BoolNet-package | Construction, Simulation and Analysis of Boolean Networks |

attractorsToLaTeX | Create LaTeX state table of attractors |

binarizeTimeSeries | Binarize a set of real-valued time series |

BoolNet | Construction, Simulation and Analysis of Boolean Networks |

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 |