├── .gitignore ├── LICENSE ├── README.md ├── data ├── README.md ├── drug_disease_overview.tsv ├── gold-standard │ └── clinical-trial.json ├── img │ └── logo.jpg ├── kg │ ├── custom_filtered_kg.tsv │ ├── openbiolink_filtered_kg.tsv │ ├── permuted_custom_filtered_kg.tsv │ └── permuted_openbiolink_filtered_kg.tsv ├── manual_drug_disease_mapping.tsv ├── prioritized_pairs.tsv └── transcriptomics │ ├── creed_harmonized_expression.json │ ├── geo_harmonized_expression.json │ ├── lc1000_harmonized_expression.json │ └── target_harmonized_expression.json ├── figures ├── figure_1.pdf └── figure_4.pdf ├── notebooks ├── 1.0-plot_kg_distributions.ipynb ├── 1.1-dataset_statistics.ipynb ├── 2.0-dataset_probabilities.ipynb ├── 3.0-kg_statistics.ipynb ├── 4.0-subgraph_full_analysis.ipynb ├── 4.1-analysis_of_pairs.ipynb ├── 5.0-benchmark_analysis.ipynb └── utils.py └── requirements.txt /.gitignore: -------------------------------------------------------------------------------- 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