Man pages for saezlab/CellNOptR
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... |
| 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"' |
| 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... |
| createAndRunILP | Creating and running the ILP problem. |
| create_binaries | Defining the set of binary variables for the ILP... |
| createILPBitstringAll | Reading the optimal solutions as bitstrings. |
| crossInhibitedData | If an inhibitor is also a measured species, replace the data... |
| crossvalidateBoolean | k-fold crossvalidation for Boolean model. |
| 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 |
| 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... |
| 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 |
| 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. |
| 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... |
| 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... |
| 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... |
| write_constraints | Writing the set of constraints for the ILP implementation of... |
| 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... |
| writeObjectiveFunction | Writing the objective function for the ILP implementation of... |
| 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... |
