CNORbool                Simple Boolean analysis standalone
CNORwrap                CNOR analysis wrapper
CNOlist-class           Class '"CNOlist"'
CNOlistDREAM            Data used for the DREAM3 challenge
CNOlistToy              Toy data
CNOlistToy2             Toy data with 2 time points
CellNOptR-package       R version of CellNOptR, boolean features
DreamModel              Model used for the DREAM3 challenge
ToyModel                Toy model
ToyModel2               Toy model
cSimulator              C-implementation of simulatorT1.
checkSignals            Check the CNOlist and model matching
compressModel           Compress a model
computeScoreT1          Compute the score of a model/data set using a
                        bitString to cut the model.
computeScoreTN          Compute the score at TN of a model/data set
                        using a bitString to cut the model.
cutAndPlot              Interface to cutAndPlotResults functions.
cutAndPlotResultsT1     Plot the results of an optimisation at t1
cutAndPlotResultsT2     Plot the results of an optimisation at t2
                        (deprecated since v1.3.28; use
                        cutAndPlotResultsTN instead)
cutAndPlotResultsTN     Plot the results of an optimisation at tN
cutModel                Cut a model structure according to a bitstring
cutNONC                 Cuts the non-observable/non-controllable
                        species from the model
cutSimList              Cut a simList structure according to a
                        bitstring
defaultParameters       Create a list of default parameters
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
gaBinaryT2              Genetic algorithm for time point 2
gaBinaryTN              Genetic algorithm for time point N
getFit                  Compute the score of a model
graph2sif               Convert graph to SIF
indexFinder             Finds the indices, in the model fields, of the
                        species that are measured/inhibited/stimulated
makeCNOlist             Make a CNOlist structure
mapBack                 Map an optimised model back onto the PKN model.
model2sif               Convert a model object in sif format
normaliseCNOlist        Normalisation for boolean modelling.
plot.CNOlist            plot a '"CNOlist"' object - methods
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
plotModel               Plot a model
plotOptimResults        Plot the data and simulated values
plotOptimResultsPDF     Plot the data and simulated values in a pdf
                        file
plotOptimResultsPan     Plots the data and simulated values from any
                        CellNOptR formalism
prep4sim                Prepare a model for simulation
preprocessing           Performs the pre-processing steps
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
sif2graph               Convert sif to graph
simulateT1              deprecated since version 1.3.28. Cut and
                        simulation of a boolean model at t1
simulateTN              Cut and simulation of a boolean model at t1
simulatorT0             Simulation of a boolean model
simulatorT1             Simulation of a boolean model
simulatorT2             Deprecated since 1.3.28. Use simulateTN
                        function instead. Simulation of a boolean model
                        for time 2
simulatorTN             Simulation of a boolean model at any time
                        points dependent on a previous one.
writeDot                Write a model, and attached features, to a dot
                        file
writeMIDAS              Write a CNOlist structure into a MIDAS 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
writeSIF                Convert a model into a SIF format and save the
                        result in a file.
writeScaffold           Writes the scaffold network to a sif file (with
                        attributes) and to a dot file
