Package: BoolNet 2.1.9

BoolNet: Construction, Simulation and Analysis of Boolean Networks

Functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks <doi:10.1093/bioinformatics/btq124>.

Authors:Christoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], Hans A. Kestler [aut, cre], Armin Biere [ctb], Troy D. Hanson [ctb]

BoolNet_2.1.9.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BoolNet/json (API)

# Install 'BoolNet' in R:

install.packages('BoolNet', repos = c('https://hkestler.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

cellcycle - Mammalian cell cycle network
examplePBN - An artificial probabilistic Boolean network
igf - Boolean model of the IGF pathway
yeastTimeSeries - Yeast cell cycle time series data

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

5.85 score 3 stars 4 packages 197 scripts 575 downloads 73 mentions 41 exports 12 dependencies

Last updated from:af3a714c5b. Checks:11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	138
linux-devel-x86_64	NOTE	157
source / vignettes	OK	177
linux-release-arm64	NOTE	143
linux-release-x86_64	NOTE	129
macos-release-arm64	NOTE	117
macos-release-x86_64	NOTE	191
macos-oldrel-arm64	NOTE	96
macos-oldrel-x86_64	NOTE	256
windows-devel	NOTE	105
windows-release	NOTE	122
windows-oldrel	NOTE	107
wasm-release	OK	108

Exports:attractorsToLaTeX binarizeTimeSeries chooseNetwork fixGenes generateCanalyzing generateNestedCanalyzing generateRandomNKNetwork generateState generateTimeSeries getAttractors getAttractorSequence getBasinOfAttraction getPathToAttractor getStateSummary getTransitionProbabilities getTransitionTable loadBioTapestry loadNetwork loadSBML markovSimulation perturbNetwork perturbTrajectories plotAttractors plotNetworkWiring plotPBNTransitions plotSequence plotStateGraph reconstructNetwork saveNetwork sequenceToLaTeX simplifyNetwork simulateSymbolicModel stateTransition symbolicToTruthTable testAttractorRobustness testIndegree testNetworkProperties testTransitionRobustness toPajek toSBML truthTableToSymbolic

Dependencies:cli cpp11 glue igraph lattice lifecycle magrittr Matrix pkgconfig rlang vctrs XML

Detailed introduction to all major features of BoolNet

Introduction | Assembling networks | Network analysis | Import and export | Appendix

Rendered fromBoolNet_package_vignette.Snwusingutils::Sweave

Last update: 2022-09-04
Started: 2013-11-20

Help page	Topics
Create LaTeX state table of attractors	attractorsToLaTeX
Binarize a set of real-valued time series	binarizeTimeSeries
Mammalian cell cycle network	cellcycle
Extract a single Boolean network from a probabilistic Boolean network	chooseNetwork
An artificial probabilistic Boolean network	examplePBN
Simulate knocked-out or over-expressed genes	fixGenes
Generate a random N-K Boolean network	generateRandomNKNetwork
Generate a state vector from single gene values	generateState
Generate time series from a network	generateTimeSeries
Generation functions for biologically relevant function classes	generateCanalyzing generateNestedCanalyzing
Identify attractors in a Boolean network	getAttractors
Decode the state sequence of a synchronous attractor	getAttractorSequence
Get states in basin of attraction	getBasinOfAttraction
Get state transitions between a state and its attractor	getPathToAttractor
Retrieve summary information on a state	getStateSummary
Get a matrix of transitions and their probabilities in probabilistic Boolean networks	getTransitionProbabilities
Retrieve the transition table of a network	getTransitionTable
Boolean model of the IGF pathway	igf
Import a network from BioTapestry	loadBioTapestry
Load a Boolean network from a file	loadNetwork
Load an SBML document	loadSBML
Identify important states in probabilistic Boolean networks	markovSimulation
Perturb a Boolean network randomly	perturbNetwork
Perturb the state trajectories and calculate robustness measures	perturbTrajectories
Plot state tables or transition graphs of attractors	plotAttractors
Plot the wiring of a Boolean network	plotNetworkWiring
Visualize the transitions in a probabilistic Boolean network	plotPBNTransitions
Plot a sequence of states	plotSequence
Visualize state transitions and attractor basins	plotStateGraph
Print attractor cycles	print.AttractorInfo
Print a Boolean network	print.BooleanNetwork
Print the results of a Markov chain simulation	print.MarkovSimulation
Print a probabilistic Boolean network	print.BooleanNetworkCollection print.ProbabilisticBooleanNetwork
Print simulation results	print.SymbolicSimulation
Print a transition table	print.BooleanStateInfo print.TransitionTable
Reconstruct a Boolean network from time series of measurements	reconstructNetwork
Save a network	saveNetwork
Create LaTeX table of state sequences	sequenceToLaTeX sequenceToLaTeX.BooleanNetwork sequenceToLaTeX.data.frame
Simplify the functions of a synchronous, asynchronous, or probabilistic Boolean network	simplifyNetwork
Simulate a symbolic Boolean network	simulateSymbolicModel
Perform a transition to the next state	stateTransition
Convert a symbolic network into a truth table representation	symbolicToTruthTable
Test properties of networks by comparing them to random networks	testAttractorRobustness testIndegree testNetworkProperties testTransitionRobustness
Export a network to the Pajek file format	toPajek
Export a network to SBML	toSBML
Convert a network in truth table representation into a symbolic representation	truthTableToSymbolic
Yeast cell cycle time series data	yeastTimeSeries

Package: BoolNet 2.1.9

BoolNet: Construction, Simulation and Analysis of Boolean Networks

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Help Manual

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