CNORwrap                CNOR analysis wrapper
CNOlistDREAM            Data used for the DREAM3 challenge
CNOlistToy              Toy data
CellNOptR-package       R version of CellNOptR, boolean features
DreamModel              Model used for the DREAM3 challenge
ToyModel                Toy mode
checkSignals            Check the CNOlist and model matching
compressModel           Compress a model
cutAndPlotResultsT1     Plot the results of an optimisation at t1
cutNONC                 Cuts the non-observable/non-controllable
                        species off the model
expandGates             Expand the gates of a model
findNONC                Find the indexes of the non-observable and non
                        controllable species
gaBinaryT1              Genetic algorithm used to optimise a model
getFit                  Compute the score of a model
indexFinder             Finds the indices, in the Model fields, of the
                        species that are measured/inhibited/stimulated
makeCNOlist             Make a CNOlist structure
normaliseCNOlist        Normalisation for boolean modelling.
plotCNOlist             Plot the data in a CNOlist
plotCNOlistLarge        Plot the data in a CNOlist, for lists with many
                        conditions.
plotCNOlistLargePDF     Plots a CNOlist into a pdf file, for lists with
                        many conditions.
plotCNOlistPDF          Plots a CNOlist into a pdf file.
plotFit                 Plot the evolution of an optimisation
plotOptimResults        Plot the data and simulated values
plotOptimResultsPDF     Plot the data and simulated values in a pdf
                        file
prep4Sim                Prepare a model for simulation
readMIDAS               Reads in a csv MIDAS file
readSif                 Read a sif file and create a model object
residualError           Compute the residual error for a dataset
simulateT1              Cut and simulation of a boolean model at t1
simulatorT1             Simulation of a boolean model
writeDot                Write a model, and attached features, to a dot
                        file
writeNetwork            Write a previous knowledge network model to a
                        sif file (with attribute files), as well as a
                        dot file
writeReport             Write a report of a CellNOptR analysis
writeScaffold           Writes the scaffold network to a sif file (with
                        attributes) and to a dot file
