BoolNet: Construction, Simulation and Analysis of Boolean Networks

Provides methods to reconstruct and generate synchronous, asynchronous, probabilistic and temporal Boolean networks, and to analyze and visualize attractors in Boolean networks.

AuthorChristoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], Hans A. Kestler [aut, cre], Armin Biere [ctb] (contributed PicoSAT code), Troy D. Hanson [ctb] (contributed uthash macros)
Date of publication2016-11-21 12:23:47
MaintainerHans A. Kestler <hans.kestler@uni-ulm.de>
LicenseArtistic-2.0
Version2.1.3

View on CRAN

Man pages

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

Files in this package

BoolNet
BoolNet/inst
BoolNet/inst/CITATION
BoolNet/inst/NEWS.Rd
BoolNet/inst/doc
BoolNet/inst/doc/BoolNet_package_vignette.R
BoolNet/inst/doc/BoolNet_package_vignette.Snw
BoolNet/inst/doc/example.btp
BoolNet/inst/doc/cellcycle.txt
BoolNet/inst/doc/BoolNet_package_vignette.pdf
BoolNet/src
BoolNet/src/boolean_network.h
BoolNet/src/common.h
BoolNet/src/symbolic_simulator.c
BoolNet/src/statespace_search.h
BoolNet/src/common.c
BoolNet/src/picosat.h
BoolNet/src/sat_search.h
BoolNet/src/attractor_info.c
BoolNet/src/random.h
BoolNet/src/uthash.h
BoolNet/src/symbolic_network.h
BoolNet/src/sat_search.c
BoolNet/src/statespace_search.c
BoolNet/src/attractor_search_interface.c
BoolNet/src/picosat.c
BoolNet/src/probabilistic_boolean_network.c
BoolNet/src/symbolic_network.c
BoolNet/src/attractor_info.h
BoolNet/src/Makevars.win
BoolNet/src/reconstruct_network.c
BoolNet/NAMESPACE
BoolNet/data
BoolNet/data/examplePBN.rda
BoolNet/data/igf.rda
BoolNet/data/yeastTimeSeries.rda
BoolNet/data/cellcycle.rda
BoolNet/R
BoolNet/R/print.SymbolicSimulation.R BoolNet/R/getPathToAttractor.R BoolNet/R/print.MarkovSimulation.R BoolNet/R/loadSBML.R BoolNet/R/getTransitionTable.R BoolNet/R/getTransitionProbabilities.R BoolNet/R/helpers.R BoolNet/R/markovSimulation.R BoolNet/R/generateRandomStartStates.R BoolNet/R/getBasinOfAttraction.R BoolNet/R/print.ProbabilisticBooleanNetwork.R BoolNet/R/plotNetworkWiring.R BoolNet/R/print.BooleanNetwork.R BoolNet/R/plotPBNTransitions.R BoolNet/R/generateState.R BoolNet/R/zeta.R BoolNet/R/toSBML.R BoolNet/R/scanStatistic.R BoolNet/R/fixGenes.R BoolNet/R/loadNetwork.R BoolNet/R/print.AttractorInfo.R BoolNet/R/plotAttractors.R BoolNet/R/sequenceToLaTeX.R BoolNet/R/saveNetwork.R BoolNet/R/perturbTrajectories.R BoolNet/R/stateTransition.R BoolNet/R/binarizeTimeSeries.R BoolNet/R/toPajek.R BoolNet/R/generateTimeSeries.R BoolNet/R/print.SymbolicBooleanNetwork.R BoolNet/R/reconstructNetwork.R BoolNet/R/simplifyNetwork.R BoolNet/R/print.BooleanStateInfo.R BoolNet/R/simulateSymbolicModel.R BoolNet/R/getAttractorSequence.R BoolNet/R/symbolicToTruthTable.R BoolNet/R/parseBooleanFunction.R BoolNet/R/loadBioTapestry.R BoolNet/R/attractorsToLaTeX.R BoolNet/R/edgeDetector.R BoolNet/R/plotSequence.R BoolNet/R/testNetworkProperties.R BoolNet/R/plotStateGraph.R BoolNet/R/getAttractors.R BoolNet/R/truthTableToSymbolic.R BoolNet/R/perturbNetwork.R BoolNet/R/getStateSummary.R BoolNet/R/print.TransitionTable.R BoolNet/R/generateRandomNKNetwork.R BoolNet/R/chooseNetwork.R
BoolNet/vignettes
BoolNet/vignettes/BoolNet_package_vignette.bib
BoolNet/vignettes/BoolNet_package_vignette.Snw
BoolNet/vignettes/biotap_model.png
BoolNet/vignettes/pajek.png
BoolNet/vignettes/biotap_sim_properties.png
BoolNet/vignettes/biotap_initval.png
BoolNet/vignettes/biotap_logic.png
BoolNet/MD5
BoolNet/build
BoolNet/build/vignette.rds
BoolNet/DESCRIPTION
BoolNet/man
BoolNet/man/reconstructNetwork.Rd BoolNet/man/plotAttractors.Rd BoolNet/man/igf.Rd BoolNet/man/stateTransition.Rd BoolNet/man/plotPBNTransitions.Rd BoolNet/man/getTransitionTable.Rd BoolNet/man/getStateSummary.Rd BoolNet/man/plotNetworkWiring.Rd BoolNet/man/markovSimulation.Rd BoolNet/man/symbolicToTruthTable.Rd BoolNet/man/yeastTimeSeries.Rd BoolNet/man/binarizeTimeSeries.Rd BoolNet/man/toSBML.Rd BoolNet/man/generationFunctions.Rd BoolNet/man/fixGenes.Rd BoolNet/man/generateState.Rd BoolNet/man/getBasinOfAttraction.Rd BoolNet/man/loadSBML.Rd BoolNet/man/perturbNetwork.Rd BoolNet/man/BoolNet-package.Rd BoolNet/man/getAttractors.Rd BoolNet/man/attractorsToLaTeX.Rd BoolNet/man/cellcycle.Rd BoolNet/man/testNetworkProperties.Rd BoolNet/man/sequenceToLaTeX.Rd BoolNet/man/simplifyNetwork.Rd BoolNet/man/plotStateGraph.Rd BoolNet/man/plotSequence.Rd BoolNet/man/print.AttractorInfo.Rd BoolNet/man/perturbTrajectories.Rd BoolNet/man/examplePBN.Rd BoolNet/man/print.TransitionTable.Rd BoolNet/man/simulateSymbolicModel.Rd BoolNet/man/print.MarkovSimulation.Rd BoolNet/man/print.ProbabilisticBooleanNetwork.Rd BoolNet/man/loadBioTapestry.Rd BoolNet/man/truthTableToSymbolic.Rd BoolNet/man/generateRandomNKNetwork.Rd BoolNet/man/chooseNetwork.Rd BoolNet/man/loadNetwork.Rd BoolNet/man/toPajek.Rd BoolNet/man/saveNetwork.Rd BoolNet/man/print.SymbolicSimulation.Rd BoolNet/man/getTransitionProbabilities.Rd BoolNet/man/getAttractorSequence.Rd BoolNet/man/print.BooleanNetwork.Rd BoolNet/man/getPathToAttractor.Rd BoolNet/man/generateTimeSeries.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.