.coveragerc
.gitignore
.readthedocs.yml
AUTHORS.rst
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE.txt
MANIFEST.in
README.md
README.rst
pyproject.toml
setup.cfg
setup.py
tox.ini
docs/Makefile
docs/authors.rst
docs/changelog.rst
docs/conf.py
docs/contributing.rst
docs/index.rst
docs/license.rst
docs/readme.rst
docs/requirements.txt
docs/_static/.gitignore
src/NetAnalyzer/__init__.py
src/NetAnalyzer/adv_mat_calc.py
src/NetAnalyzer/cli_manager.py
src/NetAnalyzer/graph2sim.py
src/NetAnalyzer/integration.py
src/NetAnalyzer/main_modules.py
src/NetAnalyzer/net_parser.py
src/NetAnalyzer/net_plotter.py
src/NetAnalyzer/netanalyzer.py
src/NetAnalyzer/performancer.py
src/NetAnalyzer/ranker.py
src/NetAnalyzer/seed_parser.py
src/NetAnalyzer.egg-info/PKG-INFO
src/NetAnalyzer.egg-info/SOURCES.txt
src/NetAnalyzer.egg-info/dependency_links.txt
src/NetAnalyzer.egg-info/entry_points.txt
src/NetAnalyzer.egg-info/not-zip-safe
src/NetAnalyzer.egg-info/requires.txt
src/NetAnalyzer.egg-info/top_level.txt
src/NetAnalyzer/templates/net_explorer.txt
src/NetAnalyzer/templates/network.txt
tests/__init__.py
tests/conftest.py
tests/test_cli_manager.py
tests/test_integrate.py
tests/test_kernel.py
tests/test_netparser.py
tests/test_network.py
tests/test_ranker.py
tests/data/bipartite_network_for_validating.txt
tests/data/clusters_network_for_validating.txt
tests/data/comunities_network_for_validating.txt
tests/data/cosine_results.txt
tests/data/counts_results.txt
tests/data/counts_results_with_deleted.txt
tests/data/csi_results.txt
tests/data/geometric_results.txt
tests/data/hyi_results.txt
tests/data/jaccard_results.txt
tests/data/minicluster
tests/data/monopartite_network_bin_matrix.npy
tests/data/monopartite_network_for_validating.txt
tests/data/monopartite_network_matrix
tests/data/monopartite_network_node_names.txt
tests/data/monopartite_network_weights_for_validating.txt
tests/data/monopartite_network_with_autorrelations.txt
tests/data/non_connected_network.txt
tests/data/pcc_results.txt
tests/data/simpson_results.txt
tests/data/transference_results.txt
tests/data/tripartite_network_for_validating.txt
tests/data/tripartite_network_weighted_for_validating.txt
tests/data/data_integrate/asym_kernel1.npy
tests/data/data_integrate/asym_kernel2.npy
tests/data/data_integrate/kernel1.lst
tests/data/data_integrate/kernel1.npy
tests/data/data_integrate/kernel2.lst
tests/data/data_integrate/kernel2.npy
tests/data/data_integrate/negative_kernel1.npy
tests/data/data_integrate/negative_kernel2.npy
tests/data/data_kernel/adj_mat.lst
tests/data/data_kernel/adj_mat.npy
tests/data/data_kernel/ct.npy
tests/data/data_kernel/ct_colIds
tests/data/data_kernel/ct_rowIds
tests/data/data_kernel/el.npy
tests/data/data_kernel/get_kernels_refs.py
tests/data/data_kernel/ka_normalized.npy
tests/data/data_kernel/ka_normalized_colIds
tests/data/data_kernel/ka_normalized_rowIds
tests/data/data_kernel/md1.npy
tests/data/data_kernel/me.npy
tests/data/data_kernel/node2vec.npy
tests/data/data_kernel/node2vec_colIds
tests/data/data_kernel/node2vec_rowIds
tests/data/data_kernel/rf.npy
tests/data/data_kernel/rl0_5.npy
tests/data/data_kernel/vn0_5.npy
tests/data/data_ranker/bigseed
tests/data/data_ranker/cross_validation_by_seedgene_results
tests/data/data_ranker/filter_results
tests/data/data_ranker/genes2filter_for_validating
tests/data/data_ranker/kernel_for_validating
tests/data/data_ranker/kernel_for_validating.lst
tests/data/data_ranker/leave_one_out_by_seedgene_results
tests/data/data_ranker/monopartite_network_weighted_for_validating.txt
tests/data/data_ranker/rank_by_seedgene_results
tests/data/data_ranker/ranked_genes
tests/data/data_ranker/seed_genes_for_validating
tests/data/data_ranker/seed_genes_for_validating_withNotInkernels
tests/data/data_ranker/seed_weighted_for_validating
tests/data/data_ranker/tagged_file
tests/data/data_ranker/top_results
tests/data/input_scripts/integrate_kernels/asym_kernel1.npy
tests/data/input_scripts/integrate_kernels/asym_kernel2.npy
tests/data/input_scripts/integrate_kernels/create_temporal_big_matrices.py
tests/data/input_scripts/integrate_kernels/int_geometric_mean.lst
tests/data/input_scripts/integrate_kernels/int_geometric_mean.npy
tests/data/input_scripts/integrate_kernels/int_max.lst
tests/data/input_scripts/integrate_kernels/int_max.npy
tests/data/input_scripts/integrate_kernels/int_mean.lst
tests/data/input_scripts/integrate_kernels/int_mean.npy
tests/data/input_scripts/integrate_kernels/int_mean_asym.lst
tests/data/input_scripts/integrate_kernels/int_mean_asym.npy
tests/data/input_scripts/integrate_kernels/int_mean_by_presence.lst
tests/data/input_scripts/integrate_kernels/int_mean_by_presence.npy
tests/data/input_scripts/integrate_kernels/int_mean_by_presence_asym.lst
tests/data/input_scripts/integrate_kernels/int_mean_by_presence_asym.npy
tests/data/input_scripts/integrate_kernels/int_median.lst
tests/data/input_scripts/integrate_kernels/int_median.npy
tests/data/input_scripts/integrate_kernels/kernel1.lst
tests/data/input_scripts/integrate_kernels/kernel1.npy
tests/data/input_scripts/integrate_kernels/kernel2.lst
tests/data/input_scripts/integrate_kernels/kernel2.npy
tests/data/input_scripts/net_explorer/net1.lst
tests/data/input_scripts/net_explorer/net1.npy
tests/data/input_scripts/net_explorer/net2.lst
tests/data/input_scripts/net_explorer/net2.npy
tests/data/input_scripts/net_explorer/seeds
tests/data/input_scripts/netanalyzer/attributes/graph_attributes.txt
tests/data/input_scripts/netanalyzer/attributes/node_attributes_nonsumm.txt
tests/data/input_scripts/netanalyzer/attributes/node_attributes_summ.txt
tests/data/input_scripts/netanalyzer/clustering/clusters_toy.txt
tests/data/input_scripts/netanalyzer/clustering/comparing_clusters.txt
tests/data/input_scripts/netanalyzer/clustering/der_discovered_clusters.txt
tests/data/input_scripts/netanalyzer/clustering/expand_clusters.txt
tests/data/input_scripts/netanalyzer/clustering/group_metrics.txt
tests/data/input_scripts/netanalyzer/clustering/group_metrics2.txt
tests/data/input_scripts/netanalyzer/clustering/group_metrics_non_connected.txt
tests/data/input_scripts/netanalyzer/clustering/group_metrics_summarized.txt
tests/data/input_scripts/netanalyzer/clustering/group_metrics_summarized2.txt
tests/data/input_scripts/netanalyzer/clustering/non_connected_network.txt
tests/data/input_scripts/netanalyzer/clustering/rber_pots_discovered_clusters.txt
tests/data/input_scripts/netanalyzer/dsl/ct.npy
tests/data/input_scripts/netanalyzer/dsl/ct_colIds
tests/data/input_scripts/netanalyzer/dsl/ct_rowIds
tests/data/input_scripts/netanalyzer/dsl/filter_cutoff
tests/data/input_scripts/netanalyzer/dsl/filter_dsl
tests/data/input_scripts/netanalyzer/dsl/filter_with_count.npy
tests/data/input_scripts/netanalyzer/dsl/filter_with_count_colIds
tests/data/input_scripts/netanalyzer/dsl/filter_with_count_rowIds
tests/data/input_scripts/netanalyzer/dsl/jaccard_count_filter_dsl
tests/data/input_scripts/netanalyzer/dsl/jaccard_dsl
tests/data/input_scripts/netanalyzer/dsl/jaccard_results.txt
tests/data/input_scripts/netanalyzer/dsl/kernel_dsl
tests/data/input_scripts/netanalyzer/dsl/similarity_dsl
tests/data/input_scripts/netanalyzer/dsl/output/ct.npy
tests/data/input_scripts/netanalyzer/dsl/output/ct_colIds
tests/data/input_scripts/netanalyzer/dsl/output/ct_rowIds
tests/data/input_scripts/netanalyzer/dsl/output/filter_cutoff
tests/data/input_scripts/netanalyzer/dsl/output/filter_with_count.npy
tests/data/input_scripts/netanalyzer/dsl/output/filter_with_count_colIds
tests/data/input_scripts/netanalyzer/dsl/output/filter_with_count_rowIds
tests/data/input_scripts/netanalyzer/dsl/output/jaccard_results.txt
tests/data/input_scripts/randomize_clustering/random_clusters.txt
tests/data/input_scripts/randomize_clustering/random_minicluster.txt
tests/data/input_scripts/randomize_network/random_net_same_seed.txt
tests/data/input_scripts/ranker/output_ranker_discarded
tests/data/input_scripts/ranker/ranker_by_seed_file_nonseeded_results_all_candidates
tests/data/input_scripts/ranker/ranker_by_seed_file_results_all_candidates
tests/data/input_scripts/ranker/ranker_by_seed_file_results_header_all_candidates
tests/data/input_scripts/ranker/ranker_by_seed_file_results_tagged_all_candidates
tests/data/input_scripts/ranker/ranker_by_seed_file_results_type_added_all_candidates
tests/data/input_scripts/ranker/ranker_by_seed_file_results_type_added_header_all_candidates
tests/data/input_scripts/ranker/ranker_by_seed_file_weighted_results_all_candidates
tests/data/input_scripts/ranker/ranker_by_seed_string_results_all_candidates
tests/data/input_scripts/ranker/ranker_cross_validation_all_by_seed_results_all_candidates
tests/data/input_scripts/ranker/ranker_cross_validation_by_seed_results_all_candidates
tests/data/input_scripts/ranker/ranker_cross_validation_by_seed_results_bigseed_all_candidates
tests/data/input_scripts/ranker/ranker_cross_validation_by_seed_results_remove_seed_all_candidates
tests/data/input_scripts/ranker/ranker_filter_results_all_candidates
tests/data/input_scripts/ranker/ranker_leave_one_out_by_seed_nonseed_results_all_candidates
tests/data/input_scripts/ranker/ranker_leave_one_out_by_seed_results_all_candidates
tests/data/input_scripts/ranker/ranker_leave_one_out_by_seed_results_bigseed_all_candidates
tests/data/input_scripts/ranker/ranker_leave_one_out_by_seed_results_header_all_candidates
tests/data/input_scripts/ranker/ranker_propagate_normalized_all_candidates
tests/data/input_scripts/ranker/ranker_propagate_not_normalized_all_candidates
tests/data/input_scripts/ranker/ranker_propagate_with_restart_all_candidates
tests/data/input_scripts/ranker/ranker_top_results
tests/data/input_scripts/ranker/ranker_whitelist_results_all_candidates
tests/data/input_scripts/ranker/whitelist
tests/data/input_scripts/text2binary_matrix/cutoff_binarizado.npy
tests/data/input_scripts/text2binary_matrix/cutoff_no_binarizado.npy
tests/data/input_scripts/text2binary_matrix/matrix_from_pairs
tests/data/input_scripts/text2binary_matrix/matrix_from_pairs.lst
tests/data/input_scripts/text2binary_matrix/set_diagonal_matrix.npy
tests/data/input_scripts/text2binary_matrix/statistics_from_text2bin
tests/data/input_scripts/text2binary_matrix/test_matrix
tests/data/input_scripts/text2binary_matrix/test_matrix_bin.npy
tests/data/input_scripts/text2binary_matrix/test_matrixfrommatrix
tests/data/input_scripts/text2binary_matrix/test_pairs