LICENSE
MANIFEST.in
README.md
setup.cfg
setup.py
assets/BioNeuralNet.png
assets/BioNeuralNet1.png
assets/BioNeuralNet2.png
assets/DPMON.png
assets/LOGO_TB.png
assets/LOGO_TB.svg
assets/LOGO_WB.png
assets/LOGO_WB.svg
assets/Overview.png
assets/SubjectRepresentation.png
assets/ccrcc_search.png
assets/clustercorrelation.png
assets/cptac_clinical.png
assets/cptac_genomics.png
assets/cptac_proteomics.png
assets/cptac_search.png
assets/enchaned_w_omics.png
assets/forum.png
assets/geometric.png
assets/hybrid_clustering.png
assets/images_download.png
assets/plot_embeddings.png
assets/plot_network.png
assets/pytorch.png
assets/raw_enriched_comparison.png
assets/raw_vs_enchances_jyp.png
assets/repo.png
assets/variance_by_feature.png
assets/variance_distribution.png
bioneuralnet/__init__.py
bioneuralnet.egg-info/PKG-INFO
bioneuralnet.egg-info/SOURCES.txt
bioneuralnet.egg-info/dependency_links.txt
bioneuralnet.egg-info/requires.txt
bioneuralnet.egg-info/top_level.txt
bioneuralnet/clustering/__init__.py
bioneuralnet/clustering/correlated_louvain.py
bioneuralnet/clustering/correlated_pagerank.py
bioneuralnet/clustering/hybrid_louvain.py
bioneuralnet/datasets/__init__.py
bioneuralnet/datasets/dataset_loader.py
bioneuralnet/datasets/example1/X1.csv
bioneuralnet/datasets/example1/X2.csv
bioneuralnet/datasets/example1/Y.csv
bioneuralnet/datasets/example1/clinical_data.csv
bioneuralnet/datasets/monet/clinical_data.csv
bioneuralnet/datasets/monet/gene_data.csv
bioneuralnet/datasets/monet/mirna_data.csv
bioneuralnet/datasets/monet/phenotype.csv
bioneuralnet/datasets/monet/rppa_data.csv
bioneuralnet/downstream_task/__init__.py
bioneuralnet/downstream_task/dpmon.py
bioneuralnet/downstream_task/subject_representation.py
bioneuralnet/external_tools/SmCCNet.R
bioneuralnet/external_tools/WGCNA.R
bioneuralnet/external_tools/__init__.py
bioneuralnet/external_tools/cptac_wrapper.py
bioneuralnet/external_tools/node2vec.py
bioneuralnet/external_tools/smccnet.py
bioneuralnet/external_tools/wgcna.py
bioneuralnet/metrics/__init__.py
bioneuralnet/metrics/correlation.py
bioneuralnet/metrics/evaluation.py
bioneuralnet/metrics/plot.py
bioneuralnet/network_embedding/__init__.py
bioneuralnet/network_embedding/gnn_embedding.py
bioneuralnet/network_embedding/gnn_models.py
bioneuralnet/subject_representation/__init__.py
bioneuralnet/subject_representation/subject_representation.py
bioneuralnet/utils/__init__.py
bioneuralnet/utils/logger.py
bioneuralnet/utils/preprocess.py
bioneuralnet/utils/rdata_convert.py
bioneuralnet/utils/rdata_to_df.R
bioneuralnet/utils/variance.py
docs/requirements.txt
docs/source/BioNeuralNet.ipynb
docs/source/TOPMED.ipynb
docs/source/clustering.rst
docs/source/conf.py
docs/source/downstream_tasks.rst
docs/source/faq.rst
docs/source/future.rst
docs/source/gnns.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/metrics.rst
docs/source/user_api.rst
docs/source/utils.rst
docs/source/_static/BioNeuralNet.png
docs/source/_static/BioNeuralNet1.png
docs/source/_static/BioNeuralNet2.png
docs/source/_static/DPMON.png
docs/source/_static/LOGO_TB.png
docs/source/_static/LOGO_TB.svg
docs/source/_static/LOGO_WB.png
docs/source/_static/LOGO_WB.svg
docs/source/_static/Overview.png
docs/source/_static/SubjectRepresentation.png
docs/source/_static/ccrcc_search.png
docs/source/_static/clustercorrelation.png
docs/source/_static/cptac_clinical.png
docs/source/_static/cptac_genomics.png
docs/source/_static/cptac_proteomics.png
docs/source/_static/cptac_search.png
docs/source/_static/geometric.png
docs/source/_static/hybrid_clustering.png
docs/source/_static/images_download.png
docs/source/_static/plot_embeddings.png
docs/source/_static/plot_network.png
docs/source/_static/pytorch.png
docs/source/_static/raw_enriched_comparison.png
docs/source/_static/raw_vs_enchances_jyp.png
docs/source/_static/repo.png
docs/source/_static/variance_by_feature.png
docs/source/_static/variance_distribution.png
docs/source/examples/correlated_hybrid_louvain.py
docs/source/examples/correlated_louvain_example.py
docs/source/examples/correlation_metrics.py
docs/source/examples/dpmon_example.py
docs/source/examples/example_1.py
docs/source/examples/example_2.py
docs/source/examples/gnn_embedding_example.py
docs/source/examples/node2vec_example.py
docs/source/examples/smccnet_example.py
docs/source/examples/subject_representation_example.py
docs/source/examples/wgcna_example.py
docs/source/external_tools/Graph_Construction.rst
docs/source/external_tools/index.rst
docs/source/tutorials/Disease_Prediction.rst
docs/source/tutorials/Graph_Clustering.rst
docs/source/tutorials/Graph_Embedding.rst
docs/source/tutorials/Subject_Representation.rst
docs/source/tutorials/example_1.rst
docs/source/tutorials/example_2.rst
docs/source/tutorials/index.rst
tests/test_correlated_louvain.py
tests/test_correlated_pagerank.py
tests/test_dpmon.py
tests/test_gnn_embedding.py
tests/test_hybrid_louvain.py
tests/test_metrics.py
tests/test_smccnet.py
tests/test_subject_representation.py
tests/test_utils.py
tests/test_wgcna.py