├── .gitignore ├── LICENSE ├── README.md ├── compute_mutation_probabilities.py ├── examples ├── README.md ├── generate_data.py ├── pancan │ ├── .gitignore │ ├── Makefile │ └── README.md └── simple │ ├── README.md │ ├── adjacency_list.tsv │ └── commands.sh ├── experiments └── eccb2016 │ ├── .gitignore │ ├── README.md │ ├── commands.sh │ ├── requirements.txt │ └── scripts │ ├── helper.py │ ├── pairs_summary.py │ ├── permutation_test_helper.py │ ├── permute_single_matrix.py │ ├── pval_correlations.py │ ├── reconcile_grid_permutation_test.py │ ├── remove_genes_with_no_length.py │ ├── results_table.py │ ├── sample_mutation_frequency_plot.py │ ├── triple_pval_scatter.py │ ├── unweighted_comparison.py │ └── weights_matrix.py ├── find_exclusive_sets.py ├── find_sets.py ├── process_mutations.py ├── requirements.txt ├── viz ├── .bowerrc ├── .gitignore ├── README.md ├── bower.json ├── generate_viz_data.py ├── requirements.txt ├── server.py └── template.html └── wext ├── __init__.py ├── constants.py ├── enumerate_sets.py ├── exact.py ├── exclusivity_tests.py ├── i_o.py ├── mcmc.py ├── saddlepoint.py ├── setup.cfg ├── setup.py ├── src ├── c │ ├── comet_exact_test.c │ ├── poibinmodule.c │ ├── poibinmodule.h │ └── wext_exact_test.c └── fortran │ └── bipartite_edge_swap_module.f95 └── statistics.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphael-group/wext/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphael-group/wext/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphael-group/wext/HEAD/README.md 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