BoolNet: Construction, Simulation and Analysis of Boolean Networks

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

Author
Christoph 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 publication
2016-11-21 12:23:47
Maintainer
Hans A. Kestler <hans.kestler@uni-ulm.de>
License
Artistic-2.0
Version
2.1.3

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