├── README.md ├── centrality_analysis ├── README.md ├── centrality_analysis.Rmd ├── centrality_analysis.ipynb └── centrality_analysis.nb.html ├── community_detection ├── README.md ├── community_detection_modularity_nonoverlap.Rmd ├── community_detection_modularity_nonoverlap.ipynb ├── community_detection_modularity_nonoverlap.nb.html ├── community_detection_modularity_overlap.Rmd ├── community_detection_modularity_overlap.nb.html ├── community_detection_topological_overlap.Rmd ├── community_detection_topological_overlap.ipynb └── community_detection_topological_overlap.nb.html ├── correlation_networks ├── README.md ├── correlation_compositional.Rmd ├── correlation_compositional.nb.html ├── correlation_thresholding.Rmd └── correlation_thresholding.nb.html ├── data ├── AraMetLeaves.csv ├── README.txt ├── breast_cancer_directed_ppi_Kanhaiya_etal_2017.csv ├── breast_cancer_essential_proteins.csv ├── drug_target_proteins.csv ├── eco_EM+TCA.txt ├── ecoli_ppi_Hu_etal_2009.txt ├── ecoli_proteins_essentiality_Baba2006MSB.txt ├── ecoli_regDB5.txt ├── human_functional_brain_network_1000_Functional_Connectomes.txt ├── human_ppi_hippie_v2.2.txt ├── human_structural_brain_network_Ardesch_2019.txt ├── karate.GraphML ├── marine_food_web_pnas_102_15_5443_01562.txt ├── metabolic_ecoli.txt ├── metabolic_human.txt ├── metabolic_yeast.txt ├── protein_structure_1A6N_A.txt ├── protein_structure_1BKS_A.txt ├── protein_structure_2VIK_A.txt ├── terrestrial_food_web_caribbean.txt ├── yeast_ppi_Batada_etal_2006.txt └── yeast_proteins_essentiality_OGEE.txt ├── introduction ├── README.md ├── load_plot_processing.Rmd ├── load_plot_processing.ipynb ├── load_plot_processing.nb.html ├── network_matrix.Rmd ├── network_matrix.ipynb ├── network_matrix.nb.html ├── path_finding.Rmd ├── path_finding.ipynb └── path_finding.nb.html ├── network_controllability ├── README.md ├── network_controllability_analysis.Rmd ├── network_controllability_analysis.ipynb ├── network_controllability_analysis.nb.html ├── network_controllability_domination.Rmd ├── network_controllability_domination.ipynb ├── network_controllability_domination.nb.html ├── network_controllability_matching.Rmd ├── network_controllability_matching.ipynb └── network_controllability_matching.nb.html ├── network_models ├── README.md ├── erdos_renyi_model.Rmd ├── erdos_renyi_model.ipynb ├── erdos_renyi_model.nb.html ├── lattice_Watts-Strogatz_model.Rmd ├── lattice_Watts-Strogatz_model.nb.html ├── lattice_Watts_Strogatz_model.ipynb ├── network_statistical_analysis.Rmd ├── network_statistical_analysis.ipynb ├── network_statistical_analysis.nb.html ├── scale-free_network_model.Rmd ├── scale-free_network_model.nb.html └── scale_free_network_model.ipynb ├── network_motifs ├── README.md ├── network_motif_analysis.Rmd ├── network_motif_analysis.nb.html ├── subgraphs_random_networks.Rmd └── subgraphs_random_networks.nb.html ├── network_property ├── README.md ├── network_property.Rmd ├── 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