Files in saezlab/PHONEMeS-ILP

Building logic-based models from discovery high-content phosphoproteomics data

R/AllClasses.R R/BMsim.R R/PKN_list.R R/PKNlist.R R/all_constraints.R R/assignAttributes.R R/assignAttributes_tp.R R/assign_tp_attributes.R R/buildDataMatrix.R R/buildDataObject.R R/buildInputs.R R/buildNetwork.R R/buildNw.R R/buildPKN.R R/build_Nw.R R/build_Nw_Inv.R R/build_PKN.R R/build_PKN_Inv.R R/checkInputs.R R/combine_networks.R R/createModel.R R/createSIF.R R/create_binaries.R R/create_binary_variables_for_x_vector.R R/create_binary_variables_for_y_vector.R R/create_binary_variables_for_z_vector.R R/create_orin_orout_variables.R R/dataBycond.R R/dataTable.R R/integratorWeights.R R/intermediateWeights.R R/limmaWrapper.R R/mInw.R R/makeContrastAlt.R R/nodeAttr.R R/nodesData.R R/oRes.R R/pathsD.R R/plotoRes.R R/readOutSIF.R R/readOutSIFAll.R R/removeRedundantEdges.R R/removeRedundantNodes.R R/run1model.R R/runLimma.R R/runPHONEMeS.R R/runPHONEMeS_Downsampling.R R/runPHONEMeS_UD.R R/runPHONEMeS_mult.R R/simulateT1.R R/sinkWeights.R R/solve_with_cbc.R R/solve_with_cplex.R R/solve_with_cplex_downsampling.R R/solve_with_cplex_tp.R R/ttopFormatter.R R/writeFile.R R/write_boundaries.R R/write_constraints_1.R R/write_constraints_2.R R/write_constraints_2_ud.R R/write_constraints_3.R R/write_constraints_4.R R/write_constraints_5.R R/write_constraints_5_ud.R R/write_equality_constraints.R R/write_in_out_constraints.R R/write_lp_file.R R/write_lp_file_1.R R/write_lp_file_2.R R/write_lp_file_downsampling.R R/write_lp_file_inv_1.R R/write_lp_file_inv_2.R R/write_objective_function.R R/write_self_activating_constraints.R R/write_time_point_constraints.R README.md inst/PHONEMeS_example/Cluster/import_3.R inst/PHONEMeS_example/Cluster/import_4.R inst/PHONEMeS_example/Cluster/import_5.R inst/PHONEMeS_example/Cluster/import_6.R inst/PHONEMeS_example/Cluster/import_7.R inst/PHONEMeS_example/Cluster/import_8.R inst/PHONEMeS_example/Cluster/processGx_3.R inst/PHONEMeS_example/Cluster/processGx_4.R inst/PHONEMeS_example/Cluster/processGx_5.R inst/PHONEMeS_example/Cluster/processGx_6.R inst/PHONEMeS_example/Cluster/processGx_7.R inst/PHONEMeS_example/Cluster/processGx_8.R inst/PHONEMeS_example/Cluster/scriptGxopt_50models_3.R inst/PHONEMeS_example/Cluster/scriptGxopt_50models_4.R inst/PHONEMeS_example/Cluster/scriptGxopt_50models_5.R inst/PHONEMeS_example/Cluster/scriptGxopt_50models_6.R inst/PHONEMeS_example/Cluster/scriptGxopt_50models_7.R inst/PHONEMeS_example/Cluster/scriptGxopt_50models_8.R inst/PHONEMeS_example/combOptim.R inst/PHONEMeS_example/postOptim.R inst/PHONEMeS_example/prepOptim.R inst/doc/PHONEMeS_HowTo.pdf man/BMsim.Rd man/GMMbyCond-class.Rd man/GMMres-class.Rd man/ModelList-class.Rd man/OptParam-class.Rd man/PHONEMeS-package.Rd man/PKNlist-class.Rd man/PKNlist.Rd man/assignAttributes.Rd man/buildInputs.Rd man/buildNw.Rd man/buildPKN.Rd man/createModel.Rd man/dataBycond.Rd man/dataTable.Rd man/integratorWeights.Rd man/intermediateWeights.Rd man/mInw.Rd man/nodeAttr.Rd man/nodesData.Rd man/oRes.Rd man/pathsD.Rd man/plotoRes.Rd man/run1model.Rd man/runLimma.Rd man/runPHONEMeS.Rd man/runPHONEMeS_Downsampling.Rd man/runPHONEMeS_UD.Rd man/runPHONEMeS_mult.Rd man/simulateT1.Rd man/sinkWeights.Rd