├── .gitattributes ├── .github └── workflows │ └── build.yml ├── .gitignore ├── LICENSE ├── README.md ├── docs ├── example_data │ ├── 5nodes_10regions_10000reads_test_cell_node_ids.tsv │ ├── 5nodes_10regions_10000reads_test_d_mat.csv │ ├── 5nodes_10regions_10000reads_test_d_mat_segmented_counts.txt │ ├── 5nodes_10regions_10000reads_test_d_mat_segmented_counts_cluster_assignments.txt │ ├── 5nodes_10regions_10000reads_test_d_mat_segmented_counts_cluster_sizes.txt │ ├── 5nodes_10regions_10000reads_test_d_mat_segmented_counts_condensed.txt │ ├── 5nodes_10regions_10000reads_test_ground_truth.csv │ ├── 5nodes_10regions_10000reads_test_region_sizes.txt │ ├── 5nodes_10regions_10000reads_test_tree.txt │ ├── cluster_acceptance_ratio.csv │ ├── cluster_attachment_scores.csv │ ├── cluster_cell_node_ids.tsv │ ├── cluster_cell_region_cnvs.csv │ ├── cluster_gamma_values.csv │ ├── cluster_inferred_cnvs.csv │ ├── cluster_markov_chain.csv │ ├── cluster_rel_markov_chain.csv │ ├── cluster_tree_inferred.graphviz │ ├── cluster_tree_inferred.pdf │ ├── cluster_tree_inferred.txt │ ├── test_acceptance_ratio.csv │ ├── test_attachment_scores.csv │ ├── test_cell_node_ids.tsv │ ├── test_cell_region_cnvs.csv │ ├── test_gamma_values.csv │ ├── test_inferred_cnvs.csv │ ├── test_markov_chain.csv │ ├── test_rel_markov_chain.csv │ ├── test_segmented_region_sizes.txt │ ├── test_segmented_regions.txt │ ├── test_tree_inferred.graphviz │ ├── test_tree_inferred.pdf │ └── test_tree_inferred.txt ├── notebooks │ ├── 10X_example.ipynb │ └── tutorial.ipynb └── tutorial.md ├── logo.png ├── pyscicone ├── MANIFEST.in ├── README.md ├── default.profraw ├── environment.yml ├── requirements.txt ├── scicone │ ├── __init__.py │ ├── bin │ │ ├── breakpoint_detection │ │ ├── inference │ │ ├── linux-breakpoint_detection │ │ ├── linux-inference │ │ ├── linux-score │ │ ├── linux-simulation │ │ ├── linux-tests │ │ ├── score │ │ ├── simulation │ │ └── tests │ ├── constants.py │ ├── data │ │ └── cancer_gene_census.csv │ ├── plotting.py │ ├── scicone.py │ ├── tree.py │ ├── utils.py │ └── utils_10x.py ├── setup.py └── tests │ └── test_scicone.py ├── reproducibility └── simulations │ ├── aggregate_simulation_results.py │ ├── benchmark.json │ ├── benchmark.smk │ ├── conet_comparison.json │ ├── conet_comparison.smk │ ├── conet_comparisons │ ├── conet_tree_distances.py │ ├── default │ │ ├── Snakefile │ │ └── config.json │ └── low_sd │ │ ├── Snakefile │ │ └── config.json │ ├── other_methods │ ├── HMMCopyInference.R │ ├── HierarchicalCopyInference.R │ ├── ginkgo.R │ ├── medalt │ │ ├── ComputeDistance.py │ │ ├── Edmonds.py │ │ ├── Kruskal.py │ │ ├── mdmst.py │ │ └── medalt.py │ ├── run_conet.py │ └── scope.R │ ├── readme.md │ └── run_scicone_recommended_params.py ├── scicone ├── CMakeLists.txt ├── Config.h.in ├── include │ ├── cxxopts.hpp │ ├── xxhash.c │ └── xxhash.h ├── reference.md ├── simulations │ ├── Simulation.h │ ├── run_simulations.cpp │ └── sample_simulation │ │ ├── 10nodes_10regions_1000reads_sim_tiny_d_mat.txt │ │ ├── 10nodes_10regions_1000reads_sim_tiny_ground_truth.txt │ │ ├── 10nodes_10regions_1000reads_sim_tiny_region_sizes.txt │ │ └── 10nodes_10regions_1000reads_sim_tiny_tree.txt ├── src │ ├── CustomExceptions.h │ ├── Inference.h │ ├── Lgamma.cpp │ ├── Lgamma.h │ ├── MathOp.cpp │ ├── MathOp.h │ ├── Node.h │ ├── SignalProcessing.cpp │ ├── SignalProcessing.h │ ├── SingletonRandomGenerator.h │ ├── Tree.h │ ├── Utils.cpp │ ├── Utils.h │ ├── breakpoint_detection.cpp │ ├── globals.cpp │ ├── infer_trees.cpp │ └── score_tree.cpp └── tests │ ├── bp_detection │ └── 10nodes_40regions_100000reads_sim_tiny_1000bins_d_mat.csv │ ├── run_tests.cpp │ ├── save_root_score_per_nu.cpp │ ├── trees_to_validate │ ├── invalid_tree_2.txt │ ├── invalid_tree_3.txt │ ├── invalid_tree_4.txt │ ├── valid_tree_1.txt │ └── valid_tree_2.txt │ └── validation.h └── scripts ├── compute_pdist.py ├── compute_tree_distances.py ├── condense_clusters.py ├── convert_to_graphviz.py 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