├── .gitignore ├── README.md ├── RWR-M.zip ├── RWR-MH.zip └── Scripts_and_Files ├── LOOCV ├── Disgenet_Generation_Input_LOOCV.R ├── Geometric_Mean.cpp ├── LOOCV_Merged_Networks.R ├── LOOCV_Multiplex_Heterogeneous.R ├── LOOCV_Multiplex_Monoplex.R ├── LOOCV_Utils.R ├── OMIM_Generation_Input_LOOCV.R └── get_transition_multiplex_rcpp.cpp ├── Network_Generation ├── .Rhistory ├── Generate_Coexpression_Network.R ├── Generate_Disease_Network_1.R ├── Generate_Disease_Network_2.R ├── Generate_PPI_Network.R ├── Generate_Pathway_Network.R ├── Network_Generation_Utils.R └── network_files │ ├── AllPathways_2016-11-24.gr │ ├── Co-Expression_2016-11-23.gr │ ├── DiseaseSimilarity_2016-12-06.gr │ └── PPI_2016-11-23.gr ├── Results_31 ├── CDF_Plots_Generation.R ├── Co-expression.txt ├── PPI.txt ├── PPI_Co-expression.txt ├── PPI_Pathways.txt ├── PPI_Pathways_Coex.txt ├── Pathways.txt └── Pathways_Coex.txt ├── Results_32 ├── CDF_Plots_Generation_Multigraph.R ├── Merged_PPI_PATH_COEX.txt └── Multiplex_PPI_PATH_COEX.txt ├── Results_33 ├── CDF_Plots_Generation_Heterogeneous.R ├── Monoplex.txt ├── Multiplex.txt ├── Multiplex_Heterogeneous.txt └── PPI_Heterogeneous.txt ├── Results_34 ├── CDF_Plots_Generation_Parameters.R ├── delta │ ├── delta_01.txt │ ├── delta_05.txt │ └── delta_09.txt ├── eta │ ├── eta_01.txt │ ├── eta_05.txt │ └── eta_09.txt ├── lambda │ ├── lambda_01.txt │ ├── lambda_05.txt │ └── lambda_09.txt ├── restart │ ├── restart_01.txt │ ├── restart_03.txt │ ├── restart_05.txt │ ├── restart_07.txt │ └── restart_09.txt └── tau │ ├── tau_1_01_19.txt │ ├── tau_1_19_01.txt │ └── tau_1_1_1.txt └── Results_35 ├── Short ├── Results_ShortSyndrome_PIK3R1_25.gr ├── Results_ShortSyndrome_PIK3R1_Diseases.txt └── Results_ShortSyndrome_PIK3R1_Genes.txt └── WRS ├── Network_WRS_Top25.gr ├── Ranking_Diseases_WRS.txt └── Ranking_Genes_WRS.txt /.gitignore: -------------------------------------------------------------------------------- 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