Files in CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

R/toSBML.R R/crossvalidateBoolean.R R/toSBMLStandard.R R/simulatorTN.R R/cSimulator.R R/rSimulatorT1.R R/createAndRunILP.R R/readSBMLQual.R R/gaBinaryTN.R R/normaliseCNOlist.R R/findNONC.R R/link_midas_colnames_to_namesSpecies.R R/create_binary_variables_for_y_vector.R R/gaBinaryT2.R R/randomizeCNOlist.R R/writeScaffold.R R/mapBack.R R/writeSIF.R R/plotOptimResultsPDF.R R/CNOdata.R R/plotOptimResults.R R/sif2graph.R R/readSIF.R R/writeCplexCommandFile.R R/exhaustive.R R/cutAndPlotResultsTN.R R/compressModel.R R/cutModel.R R/cleanupILP.R R/create_binary_variables_for_all_species_in_experiment_k_i.R R/checkSignals.R R/cutSimList.R R/plotCNOlist2.R R/writeConstraint3.R R/CNOlist.R R/write_constraints.R R/plotCNOlistLargePDF.R R/prep4sim.R R/model2igraph.R R/cutAndPlotResultsT1.R R/cutAndPlot.R R/invokeCPLEX.R R/create_binary_variables_for_all_reactions_z_i_in_experiment_k_i.R R/CNORbool.R R/makeCNOlist.R R/simulatorT2.R R/plotCNOlistPDF.R R/ilpBinaryTN.R R/gaBinaryT1.R R/model2sif.R R/readRules.R R/writeFile.R R/writeBoundsForEdges_y_i.R R/writeNetwork.R R/plotFit.R R/computeScoreT1.R R/writeObjectiveFunction.R R/createILPBitstringAll.R R/ilpBinaryT2.R R/plotModel.R R/CellNOptR-internal.R R/residualError.R R/simulatorT1.R R/defaultParameters.R R/cutCNOlist.R R/ilpBinaryT1.R R/cutNONC.R R/expandGates.R R/plotCNOlist.R R/getFit.R R/buildBitString.R R/computeScoreTN.R R/writeMIDAS.R R/plotOptimResultsPan.R R/writeReport.R R/plotCNOlistLarge.R R/write_bounds.R R/deprecated.R R/CNORwrap.R R/preprocessing.R R/graph2sif.R R/crossInhibitedData.R R/readMIDAS.R R/simulateTN.R R/simulatorT0.R R/indexFinder.R R/writeDot.R R/create_binaries.R vignettes/CellNOptR0_1flowchart.pdf vignettes/Fig8.pdf vignettes/model_3.pdf vignettes/Fig7.pdf vignettes/Fig3.pdf vignettes/model_2.pdf vignettes/Fig4.pdf vignettes/CellNOptR-examples.R vignettes/Fig2.pdf vignettes/ilp_fit.pdf vignettes/Fig6.pdf vignettes/model_1.pdf man/makeCNOlist.Rd man/gaBinaryT2.Rd man/CellNOptR-package.Rd man/cSimulator.Rd man/CNORbool.Rd man/create_binaries.Rd man/readMIDAS.Rd man/ToyModel2.Rd man/DreamModel.Rd man/ilpBinaryT1.Rd man/plotFit.Rd man/computeScoreTN.Rd man/plotOptimResults.Rd man/toSBML.Rd man/CNOlist-class.Rd man/findNONC.Rd man/model2igraph.Rd man/normaliseCNOlist.Rd man/expandGates.Rd man/mapBack.Rd man/cutAndPlotResultsT1.Rd man/gaBinaryT1.Rd man/plotCNOlistLargePDF.Rd man/simulateTN.Rd man/CNOlistToyMMB.Rd man/CNOlistToy.Rd man/readBND.Rd man/writeObjectiveFunction.Rd man/plotCNOlistLarge.Rd man/writeReport.Rd man/simulatorT1.Rd man/defaultParameters.Rd man/writeMIDAS.Rd man/buildBitString.Rd man/getFit.Rd man/randomizeCNOlist.Rd man/residualError.Rd man/CNOdata.Rd man/createAndRunILP.Rd man/build_sif_table_from_rule.Rd man/writeNetwork.Rd man/simulatorT0.Rd man/crossInhibitedData.Rd man/sif2graph.Rd man/plotOptimResultsPDF.Rd man/createILPBitstringAll.Rd man/cutAndPlotResultsTN.Rd man/gaBinaryTN.Rd man/graph2sif.Rd man/plotOptimResultsPan.Rd man/model2sif.Rd man/writeScaffold.Rd man/readBNET.Rd man/simulatorTN.Rd man/plotCNOlist.Rd man/cutModel.Rd man/preprocessing.Rd man/readSIF.Rd man/computeScoreT1.Rd man/CNOlistToy2.Rd man/CNOlistDREAM.Rd man/CNORwrap.Rd man/exhaustive.Rd man/readSBMLQual.Rd man/checkSignals.Rd man/cutCNOlist.Rd man/compressModel.Rd man/ilpBinaryT2.Rd man/invokeCPLEX.Rd man/cutAndPlot.Rd man/write_bounds.Rd man/simulatorT2.Rd man/plotCNOlistPDF.Rd man/writeFile.Rd man/cutSimList.Rd man/plot-methods.Rd man/internals.Rd man/cutNONC.Rd man/writeSIF.Rd man/write_constraints.Rd man/CNOlist-methods.Rd man/simulateT1.Rd man/indexFinder.Rd man/ToyModel.Rd man/ilpBinaryTN.Rd man/plotCNOlist2.Rd man/prep4sim.Rd man/crossvalidateBoolean.Rd man/plotModel.Rd man/writeDot.Rd tests/test_import_rules.R tests/test_gaBinaryT1.R tests/test_gaBinaryT2.R tests/test_simulateTN.R tests/test_priorBitString.R tests/test_manySteadyStates.R tests/test_gaBinaryT3.R inst/doc/CellNOptR-vignette.pdf inst/doc/CellNOptR-vignette.R