├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── ddot ├── Ontology.py ├── __init__.py ├── config.py ├── ontology_style.cx ├── passthrough_style.cx ├── site.cfg ├── tohiview.py └── utils.py ├── docker ├── Dockerfile-anaconda2 ├── Dockerfile-anaconda3 ├── build_docker.sh └── push_docker.sh ├── docs ├── .ipynb_checkpoints │ └── install-checkpoint.rst ├── Makefile ├── conf.py ├── fango.png ├── index.rst ├── install.rst ├── intro.rst ├── make.bat ├── ontology.rst ├── requirements.txt ├── software_pipeline_1dec2017.png ├── software_pipeline_23jan2018.png ├── software_pipeline_6jul2017.png ├── toy_ontology.ai ├── toy_ontology.png ├── toy_ontology_S1.ai ├── toy_ontology_S1.png ├── toy_ontology_alignment.ai ├── toy_ontology_alignment.png ├── toy_ontology_dag2tree.ai ├── toy_ontology_dag2tree.png ├── toy_ontology_delete_not_transitive.ai ├── toy_ontology_delete_not_transitive.png ├── toy_ontology_delete_transitive.ai ├── toy_ontology_delete_transitive.png ├── toy_ontology_propagate_gene_term.ai ├── toy_ontology_propagate_gene_term.png ├── toy_ontology_propagate_term_term.ai ├── toy_ontology_propagate_term_term.png ├── toy_ontology_spanning_tree.ai ├── toy_ontology_spanning_tree.png ├── tutorial.rst └── utils.rst ├── examples ├── 1.0.0 │ ├── .ipynb_checkpoints │ │ └── Tutorial-checkpoint.ipynb │ ├── Load_example_datasets.ipynb │ ├── Make_disease_gene_ontologies.ipynb │ ├── Process_the_Gene_Ontology.ipynb │ ├── Tutorial.ipynb │ └── disease_gene_ontologies.txt └── 1.0.1_HiView_tutorial │ ├── .ipynb_checkpoints │ └── hiview_tutorial-checkpoint.ipynb │ ├── data │ ├── net_links.txt │ ├── test1.ont │ ├── test2.ont │ ├── test2_score.txt │ ├── test2_ww.ont │ ├── test3_binarysample.txt │ ├── test3_coxsample.txt │ ├── test3_ppisample.txt │ └── test4_nodeattr.txt │ ├── fig │ ├── fig1.png │ ├── fig2.png │ ├── fig3.png │ ├── fig4.png │ └── fig5.png │ ├── hiview_tutorial.ipynb │ ├── term_2_uuid.test2 │ ├── term_2_uuid.test2.1 │ └── term_2_uuid.test3 ├── 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