saezlab/CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

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Search the saezlab/CellNOptR package
Functions
287
Source code
99
Man pages
90
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saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
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API

API for saezlab/CellNOptR
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Global functions
.add_dummies Source code
.cutCNOlistModel Source code
.cutCNOlistTimeIndices Source code
.error.bar Source code Source code
.int2dec Source code Source code
CNORbool Man page Source code
CNORwrap Man page Source code
CNOdata Man page Source code
CNOlist Man page Source code
CNOlist,ANY Man page
CNOlist-class Man page
CNOlist-methods Man page
CNOlistDREAM Man page
CNOlistToy Man page
CNOlistToy2 Man page
CNOlistToyMMB Man page
CellNOptR Man page
CellNOptR-package Man page
DreamModel Man page
ToyModel Man page
ToyModel2 Man page
addPriorKnowledge Source code Source code
buildBitString Man page Source code
build_sif_table_from_rule Man page Source code
cSimulator Man page Source code
checkSignals Man page Source code
clean_dot Source code
cleanupILP Source code
cnodata Man page
compareNA Source code
compatCNOlist Man page
compatCNOlist,CNOlist Man page
compatCNOlist,CNOlist,CNOlist-method Man page
compatCNOlist,CNOlist-method Man page
compressModel Man page Source code
computeScoreT1 Man page Source code
computeScoreTN Man page Source code
createAndRunILP Man page Source code
createEdgeAttrs Source code
createILPBitstringAll Man page Man page Source code
createNodeAttrs Source code
create_binaries Man page Man page Source code
create_binary_variables_for_all_reactions_z_i_in_experiment_k_i Source code
create_binary_variables_for_all_species_in_experiment_k_i Source code
create_binary_variables_for_y_vector Source code
create_layout Source code
crossInhibitedData Man page Source code
crossvalidateBoolean Man page Source code
cutAndPlot Man page Source code
cutAndPlotResultsT1 Man page Source code
cutAndPlotResultsTN Man page Source code
cutCNOlist Man page Source code
cutModel Man page Source code
cutNONC Man page Source code
cutSimList Man page Source code
defaultParameters Man page Source code
exhaustive Man page Source code
expandGates Man page Source code
findNONC Man page Source code
gaBinaryT1 Man page Source code
gaBinaryT2 Source code
gaBinaryTN Man page Source code
getCues Man page
getCues,CNOlist Man page
getCues,CNOlist-method Man page
getDotInfo Source code
getFit Man page Source code
getInhibitors Man page
getInhibitors,CNOlist Man page
getInhibitors,CNOlist-method Man page Man page
getNetworkInfo Source code
getSifInfo Source code
getSignals Man page
getSignals,CNOlist Man page
getSignals,CNOlist,CNOlist-method Man page
getSignals,CNOlist-method Man page
getStimuli Man page
getStimuli,CNOlist Man page
getStimuli,CNOlist,CNOlist-method Man page
getStimuli,CNOlist-method Man page
getTimepoints Man page
getTimepoints,CNOlist Man page
getTimepoints,CNOlist,CNOlist-method Man page
getTimepoints,CNOlist-method Man page
getVariances Man page
getVariances,CNOlist Man page
getVariances,CNOlist,CNOlist-method Man page
getVariances,CNOlist-method Man page
graph2sif Man page Source code
ilpBinaryT1 Man page Source code
ilpBinaryT2 Man page Source code
ilpBinaryTN Man page Source code
indexFinder Man page Source code
inhibitors Source code
internal_CNOlist_from_file Source code
internal_CNOlist_from_makeCNOlist Source code
internal_compatCNOlist Source code
internal_simulateT1 Source code
internal_simulateTN Source code
internals Man page
invokeCPLEX Man page Man page Source code
length Man page
length,CNOlist Man page
length,CNOlist,ANY-method Man page
length,CNOlist-method Man page
link_midas_colnames_to_namesSpecies Source code
makeCNOlist Man page Source code
mapBack Man page Source code
model2igraph Man page Source code
model2sif Man page Source code
normaliseCNOlist Man page Source code
pknmodel Man page
plot Man page
plot,CNOlist Man page
plot,CNOlist,ANY Man page
plot,CNOlist,ANY,CNOlist-method Man page
plot,CNOlist,ANY-method Man page
plot,CNOlist,CNOlist Man page
plot,CNOlist,CNOlist,CNOlist-method Man page Man page Man page
plot,CNOlist,CNOlist,CNOlist-methods Man page
plot,CNOlist,CNOlist-method Man page
plot,CNOlist,missing,CNOlist-method Man page
plot,CNOlist,missing-method Man page
plot,CNOlist-method Man page
plot.CNOlist Man page
plotCNOlist Man page Source code
plotCNOlist2 Man page Source code
plotCNOlistLarge Man page Source code
plotCNOlistLargePDF Man page Source code
plotCNOlistPDF Man page Source code
plotFit Man page Source code
plotModel Man page Source code
plotOptimResults Man page Source code
plotOptimResultsPDF Man page Source code
plotOptimResultsPan Man page Source code
prep4Sim Man page Source code
prep4sim Man page Source code
preprocessing Man page Source code
rSimulatorT1 Source code
randomize Man page
randomize,CNOlist Man page
randomize,CNOlist,CNOlist-method Man page
randomize,CNOlist-method Man page
randomizeCNOlist Man page Source code
readBND Man page Source code
readBNET Man page Source code
readErrors Man page
readErrors,CNOlist Man page
readErrors,CNOlist,CNOlist-method Man page
readErrors,CNOlist-method Man page
readMIDAS Man page Source code
readMidas Man page
readSBMLQual Man page Man page Source code
readSIF Man page Source code
readSif Man page Source code
residualError Man page Source code
setEdgeRenderInfo Source code
setNodeRenderInfo Source code
setSignals<- Man page
setSignals<-,CNOlist Man page
setSignals<-,CNOlist,CNOlist-method Man page
setSignals<-,CNOlist-method Man page
sif2graph Man page Source code
signals Source code
simulateT1 Man page Source code
simulateT2 Source code
simulateTN Man page Source code
simulatorT0 Man page Source code
simulatorT1 Man page Source code
simulatorT2 Man page Source code
simulatorTN Man page Source code
stimuli Source code
toSBML Man page Source code
toSBMLStandard Source code
writeBoundsForEdges_y_i Source code
writeConstraint3 Source code
writeCplexCommandFile Source code
writeDot Man page Source code
writeErrors Man page
writeErrors,CNOlist Man page
writeErrors,CNOlist,CNOlist-method Man page
writeErrors,CNOlist-method Man page
writeFile Man page Source code
writeLogic Source code
writeMIDAS Man page Source code
writeNetwork Man page Source code
writeNetworkW Source code
writeObjectiveFunction Man page Man page Source code
writeReport Man page Source code
writeSIF Man page Source code
writeScaffold Man page Source code
writeScaffoldW Source code
writeSif Man page
write_bounds Man page Source code
write_constraints Man page Man page Source code
saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.

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