attractorsToLaTeX |
Create LaTeX state table of attractors |
binarizeTimeSeries |
Binarize a set of real-valued time series |
cellcycle |
Mammalian cell cycle network |
chooseNetwork |
Extract a single Boolean network from a probabilistic Boolean network |
examplePBN |
An artificial probabilistic Boolean network |
fixGenes |
Simulate knocked-out or over-expressed genes |
generateCanalyzing |
Generation functions for biologically relevant function classes |
generateNestedCanalyzing |
Generation functions for biologically relevant function classes |
generateRandomNKNetwork |
Generate a random N-K Boolean network |
generateState |
Generate a state vector from single gene values |
generateTimeSeries |
Generate time series from a network |
getAttractors |
Identify attractors in a Boolean network |
getAttractorSequence |
Decode the state sequence of a synchronous attractor |
getBasinOfAttraction |
Get states in basin of attraction |
getPathToAttractor |
Get state transitions between a state and its attractor |
getStateSummary |
Retrieve summary information on a state |
getTransitionProbabilities |
Get a matrix of transitions and their probabilities in probabilistic Boolean networks |
getTransitionTable |
Retrieve the transition table of a network |
igf |
Boolean model of the IGF pathway |
loadBioTapestry |
Import a network from BioTapestry |
loadNetwork |
Load a Boolean network from a file |
loadSBML |
Load an SBML document |
markovSimulation |
Identify important states in probabilistic Boolean networks |
perturbNetwork |
Perturb a Boolean network randomly |
perturbTrajectories |
Perturb the state trajectories and calculate robustness measures |
plotAttractors |
Plot state tables or transition graphs of attractors |
plotNetworkWiring |
Plot the wiring of a Boolean network |
plotPBNTransitions |
Visualize the transitions in a probabilistic Boolean network |
plotSequence |
Plot a sequence of states |
plotStateGraph |
Visualize state transitions and attractor basins |
print.AttractorInfo |
Print attractor cycles |
print.BooleanNetwork |
Print a Boolean network |
print.BooleanNetworkCollection |
Print a probabilistic Boolean network |
print.BooleanStateInfo |
Print a transition table |
print.MarkovSimulation |
Print the results of a Markov chain simulation |
print.ProbabilisticBooleanNetwork |
Print a probabilistic Boolean network |
print.SymbolicSimulation |
Print simulation results |
print.TransitionTable |
Print a transition table |
reconstructNetwork |
Reconstruct a Boolean network from time series of measurements |
saveNetwork |
Save a network |
sequenceToLaTeX |
Create LaTeX table of state sequences |
sequenceToLaTeX.BooleanNetwork |
Create LaTeX table of state sequences |
sequenceToLaTeX.data.frame |
Create LaTeX table of state sequences |
simplifyNetwork |
Simplify the functions of a synchronous, asynchronous, or probabilistic Boolean network |
simulateSymbolicModel |
Simulate a symbolic Boolean network |
stateTransition |
Perform a transition to the next state |
symbolicToTruthTable |
Convert a symbolic network into a truth table representation |
testAttractorRobustness |
Test properties of networks by comparing them to random networks |
testIndegree |
Test properties of networks by comparing them to random networks |
testNetworkProperties |
Test properties of networks by comparing them to random networks |
testTransitionRobustness |
Test properties of networks by comparing them to random networks |
toPajek |
Export a network to the Pajek file format |
toSBML |
Export a network to SBML |
truthTableToSymbolic |
Convert a network in truth table representation into a symbolic representation |
yeastTimeSeries |
Yeast cell cycle time series data |