CellNOptR-package |
R version of CellNOptR, boolean features |
CellNOptR |
R version of CellNOptR, boolean features |
checkSignals |
Check the CNOlist and model matching |
CNOlist |
Class '"CNOlist"' |
CNOlist,ANY |
Class '"CNOlist"' |
CNOlist-class |
Class '"CNOlist"' |
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. |
cSimulator |
C-implementation of simulatorT1. |
cutAndPlot |
Interface to cutAndPlotResults functions. |
cutAndPlotResultsT1 |
Plot the results of an optimisation at t1 |
cutAndPlotResultsT2 |
Plot the results of an optimisation at t2 (deprecated since v1.3.28; use cutAndPlotResultsTN instead) |
cutAndPlotResultsTN |
Plot the results of an optimisation at tN |
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 |
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 |
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 are measured/inhibited/stimulated |
makeCNOlist |
Make a CNOlist structure |
mapBack |
Map an optimised model back onto the PKN model. |
model2sif |
Convert a model object in sif format |
normaliseCNOlist |
Normalisation for boolean modelling. |
plot-method |
plot a '"CNOlist"' object - methods |
plot.CNOlist |
plot a '"CNOlist"' object - methods |
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 |
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 |
prep4sim |
Prepare a model for simulation |
preprocessing |
Performs the pre-processing steps |
readMIDAS |
Reads in a CSV MIDAS file |
readMidas |
Reads in a CSV MIDAS file |
readSIF |
Read a SIF file and create a model object |
readSif |
Read a SIF file and create a model object |
residualError |
Compute the residual error for a dataset |
show-method |
Class '"CNOlist"' |
sif2graph |
Convert sif to graph |
simulateT1 |
deprecated since version 1.3.28. Cut and simulation of a boolean model at t1 |
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. Simulation of a boolean model for time 2 |
simulatorTN |
Simulation of a boolean model at any time points dependent on a previous one. |
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 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 |
writeSIF |
Convert a model into a SIF format and save the result in a file. |
writeSif |
Convert a model into a SIF format and save the result in a file. |