Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data.

buildBitString | Build the final bit string vector and times vector based on a... |

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"' |

CNOlistDREAM | Data used for the DREAM3 challenge |

CNOlist-methods | List of CNOlist-class methods |

CNOlistToy | Toy data |

CNOlistToy2 | Toy data with 2 time points |

CNOlistToyMMB | Toy data |

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... |

computeScoreTN | Compute the score at TN of a model/data set using a bitString... |

cSimulator | C-implementation of simulatorT1. |

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... |

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... |

expandGates | Expand the gates of a model |

findNONC | Find the indexes of the non-observable and non controllable... |

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... |

internals | List of CellNOptR internal functions. |

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. |

plotCNOlist | Plot the data in a CNOlist |

plotCNOlist2 | Another version of plotCNOlist that allows to plot 2 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... |

plotCNOlistPDF | Plots a CNOlist into a pdf file. |

plotFit | Plot the evolution of an optimisation |

plot-methods | plot a '"CNOlist"' object - methods |

plotModel | Plot a model |

plotOptimResults | Plot the data and simulated values |

plotOptimResultsPan | Plots the data and simulated values from any CellNOptR... |

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. |

readMIDAS | Reads in a CSV MIDAS file |

readSBMLQual | Read a SBMLQual document and returns a SIF object (as... |

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... |

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.... |

simulatorTN | Simulation of a boolean model at any time points dependent on... |

ToyModel | Toy model |

ToyModel2 | Toy model |

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... |

writeReport | Write a report of a CellNOptR analysis |

writeScaffold | Writes the scaffold network to a sif file (with attributes)... |

writeSIF | Convert a model into a SIF format and save the result in a... |

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