CNORbool                Simple Boolean analysis standalone
CNORwrap                CNOR analysis wrapper
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
CellNOptR-package       R version of CellNOptR, boolean features
DreamModel              Model used for the DREAM3 challenge
ToyModel                Toy model
ToyModel2               Toy model
build_sif_table_from_rule
                        Build a SIF table from a logic rule written in
                        a string
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.
createAndRunILP         Creating and running the ILP problem.
createILPBitstringAll   Reading the optimal solutions as bitstrings.
create_binaries         Defining the set of binary variables for the
                        ILP implementation of CellNOptR.
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
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
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
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
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
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
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.
