.editorconfig
.gitignore
.travis.yml
AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENSE
LICENSE.txt
MANIFEST.in
README.md
README.rst
requirements.txt
requirements_dev.txt
requirements_stateoftheinteractomes.txt
setup.cfg
setup.py
tox.ini
Data/Ensembl_export_Dec20_2023.txt.gz
Data/HGNC_download_Dec20_2023.txt
Data/HPA_normal_tissue_expression.tsv.gz
Data/PathwayCommons12.dip.hgnc.txt.clean.gz
Data/Wan_2015_PPIs.txt
Data/corum.pc_net.txt
Data/disgen.genesets
Data/disgen_strict30.genesets
Data/disgen_strict30.genesets.reduced
Data/example_edge_counts.txt
Data/example_network_names.txt
Data/example_prefix_file.txt
Data/experimental.genesets
Data/gene2go.gz
Data/gene_citation_counts_Dec20_2023.txt
Data/gene_conservation_scores.txt
Data/go_min10.genesets
Data/gtex_median_processed_1.tsv.gz
Data/gwas.genesets
Data/gwas_20230727.genesets
Data/gwas_strict15.genesets
Data/gwas_strict15.genesets.reduced
Data/network_optimal_alphas.txt
Data/panther.pc_net.txt
Data/pid2_combined_via_ndex.tsv
Data/protein_coding_genes.txt
Data/ranked_networks.tsv
Data/sizetest_prefixes.txt
Data/uniprot_data_id_length_mass_2023-12-20.tsv
Data/uniprot_data_id_sequence_xref_geneid_2024-02-05.tsv
ExampleUsage/AF_AlphaFold.README.md
ExampleUsage/AF_fasta_pairs.sh
ExampleUsage/AF_get_fastas.sh
ExampleUsage/GSR_GeneSetRecovery.README.md
ExampleUsage/GSR_process_genesets.sh
ExampleUsage/GSR_run_evaluation.sh
ExampleUsage/IP_InteractionPrediction.README.md
ExampleUsage/IP_createFolds.sh
ExampleUsage/IP_make_csvs.sh
ExampleUsage/IP_run_L3.sh
ExampleUsage/IP_run_MPS_topology.sh
ExampleUsage/IP_run_coverage.sh
ExampleUsage/IP_run_external.sh
ExampleUsage/IP_run_heldout.sh
ExampleUsage/NP_NetworkProcessing.README.md
ExampleUsage/NP_process_data.sh
ExampleUsage/PC_PCNets.README.md
ExampleUsage/PC_create_composites.sh
ExampleUsage/process_data_job.sh
ExampleUsage/run_L3_prediction.sh
ExampleUsage/run_MPS_prediction.sh
ExampleUsage/run_MPS_topology.sh
ExampleUsage/run_composite.sh
ExampleUsage/run_single_evaluation.sh
StateOfTheInteractomes_Notebooks/1_Statistics_and_Representation.ipynb
StateOfTheInteractomes_Notebooks/2_GO_analysis.ipynb
StateOfTheInteractomes_Notebooks/3_Gene_Set_Recovery.ipynb
StateOfTheInteractomes_Notebooks/4_Composite_networks.ipynb
StateOfTheInteractomes_Notebooks/5_Interaction_and_Complex_Prediction.ipynb
StateOfTheInteractomes_Notebooks/6_AlphaFold_Assessment.ipynb
StateOfTheInteractomes_Notebooks/README.md
StateOfTheInteractomes_Notebooks/go.obo
StateOfTheInteractomes_Notebooks/Data/Fig1A_network_feature_data.csv
StateOfTheInteractomes_Notebooks/Data/Fig1B_network_sizes.csv
StateOfTheInteractomes_Notebooks/Data/Fig2A_gene_annotations.csv
StateOfTheInteractomes_Notebooks/Data/Fig2C_bias_results.csv
StateOfTheInteractomes_Notebooks/Data/Fig2G_interaction_coverage.csv
StateOfTheInteractomes_Notebooks/Data/Fig2H_chrom_bin_data.npy
StateOfTheInteractomes_Notebooks/Data/Fig2H_citation_bin_data.npy
StateOfTheInteractomes_Notebooks/Data/Fig2H_citation_bin_data.txt.npy
StateOfTheInteractomes_Notebooks/Data/Fig2H_mrna_bin_data.npy
StateOfTheInteractomes_Notebooks/Data/Fig2H_prot_bin_data.npy
StateOfTheInteractomes_Notebooks/Data/Fig2I_go_bin_data.csv
StateOfTheInteractomes_Notebooks/Data/Fig3B_all_network_ranks.csv
StateOfTheInteractomes_Notebooks/Data/Fig3D_type_specific_results.csv
StateOfTheInteractomes_Notebooks/Data/Fig4B_performance_results.csv
StateOfTheInteractomes_Notebooks/Data/Fig4C_performance_results.csv
StateOfTheInteractomes_Notebooks/Data/Fig4D_network_sizes.csv
StateOfTheInteractomes_Notebooks/Data/Fig5D_interaction_coverage.csv
StateOfTheInteractomes_Notebooks/Data/Fig5D_interaction_coverage_revised.csv
StateOfTheInteractomes_Notebooks/Data/Fig5_Random_AF_results.csv
StateOfTheInteractomes_Notebooks/Data/Fig6F_corum_complex_results.csv
StateOfTheInteractomes_Notebooks/Data/FigS1c_experimental_node_counts.csv
StateOfTheInteractomes_Notebooks/Data/FigS2_tissue_mrna_data.tsv
StateOfTheInteractomes_Notebooks/Data/FigS3_tissue_prot_data.tsv
StateOfTheInteractomes_Notebooks/Data/FigS4B_interaction_density_tissue.tsv
StateOfTheInteractomes_Notebooks/Data/FigS4C_F_gene_function_prediction_results.tsv
StateOfTheInteractomes_Notebooks/Data/FigS5C_slope_data.tsv
StateOfTheInteractomes_Notebooks/Data/FigS5D_type_specific_stats.tsv
StateOfTheInteractomes_Notebooks/Data/FigS5E_Jaccard_mat.tsv
StateOfTheInteractomes_Notebooks/Data/FigS6EFGH_complex_prediciton.csv
StateOfTheInteractomes_Notebooks/Data/FigS6F_corum_complexes.txt
StateOfTheInteractomes_Notebooks/Data/FigS6_corum_panther_overlap.txt
StateOfTheInteractomes_Notebooks/Data/FigS7_pdb_edge_list.txt
StateOfTheInteractomes_Notebooks/Data/FigS7_pdb_node_list.txt
StateOfTheInteractomes_Notebooks/Data/TableS2.txt
StateOfTheInteractomes_Notebooks/Data/TableS3.txt
StateOfTheInteractomes_Notebooks/Data/TableS4.txt
StateOfTheInteractomes_Notebooks/Data/TableS5.txt
StateOfTheInteractomes_Notebooks/Data/TableS7.txt
StateOfTheInteractomes_Notebooks/Data/TableS8.txt
StateOfTheInteractomes_Notebooks/Data/corum_complex_info.tsv
StateOfTheInteractomes_Notebooks/Data/gene_conservation_scores.txt
StateOfTheInteractomes_Notebooks/Data/network_classifications.txt
StateOfTheInteractomes_Notebooks/Data/network_names_final.txt
StateOfTheInteractomes_Notebooks/Data/revision_prefixes.txt
StateOfTheInteractomes_Notebooks/Figures/Fig1A_network_features_bar.jpg
StateOfTheInteractomes_Notebooks/Supplemental_Code/EGAD_README.md
StateOfTheInteractomes_Notebooks/Supplemental_Code/HiDeF_README.md
StateOfTheInteractomes_Notebooks/Supplemental_Code/PDB_processing.py
StateOfTheInteractomes_Notebooks/Supplemental_Code/corum_processing.py
StateOfTheInteractomes_Notebooks/Supplemental_Code/egad_GBA.R
StateOfTheInteractomes_Notebooks/Supplemental_Code/egad_go_associations.tsv
StateOfTheInteractomes_Notebooks/Supplemental_Code/egad_run.sh
StateOfTheInteractomes_Notebooks/Supplemental_Code/hidef_run.sh
StateOfTheInteractomes_Notebooks/Supplemental_Code/phyloP_README.md
StateOfTheInteractomes_Notebooks/Supplemental_Code/phyloP_aggregation.py
StateOfTheInteractomes_Notebooks/Supplemental_Code/phyloP_classify_chrs.sh
StateOfTheInteractomes_Notebooks/Supplemental_Code/phyloP_run_cds.sh
StateOfTheInteractomes_Notebooks/Supplemental_Code/phyloP_run_pergene.sh
StateOfTheInteractomes_Notebooks/Supplemental_Code/phyloP_run_wig_bed.sh
data_configs/dip.config
data_configs/pid2.config
data_configs/template.config
data_configs/wan.config
docker/Dockerfile
docs/Makefile
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/devbranches.rst
docs/developer.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/integrationtesting.rst
docs/make.bat
docs/modules.rst
docs/neteval.rst
docs/newrelease.rst
docs/pypircfile.rst
docs/usage.rst
docs/versioningscheme.rst
neteval/L3_prediction.sh
neteval/Timer.py
neteval/__init__.py
neteval/alphafold_results.py
neteval/community_annotation.py
neteval/data_import_export_tools.py
neteval/edge_prediction.py
neteval/gene_mapper.py
neteval/gene_set_recovery_results.py
neteval/get_disgen_associations.py
neteval/get_gwas_associations.py
neteval/gsea_functions.py
neteval/net_to_csv.sh
neteval/netevalcmd.py
neteval/network_constructor.py
neteval/network_evaluation_functions.py
neteval/network_propagation.py
neteval/network_statistics.py
neteval/node_annotation.py
neteval/prepare_evaluation_data.py
neteval/process_data.py
neteval/processing_functions.py
neteval/query_ensembl.py
neteval/query_hgnc.py
neteval/query_uniprot.py
neteval/run_network_evaluation.py
neteval/shuffle_networks.py
neteval/type_mapper.py
neteval.egg-info/PKG-INFO
neteval.egg-info/SOURCES.txt
neteval.egg-info/dependency_links.txt
neteval.egg-info/not-zip-safe
neteval.egg-info/requires.txt
neteval.egg-info/top_level.txt
tests/__init__.py
tests/test_NetevalRunner.py
tests/test_dit.py
tests/test_edge_prediction.py
tests/test_evaluation.py
tests/test_gene_mapper.py
tests/test_integration_neteval.py
tests/test_netevalcmd.py
tests/test_processing_functions.py
tests/test_profiler.py
tests/test_shuffle.py
tests/test_type_mapper.py
tests/data/BIND_v8_shuffled.txt
tests/data/create_toy_obo.py
tests/data/edge_only_symbol.txt
tests/data/example_GS_edges.txt
tests/data/example_genesets.txt
tests/data/example_graph.txt
tests/data/example_graph_attributes.txt
tests/data/export_test_network.txt
tests/data/export_test_pcnet.txt
tests/data/pmid_assigned.txt
tests/data/pmid_evidence_test_data.txt
tests/data/pmid_unassigned.txt
tests/data/pmids.txt
tests/data/sub_go.obo
tests/data/sub_go_associations.txt