Gene ranking based on random walk with restarts in Protein Protein Interaction Networks Reference Manual – User Manual . Authors: F. Cazals and A. Jean-Marie and D. Mazauric and J. Roux and G. Sales Santa Cruz

Main classes:

SBL::SBL_PPIN_application::PPIN_application : Execution of simulations from inputs + generation of visualizations

SBL::SBL_Genetrank_gene_radar_scatter_plot::Genetrank_gene_radar : Class for the generation of a gene scatter plot

SBL::SBL_PPIN_gene_radar_scatter_plot::PPIN_gene_radar_scatter_plot : Class for the generation of a gene radar scatter plotl

SBL::SBL_Genetrank_gene_to_protein::Genetrank_Translations : Class containing the translations resulting from use of SBL::SBL_Genetrank_gene_to_protein::Genetrank_GeneProteinTranslator

SBL::SBL_Genetrank_gene_to_protein::Genetrank_GeneProteinTranslator : Class that translates between identifier types (Requires a connection)

SBL::SBL_Genetrank_network_statistical_analysis::Genetrank_network_statistical_analysis : A class performing statistical analysis on a PPIN

SBL::SBL_PPIN_simulation::Genetrank_simulation_input : Class that represents an input set for a simulation

SBL::SBL_PPIN_simulation::PPIN_simulation_result : Class that gives an interface for getting the results of a simulation

SBL::SBL_PPIN_simulation::PPIN_simulation : Class that performs a simulation

SBL::SBL_PPIN_simulation_statistics::PPIN_simulation_visualizations : Generation of visualization for the results of a simulation

SBL::SBL_PPIN_simulation_statistics::PPIN_simulation_statistics : Run statistics for a single simulation

SBL::SBL_PPIN_simulation_statistics::PPIN_multiple_simulation_statistics : Raw statistics for a set of simulations