CNORfuzzy: Addon to CellNOptR: Fuzzy Logic

This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).

Author
M. Morris, T. Cokelaer
Date of publication
None
Maintainer
T. Cokelaer <cokelaer@ebi.ac.uk>
License
GPL-2
Version
1.16.0

View on Bioconductor

Man pages

CNORfuzzy-package
R version of CNOFuzzy, a Constrained Fuzzy Logic Network...
CNORwrapFuzzy
CNORfuzzy analysis wrapper
compileMultiRes
Compiles results from multiple runs and produces graph for...
computeScoreFuzzy
Compute Score of a model compared to the data for a given...
defaultParametersFuzzy
Create a list of default parameters
gaDiscreteT1
Genetic algorithm used to optimise a cFL model
getRefinedModel
Refinement of Parameters of cFL model
interpretDiscreteGA
Interpreter of output of discrete genetic algorithm
plotMeanFuzzyFit
Simulates models returned from multiple cFL runs and plots...
prep4simFuzzy
Prepare a model for simulation
reduceFuzzy
Remove unnecessary interactions from cFL model
simFuzzyT1
Simulation of a cFL model
writeFuzzyNetwork
Despict the network results of training a cFL model to data...

Files in this package

CNORfuzzy/.Rinstignore
CNORfuzzy/ChangeLog
CNORfuzzy/DESCRIPTION
CNORfuzzy/NAMESPACE
CNORfuzzy/R
CNORfuzzy/R/CNORwrapFuzzy.R
CNORfuzzy/R/cSimulator.R
CNORfuzzy/R/compileMultiRes.R
CNORfuzzy/R/computeScoreFuzzy.R
CNORfuzzy/R/defaultParametersFuzzy.R
CNORfuzzy/R/gaDiscreteT1.R
CNORfuzzy/R/getEC50.R
CNORfuzzy/R/getMeanFuzzy.R
CNORfuzzy/R/getMeanModel.R
CNORfuzzy/R/getRefinedModel.R
CNORfuzzy/R/interpretDiscreteGA.R
CNORfuzzy/R/plotMeanFuzzyFit.R
CNORfuzzy/R/prep4simFuzzy.R
CNORfuzzy/R/rSimFuzzyT1.R
CNORfuzzy/R/rSimulator.R
CNORfuzzy/R/reduceFuzzy.R
CNORfuzzy/R/removeRedundant.R
CNORfuzzy/R/simFuzzyT1.R
CNORfuzzy/R/simulate.R
CNORfuzzy/R/writeFuzzyNetwork.R
CNORfuzzy/build
CNORfuzzy/build/vignette.rds
CNORfuzzy/inst
CNORfuzzy/inst/NEWS.Rd
CNORfuzzy/inst/doc
CNORfuzzy/inst/doc/CNORfuzzy-vignette.R
CNORfuzzy/inst/doc/CNORfuzzy-vignette.Rnw
CNORfuzzy/inst/doc/CNORfuzzy-vignette.pdf
CNORfuzzy/inst/unitTests
CNORfuzzy/inst/unitTests/test_CNORwrapFuzzy.R
CNORfuzzy/inst/unitTests/test_computeScore.R
CNORfuzzy/man
CNORfuzzy/man/CNORfuzzy-package.Rd
CNORfuzzy/man/CNORwrapFuzzy.Rd
CNORfuzzy/man/compileMultiRes.Rd
CNORfuzzy/man/computeScoreFuzzy.Rd
CNORfuzzy/man/defaultParametersFuzzy.Rd
CNORfuzzy/man/gaDiscreteT1.Rd
CNORfuzzy/man/getRefinedModel.Rd
CNORfuzzy/man/interpretDiscreteGA.Rd
CNORfuzzy/man/plotMeanFuzzyFit.Rd
CNORfuzzy/man/prep4simFuzzy.Rd
CNORfuzzy/man/reduceFuzzy.Rd
CNORfuzzy/man/simFuzzyT1.Rd
CNORfuzzy/man/writeFuzzyNetwork.Rd
CNORfuzzy/src
CNORfuzzy/src/simulatorT1.c
CNORfuzzy/tests
CNORfuzzy/tests/runTests.R
CNORfuzzy/vignettes
CNORfuzzy/vignettes/CNORfuzzy-vignette-FullAnalysis.pdf
CNORfuzzy/vignettes/CNORfuzzy-vignette-FullAnalysis2.pdf
CNORfuzzy/vignettes/CNORfuzzy-vignette-FullAnalysis3.pdf
CNORfuzzy/vignettes/CNORfuzzy-vignette.Rnw
CNORfuzzy/vignettes/README.txt
CNORfuzzy/vignettes/output_dream_PKN.dot
CNORfuzzy/vignettes/output_dream_PKN.png
CNORfuzzy/vignettes/output_dream_PKN.sif
CNORfuzzy/vignettes/output_dream_PKN.svg
CNORfuzzy/vignettes/output_dream_TimesPKN.EA
CNORfuzzy/vignettes/output_dream_nodesPKN.NA
CNORfuzzy/vignettes/tf1.pdf
CNORfuzzy/vignettes/tf2.pdf