build_sif_table_from_rule
                        Build a SIF table from a logic rule written in
                        a string
CellNOptR-package       R version of CellNOptR, boolean features
checkSignals            Check the CNOlist and model matching
CNOdata                 Get data from a CellNOpt data repository
CNOlist-class           Class '"CNOlist"'
CNOlist-methods         List of CNOlist-class methods
CNOlistDREAM            Data used for the DREAM3 challenge
CNOlistToy              Toy data
CNOlistToy2             Toy data with 2 time points
CNORbool                Simple Boolean analysis standalone
CNORwrap                CNOR analysis wrapper
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.
create_binaries         Defining the set of binary variables for the
                        ILP implementation of CellNOptR.
createAndRunILP         Creating and running the ILP problem.
createILPBitstringAll   Reading the optimal solutions as bitstrings.
crossInhibitedData      If an inhibitor is also a measured species,
                        replace the data with NA (when inhibited)
crossvalidateBoolean    k-fold crossvalidation for Boolean model.
cutAndPlot              Interface to cutAndPlotResults functions.
cutAndPlotResultsT1     Plot the results of an optimisation at t1
cutAndPlotResultsTN     Plot the results of an optimisation at tN
cutCNOlist              Cut a CNOlist structure according to a model
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
DreamModel              Model used for the DREAM3 challenge
exhaustive              Exhaustive search over the optimisation of a
                        PKN model on MIDAS data.
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
gaBinaryTN              Genetic algorithm for time point N
getFit                  Compute the score of a model
graph2sif               Convert graph to SIF
ilpBinaryT1             ILP method used to optimise a model
ilpBinaryT2             ILP method used to optimise a model
ilpBinaryTN             ILP method used to optimise a model
indexFinder             Finds the indices, in the model fields, of the
                        species that are measured/inhibited/stimulated
internals               List of CellNOptR internal functions.
invokeCPLEX             Solving the ILP problem with CPLEX.
makeCNOlist             Make a CNOlist structure
mapBack                 Map an optimised model back onto the PKN model.
model2igraph            Convert a model object to a igraph object
model2sif               Convert a model object in sif format
normaliseCNOlist        Normalisation for boolean modelling.
pknmodel                pknmodel
plot.CNOlist            plot a '"CNOlist"' object - methods
plotCNOlist             Plot the data in a CNOlist
plotCNOlist2            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).
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
plotOptimResultsPan     Plots the data and simulated values from any
                        CellNOptR formalism
plotOptimResultsPDF     Plot the data and simulated values in a pdf
                        file
prep4sim                Prepare a model for simulation
preprocessing           Performs the pre-processing steps
randomizeCNOlist        add noise to the data contained in a CNOlist.
readBND                 Read network from BND file
readBNET                Read network from BNET file
readMIDAS               Reads in a CSV MIDAS file
readSBMLQual            Read a SBMLQual document and returns a SIF
                        object (as returned by readSIG
readSIF                 Read a SIF file and create a model object
residualError           Compute the residual error for a dataset
sif2graph               Convert sif to graph
simulateTN              Cut and simulation of a boolean model at t1
simulatorT0             Simulation of a boolean model
simulatorT1             Simulation of a boolean model
simulatorTN             Simulation of a boolean model at any time
                        points dependent on a previous one.
toSBML                  Export the network to SBML-qual format
ToyModel                Toy model
ToyModel2               Toy model
write_bounds            Writing the set of boundaries for each integer
                        variable for the ILP implementation of
                        CellNOptR.
write_constraints       Writing the set of constraints for the ILP
                        implementation of CellNOptR.
writeDot                Write a model, and attached features, to a dot
                        file
writeFile               Writing the ILP problem.
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
writeObjectiveFunction
                        Writing the objective function for the ILP
                        implementation of CellNOptR.
writeReport             Write a report of a CellNOptR analysis
writeScaffold           Writes the scaffold network to a sif file (with
                        attributes) and to a dot file
writeSIF                Convert a model into a SIF format and save the
                        result in a file.
