├── .gitignore ├── .travis.yml ├── AUTHORS.md ├── Dockerfile ├── LICENSE ├── README.md ├── data ├── PPI_STRING_v9.mat ├── PPI_influence.mat ├── __init__.py ├── dataset.txt ├── datasetDiffused.txt └── entrez_to_idmat.mat ├── data_formatting ├── .ipynb_checkpoints │ └── STRING_PPI_data-checkpoint.ipynb ├── PPI_APID.ipynb └── PPI_STRING.ipynb ├── reproducibility ├── MatlabToPython.m ├── README.md ├── confusion_matrices.py ├── img │ ├── confusion_matrices_1.svg │ ├── confusion_matrices_2.svg │ ├── confusion_matrices_plan.svg │ ├── lamb1.svg │ ├── lamb1800.svg │ └── matlab.svg ├── nbs_functions.py ├── reproducibility.ipynb ├── reproducibility.py └── reproducibility_output │ └── README.md ├── requirements.txt ├── setup.py ├── simulation ├── .ipynb_checkpoints │ ├── DatasetsGeneration-checkpoint.ipynb │ ├── Diffusion-checkpoint.ipynb │ ├── SimulatedNetworks-checkpoint.ipynb │ └── simulation_ppi_network-checkpoint.ipynb ├── DatasetsGeneration.ipynb ├── Diffusion.ipynb ├── HofreeDataset.ipynb ├── ModelComparison.ipynb ├── ScikitLearnNMF.ipynb ├── SimulatedNetworks.ipynb ├── __pycache__ │ ├── nbs_functions.cpython-36.pyc │ └── simulation_functions.cpython-36.pyc ├── analysis.py ├── confusion_matrix.py ├── input │ └── ppi_node_position.txt ├── r_analysis │ └── from_cc_to_pac.r ├── simulation.py ├── simulation_functions.py └── simulation_nbs_functions.py ├── stratipy ├── __init__.py ├── biostat.py ├── biostat_go.py ├── biostat_plot.py ├── consensus_clustering.py ├── filtering_diffusion.py ├── formatting_data.py ├── hierarchical_clustering.py ├── load_data.py ├── nbs.py ├── nbs_class.py ├── nbs_cluster.py ├── nbs_local.py ├── nmf_bootstrap.py ├── pac.py └── parameters.py └── test ├── .cache └── v │ └── cache │ └── lastfailed ├── __init__.py ├── __pycache__ └── test_filtering_diffusion.cpython-36-PYTEST.pyc └── test_filtering_diffusion.py /.gitignore: -------------------------------------------------------------------------------- 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