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| BoolNet-package | Analyze Boolean networks |
| attractorsToLaTeX | Create LaTeX state table of attractors |
| binarizeTimeSeries | Binarize a set of real-valued time series |
| BoolNet | Analyze 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 |
| generateRandomNKNetwork | Generate a random N-K Boolean network |
| getAttractors | Identify attractors in a Boolean network |
| getBasinOfAttraction | Get states in basin of attraction |
| 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 |
| loadBioTapestry | Import a network from BioTapestry |
| loadNetwork | Load a Boolean network from a file |
| markovSimulation | Identify important states in probabilistic Boolean networks |
| perturbNetwork | Perturb a Boolean network randomly |
| 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 |
| 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.TransitionTable | Print a transition table |
| reconstructNetwork | Reconstruct a Boolean network from time series of measurements |
| simplifyNetwork | Simplify the functions of a synchronous, asynchronous, or probabilistic Boolean network |
| stateTransition | Perform a transition to the next state |
| 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 |
| toPajek | Export a network to the Pajek file format |
| yeastTimeSeries | Yeast cell cycle time series data |