Construction, Simulation and Analysis of Boolean Networks

attractorsToLaTeX | Create LaTeX state table of attractors |

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

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

cellcycle | Mammalian cell cycle network |

chooseNetwork | Extract a single Boolean network from a probabilistic Boolean... |

examplePBN | An artificial probabilistic Boolean network |

fixGenes | Simulate knocked-out or over-expressed genes |

generateRandomNKNetwork | Generate a random N-K Boolean network |

generateState | Generate a state vector from single gene values |

generateTimeSeries | Generate time series from a network |

generationFunctions | Generation functions for biologically relevant function... |

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... |

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... |

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.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... |

saveNetwork | Save a network |

sequenceToLaTeX | Create LaTeX table of state sequences |

simplifyNetwork | Simplify the functions of a synchronous, asynchronous, or... |

simulateSymbolicModel | Simulate a symbolic Boolean network |

stateTransition | Perform a transition to the next state |

symbolicToTruthTable | Convert a symbolic network into a truth table representation |

testNetworkProperties | Test properties of networks by comparing them to random... |

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... |

yeastTimeSeries | Yeast cell cycle time series data |

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