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

Functions

attractorsToLaTeX Man page
binarizeTimeSeries Man page
BoolNet Man page
BoolNet-package Man page
cellcycle Man page
chooseNetwork Man page
examplePBN Man page
fixGenes Man page
generateCanalyzing Man page
generateNestedCanalyzing Man page
generateRandomNKNetwork Man page
generateState Man page
generateTimeSeries Man page
getAttractors Man page
getAttractorSequence Man page
getBasinOfAttraction Man page
getPathToAttractor Man page
getStateSummary Man page
getTransitionProbabilities Man page
getTransitionTable Man page
igf Man page
loadBioTapestry Man page
loadNetwork Man page
loadSBML Man page
markovSimulation Man page
perturbNetwork Man page
perturbTrajectories Man page
plotAttractors Man page
plotNetworkWiring Man page
plotPBNTransitions Man page
plotSequence Man page
plotStateGraph Man page
print.AttractorInfo Man page
print.BooleanNetwork Man page
print.BooleanNetworkCollection Man page
print.BooleanStateInfo Man page
print.MarkovSimulation Man page
print.ProbabilisticBooleanNetwork Man page
print.SymbolicSimulation Man page
print.TransitionTable Man page
reconstructNetwork Man page
saveNetwork Man page
sequenceToLaTeX Man page
sequenceToLaTeX.BooleanNetwork Man page
sequenceToLaTeX.data.frame Man page
simplifyNetwork Man page
simulateSymbolicModel Man page
stateTransition Man page
symbolicToTruthTable Man page
testAttractorRobustness Man page
testIndegree Man page
testNetworkProperties Man page
testTransitionRobustness Man page
toPajek Man page
toSBML Man page
truthTableToSymbolic Man page
yeastTimeSeries Man page

Files

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

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