BoolNet: Construction, Simulation and Analysis of Boolean Networks
Version 2.1.3

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BoolNet")

Getting started

Package overview

Popular 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
getBasinOfAttraction: Get states in basin of attraction
loadNetwork: Load a Boolean network from a file
perturbNetwork: Perturb a Boolean network randomly
yeastTimeSeries: Yeast cell cycle time series data
See all...

All man pages Function index File listing

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

Files

inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/BoolNet_package_vignette.R
inst/doc/BoolNet_package_vignette.Snw
inst/doc/example.btp
inst/doc/cellcycle.txt
inst/doc/BoolNet_package_vignette.pdf
src
src/boolean_network.h
src/common.h
src/symbolic_simulator.c
src/statespace_search.h
src/common.c
src/picosat.h
src/sat_search.h
src/attractor_info.c
src/random.h
src/uthash.h
src/symbolic_network.h
src/sat_search.c
src/statespace_search.c
src/attractor_search_interface.c
src/picosat.c
src/probabilistic_boolean_network.c
src/symbolic_network.c
src/attractor_info.h
src/Makevars.win
src/reconstruct_network.c
NAMESPACE
data
data/examplePBN.rda
data/igf.rda
data/yeastTimeSeries.rda
data/cellcycle.rda
R
R/print.SymbolicSimulation.R
R/getPathToAttractor.R
R/print.MarkovSimulation.R
R/loadSBML.R
R/getTransitionTable.R
R/getTransitionProbabilities.R
R/helpers.R
R/markovSimulation.R
R/generateRandomStartStates.R
R/getBasinOfAttraction.R
R/print.ProbabilisticBooleanNetwork.R
R/plotNetworkWiring.R
R/print.BooleanNetwork.R
R/plotPBNTransitions.R
R/generateState.R
R/zeta.R
R/toSBML.R
R/scanStatistic.R
R/fixGenes.R
R/loadNetwork.R
R/print.AttractorInfo.R
R/plotAttractors.R
R/sequenceToLaTeX.R
R/saveNetwork.R
R/perturbTrajectories.R
R/stateTransition.R
R/binarizeTimeSeries.R
R/toPajek.R
R/generateTimeSeries.R
R/print.SymbolicBooleanNetwork.R
R/reconstructNetwork.R
R/simplifyNetwork.R
R/print.BooleanStateInfo.R
R/simulateSymbolicModel.R
R/getAttractorSequence.R
R/symbolicToTruthTable.R
R/parseBooleanFunction.R
R/loadBioTapestry.R
R/attractorsToLaTeX.R
R/edgeDetector.R
R/plotSequence.R
R/testNetworkProperties.R
R/plotStateGraph.R
R/getAttractors.R
R/truthTableToSymbolic.R
R/perturbNetwork.R
R/getStateSummary.R
R/print.TransitionTable.R
R/generateRandomNKNetwork.R
R/chooseNetwork.R
vignettes
vignettes/BoolNet_package_vignette.bib
vignettes/BoolNet_package_vignette.Snw
vignettes/biotap_model.png
vignettes/pajek.png
vignettes/biotap_sim_properties.png
vignettes/biotap_initval.png
vignettes/biotap_logic.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/reconstructNetwork.Rd
man/plotAttractors.Rd
man/igf.Rd
man/stateTransition.Rd
man/plotPBNTransitions.Rd
man/getTransitionTable.Rd
man/getStateSummary.Rd
man/plotNetworkWiring.Rd
man/markovSimulation.Rd
man/symbolicToTruthTable.Rd
man/yeastTimeSeries.Rd
man/binarizeTimeSeries.Rd
man/toSBML.Rd
man/generationFunctions.Rd
man/fixGenes.Rd
man/generateState.Rd
man/getBasinOfAttraction.Rd
man/loadSBML.Rd
man/perturbNetwork.Rd
man/BoolNet-package.Rd
man/getAttractors.Rd
man/attractorsToLaTeX.Rd
man/cellcycle.Rd
man/testNetworkProperties.Rd
man/sequenceToLaTeX.Rd
man/simplifyNetwork.Rd
man/plotStateGraph.Rd
man/plotSequence.Rd
man/print.AttractorInfo.Rd
man/perturbTrajectories.Rd
man/examplePBN.Rd
man/print.TransitionTable.Rd
man/simulateSymbolicModel.Rd
man/print.MarkovSimulation.Rd
man/print.ProbabilisticBooleanNetwork.Rd
man/loadBioTapestry.Rd
man/truthTableToSymbolic.Rd
man/generateRandomNKNetwork.Rd
man/chooseNetwork.Rd
man/loadNetwork.Rd
man/toPajek.Rd
man/saveNetwork.Rd
man/print.SymbolicSimulation.Rd
man/getTransitionProbabilities.Rd
man/getAttractorSequence.Rd
man/print.BooleanNetwork.Rd
man/getPathToAttractor.Rd
man/generateTimeSeries.Rd
BoolNet documentation built on May 19, 2017, 8:45 p.m.

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