CellNOptR-package | R version of CellNOptR, boolean features |
CellNOptR | R version of CellNOptR, boolean features |
checkSignals | Check the CNOlist and model matching |
CNOlistDREAM | Data used for the DREAM3 challenge |
CNOlistToy | Toy data |
CNOlistToy2 | Toy data with 2 time points |
CNORwrap | CNOR analysis wrapper |
compressModel | Compress a model |
cutAndPlotResultsT1 | Plot the results of an optimisation at t1 |
cutAndPlotResultsT2 | Plot the results of an optimisation at t2 |
cutNONC | Cuts the non-observable/non-controllable species off 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 |
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 |
getFit | Compute the score of a model |
indexFinder | Finds the indices, in the Model fields, of the species that are measured/inhibited/stimulated |
makeCNOlist | Make a CNOlist structure |
normaliseCNOlist | Normalisation for boolean modelling. |
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 |
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 |
simulateT1 | Cut and simulation of a boolean model at t1 |
simulatorT1 | Simulation of a boolean model |
simulatorT2 | Simulation of a boolean model for time 2 |
ToyModel | Toy model |
ToyModel2 | Toy model |
writeDot | Write a model, and attached features, to a dot 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 |
writeScaffold | Writes the scaffold network to a sif file (with attributes) and to a dot file |