├── 06-many_genes.ipynb │ │ ├── 07-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 07-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 07-many_samples.ipynb │ │ └── py │ │ │ ├── 04-compare_numba_ari.py │ │ │ ├── 06-many_genes.py │ │ │ └── 07-many_samples.py │ │ ├── 07_cm_optimized │ │ ├── 04-cm_ari_numba.txt │ │ ├── 04-compare_numba_ari.ipynb │ │ ├── 06-cm_many_genes.txt │ │ ├── 06-many_genes.ipynb │ │ ├── 07-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 07-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 07-many_samples.ipynb │ │ └── py │ │ │ ├── 04-compare_numba_ari.py │ │ │ ├── 06-many_genes.py │ │ │ └── 07-many_samples.py │ │ ├── 10_cm_optimized │ │ ├── 00-n_samples_large.txt │ │ ├── 00-n_samples_small.txt │ │ ├── 00-run_reference.ipynb │ │ ├── 01-cdist_parts_v00.ipynb │ │ ├── 01-n_samples_large.txt │ │ ├── 01-n_samples_small.txt │ │ ├── 02-cdist_parts_v01.ipynb │ │ ├── 02-n_samples_large.txt │ │ ├── 02-n_samples_small.txt │ │ ├── 03-cdist_parts_v02.ipynb │ │ ├── 03-n_samples_large.txt │ │ ├── 03-n_samples_small.txt │ │ ├── 04-get_parts_v00.ipynb │ │ ├── 04-n_samples_large.txt │ │ ├── 04-n_samples_small.txt │ │ ├── 05-get_parts_v01.ipynb │ │ ├── 05-n_samples_large.txt │ │ ├── 05-n_samples_small.txt │ │ ├── 06-get_parts_v02.ipynb │ │ ├── 06-n_samples_large.txt │ │ ├── 06-n_samples_small.txt │ │ ├── 07-get_parts_v03.ipynb │ │ ├── 07-n_samples_large.txt │ │ ├── 07-n_samples_small.txt │ │ ├── 08-cdist_parts_v04.ipynb │ │ ├── 08-n_samples_large_100000.txt │ │ ├── 08-n_samples_large_50000.txt │ │ ├── 08-n_samples_small_100.txt │ │ ├── 08-n_samples_small_1000.txt │ │ ├── 08-n_samples_small_50.txt │ │ ├── 08-n_samples_small_500.txt │ │ ├── 09-cdist_parts_v04.ipynb │ │ ├── 09-n_samples_large_100000.txt │ │ ├── 09-n_samples_large_50000.txt │ │ ├── 09-n_samples_small_100.txt │ │ ├── 09-n_samples_small_1000.txt │ │ ├── 09-n_samples_small_50.txt │ │ ├── 09-n_samples_small_500.txt │ │ ├── 10-cdist_parts_v04.ipynb │ │ ├── 10-n_samples_large_100000.txt │ │ ├── 10-n_samples_large_50000.txt │ │ ├── 10-n_samples_small_100.txt │ │ ├── 10-n_samples_small_1000.txt │ │ ├── 10-n_samples_small_50.txt │ │ ├── 10-n_samples_small_500.txt │ │ └── py │ │ │ ├── 00-run_reference.py │ │ │ ├── 01-cdist_parts_v00.py │ │ │ ├── 02-cdist_parts_v01.py │ │ │ ├── 03-cdist_parts_v02.py │ │ │ ├── 04-get_parts_v00.py │ │ │ ├── 05-get_parts_v01.py │ │ │ ├── 06-get_parts_v02.py │ │ │ ├── 07-get_parts_v03.py │ │ │ ├── 08-cdist_parts_v04.py │ │ │ ├── 09-cdist_parts_v04.py │ │ │ └── 10-cdist_parts_v04.py │ │ ├── 11_cm_optimized │ │ ├── 06-cm_many_genes.txt │ │ ├── 06-many_genes.ipynb │ │ ├── 07-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 07-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 07-many_samples.ipynb │ │ ├── 08-cm_many_genes.txt │ │ ├── 08-many_genes.ipynb │ │ ├── 09-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 09-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 09-many_samples.ipynb │ │ └── py │ │ │ ├── 06-many_genes.py │ │ │ ├── 07-many_samples.py │ │ │ ├── 08-many_genes.py │ │ │ └── 09-many_samples.py │ │ ├── 12_cm_optimized │ │ ├── 06-cm_many_genes.txt │ │ ├── 06-many_genes.ipynb │ │ ├── 07-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 07-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 07-many_samples.ipynb │ │ ├── 08-cm_many_genes.txt │ │ ├── 08-many_genes.ipynb │ │ ├── 09-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 09-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 09-many_samples.ipynb │ │ ├── 10-cm_many_genes.txt │ │ ├── 10-many_genes.ipynb │ │ ├── 11-cm_many_samples-default_internal_n_clusters.txt │ │ ├── 11-cm_many_samples-less_internal_n_clusters.txt │ │ ├── 11-many_samples.ipynb │ │ └── py │ │ │ ├── 06-many_genes.py │ │ │ ├── 07-many_samples.py │ │ │ ├── 08-many_genes.py │ │ │ ├── 09-many_samples.py │ │ │ ├── 10-many_genes.py │ │ │ └── 11-many_samples.py │ │ └── README.md └── run_nbs.sh ├── scripts ├── convert_ipynb_to_py.sh ├── create_docker_image.sh ├── env.sh ├── jupytext_sync.sh ├── rsync.sh ├── run_docker.sh ├── run_nbs_server.sh ├── styler.r └── touch_pys.sh ├── setup.cfg ├── setup.py └── tests ├── README.md ├── __init__.py ├── data ├── README.md ├── ccc-example-coef.pkl ├── ccc-example-data.pkl ├── ccc-random_data-coef.pkl ├── ccc-random_data-data.pkl ├── file.txt └── file2.txt ├── test_coef.py ├── test_coef_pval.py ├── 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