| R version of CellNOptR, boolean features | CellNOptR-package CellNOptR |
| Build a SIF table from a logic rule written in a string | build_sif_table_from_rule |
| Check the CNOlist and model matching | checkSignals |
| Get data from a CellNOpt data repository | CNOdata cnodata |
| Class '"CNOlist"' | CNOlist CNOlist-class compatCNOlist,CNOlist-method getCues,CNOlist-method getInhibitors,CNOlist-method getSignals,CNOlist-method getStimuli,CNOlist-method getTimepoints,CNOlist-method getVariances,CNOlist-method length,CNOlist-method plot,CNOlist,CNOlist-method randomize,CNOlist-method readErrors,CNOlist-method setSignals<-,CNOlist-method writeErrors,CNOlist-method |
| List of CNOlist-class methods | CNOlist-methods compatCNOlist compatCNOlist,CNOlist getCues getCues,CNOlist getInhibitors getInhibitors,CNOlist getSignals getSignals,CNOlist getStimuli getStimuli,CNOlist getTimepoints getTimepoints,CNOlist getVariances getVariances,CNOlist getVariances,CNOlist,CNOlist-method length length,CNOlist length,CNOlist,ANY-method plot,CNOlist,CNOlist,CNOlist-method randomize randomize,CNOlist randomize,CNOlist,CNOlist-method readErrors readErrors,CNOlist setSignals<- setSignals<-,CNOlist setSignals<-,CNOlist,CNOlist-method writeErrors writeErrors,CNOlist |
| Data used for the DREAM3 challenge | CNOlistDREAM |
| Toy data | CNOlistToy |
| Toy data with 2 time points | CNOlistToy2 |
| Simple Boolean analysis standalone | CNORbool |
| CNOR analysis wrapper | CNORwrap |
| Compress a model | compressModel |
| Compute the score of a model/data set using a bitString to cut the model. | computeScoreT1 |
| Compute the score at TN of a model/data set using a bitString to cut the model. | computeScoreTN |
| Defining the set of binary variables for the ILP implementation of CellNOptR. | create_binaries |
| Creating and running the ILP problem. | createAndRunILP |
| Reading the optimal solutions as bitstrings. | createILPBitstringAll |
| If an inhibitor is also a measured species, replace the data with NA (when inhibited) | crossInhibitedData |
| k-fold crossvalidation for Boolean model. | crossvalidateBoolean |
| Interface to cutAndPlotResults functions. | cutAndPlot |
| Plot the results of an optimisation at t1 | cutAndPlotResultsT1 |
| Plot the results of an optimisation at tN | cutAndPlotResultsTN |
| Cut a CNOlist structure according to a model | cutCNOlist |
| Cut a model structure according to a bitstring | cutModel |
| Cuts the non-observable/non-controllable species from the model | cutNONC |
| Cut a simList structure according to a bitstring | cutSimList |
| Create a list of default parameters | defaultParameters |
| Exhaustive search over the optimisation of a PKN model on MIDAS data. | exhaustive |
| Expand the gates of a model | expandGates |
| Find the indexes of the non-observable and non controllable species | findNONC |
| Genetic algorithm used to optimise a model | gaBinaryT1 |
| Genetic algorithm for time point N | gaBinaryTN |
| Compute the score of a model | getFit |
| Convert graph to SIF | graph2sif |
| ILP method used to optimise a model | ilpBinaryT1 |
| ILP method used to optimise a model | ilpBinaryT2 |
| ILP method used to optimise a model | ilpBinaryTN |
| Finds the indices, in the model fields, of the species that are measured/inhibited/stimulated | indexFinder |
| List of CellNOptR internal functions. | internals |
| Solving the ILP problem with CPLEX. | invokeCPLEX |
| Model used for the DREAM3 challenge | DreamModel |
| Make a CNOlist structure | makeCNOlist |
| Map an optimised model back onto the PKN model. | mapBack |
| Convert a model object to a igraph object | model2igraph |
| Convert a model object in sif format | model2sif |
| Normalisation for boolean modelling. | normaliseCNOlist |
| pknmodel | pknmodel |
| plot a '"CNOlist"' object - methods | plot,CNOlist,ANY-method plot.CNOlist |
| Plot the data in a CNOlist | plotCNOlist |
| Another version of plotCNOlist that allows to plot 2 cnolist in the same layout to compare them. This function uses ggplot2 library. It is recommended for small data sets (about 15 species). | plotCNOlist2 |
| Plot the data in a CNOlist, for lists with many conditions. | plotCNOlistLarge |
| Plots a CNOlist into a pdf file, for lists with many conditions. | plotCNOlistLargePDF |
| Plots a CNOlist into a pdf file. | plotCNOlistPDF |
| Plot the evolution of an optimisation | plotFit |
| Plot a model | plotModel |
| Plot the data and simulated values | plotOptimResults |
| Plots the data and simulated values from any CellNOptR formalism | plotOptimResultsPan |
| Plot the data and simulated values in a pdf file | plotOptimResultsPDF |
| Prepare a model for simulation | prep4Sim prep4sim |
| Performs the pre-processing steps | preprocessing |
| add noise to the data contained in a CNOlist. | randomizeCNOlist |
| Read network from BND file | readBND |
| Read network from BNET file | readBNET |
| Reads in a CSV MIDAS file | readMIDAS readMidas |
| Read a SBMLQual document and returns a SIF object (as returned by readSIG | readSBMLQual |
| Read a SIF file and create a model object | readSIF readSif |
| Compute the residual error for a dataset | residualError |
| Convert sif to graph | sif2graph |
| Cut and simulation of a boolean model at t1 | simulateTN |
| Simulation of a boolean model | simulatorT0 |
| Simulation of a boolean model | simulatorT1 |
| Simulation of a boolean model at any time points dependent on a previous one. | simulatorTN |
| Export the network to SBML-qual format | toSBML |
| Toy model | ToyModel |
| Toy model | ToyModel2 |
| Writing the set of boundaries for each integer variable for the ILP implementation of CellNOptR. | write_bounds |
| Writing the set of constraints for the ILP implementation of CellNOptR. | write_constraints |
| Write a model, and attached features, to a dot file | writeDot |
| Writing the ILP problem. | writeFile |
| Write a CNOlist structure into a MIDAS file | writeMIDAS |
| Write a previous knowledge network model to a sif file (with attribute files), as well as a dot file | writeNetwork |
| Writing the objective function for the ILP implementation of CellNOptR. | writeObjectiveFunction |
| Write a report of a CellNOptR analysis | writeReport |
| Writes the scaffold network to a sif file (with attributes) and to a dot file | writeScaffold |
| Convert a model into a SIF format and save the result in a file. | writeSIF writeSif |
