Files in CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
ChangeLog
.Rinstignore
NAMESPACE
DESCRIPTION
build/vignette.rds
src/simulatorTN.c
src/Makevars
src/getFit.c
src/simulatorT1.c
data/CNOlistToy.RData
data/CNOlist_ToyPB.RData
data/ToyModel2.RData
data/ToyModel.RData
data/CNOlistToyMMB.RData
data/CNOlistToy2.RData
data/PKN_ToyPB.RData
data/DreamModel.RData
data/CNOlistDREAM.RData
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/CellNOptR-vignette.Rnw
vignettes/Fig3.pdf
vignettes/model_2.pdf
vignettes/Fig4.pdf
vignettes/CellNOptR-examples.R
vignettes/Fig2.pdf
vignettes/Fig5.png
vignettes/ilp_fit.pdf
vignettes/Fig6.pdf
vignettes/model_1.pdf
vignettes/Fig1.png
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/NEWS.Rd
inst/CITATION
inst/doc/CellNOptR-vignette.pdf
inst/doc/CellNOptR-vignette.Rnw
inst/doc/CellNOptR-vignette.R
inst/ToyModel/ToyModelMMB2.sif
inst/ToyModel/ToyDataMMB.csv
inst/ToyModel/ToyPKNMMB.sif
inst/ToyModelT3/ToyDataT3.csv
inst/ToyModelT3/ToyModelT3.sif
inst/templates/logo_saezrodriguez_mid.gif
inst/templates/phinou.jpeg
inst/templates/Rlogo.png
inst/templates/bordercorner2.jpg
inst/templates/CNOR.css
inst/templates/bordercorner.jpg
inst/DREAMmodel/LiverPKNDREAM.sif
inst/DREAMmodel/LiverDataDREAMMIDAS.csv
