Package: CNORode 1.47.0

Attila Gabor

CNORode: ODE add-on to CellNOptR

Logic based ordinary differential equation (ODE) add-on to CellNOptR.

Authors:David Henriques, Thomas Cokelaer, Attila Gabor, Federica Eduati, Enio Gjerga

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CNORode.pdf |CNORode.html✨
CNORode/json (API)
NEWS

# Install 'CNORode' in R:
install.packages('CNORode', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:CNORode-1.47.0(bioc 3.20)CNORode-1.46.0(bioc 3.19)

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

bioconductor-package

19 exports 1.75 score 63 dependencies 1 dependents 5 mentions

Last updated 2 months agofrom:b6b1538126

Exports:createLBodeContParsdefaultParametersGAdefaultParametersSSmgetLBodeContObjFunctiongetLBodeDataSimgetLBodeMINLPObjFunctiongetLBodeModelSimgetLBodeSimFunctiongetStatesincidence2AdjacencyminlpLBodeSSmparEstimationLBodeparEstimationLBodeGAparEstimationLBodeSSmplotLBodeFitnessplotLBodeModelSimrunCNORodesimdata2cnolistsimulate

Dependencies:base64encBHBiocGenericsbitopsbslibcachemCellNOptRclicolorspacecpp11digestevaluatefansifarverfastmapfontawesomefsgenalgggplot2gluegraphgtablehighrhtmltoolsigraphisobandjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigR6rappdirsRBGLRColorBrewerRCurlRgraphvizrlangrmarkdownsassscalesstringistringrtibbletinytexutf8vctrsviridisLitewithrxfunXMLyaml

Training Signalling Pathway Maps to Biochemical Data with Logic-Based Ordinary Differential Equations

David Henriques, Thomas Cokelaer, Enio Gjerga, Attila Gabor

Rendered fromCNORode-vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2024-02-27
Started: 2024-01-24

Readme and manuals

Help Manual

Help pageTopics
A cnodata from CellNoptRcnodata
A cnolist from CellNoptRcnolist
A cnolist from CellNoptRcnolistCNORodeExample
Logic based ODE extension for CellNOptRCNORode
Create a list with ODE parameter information needed to perform parameter estimationcreateLBodeContPars
Crossvalidate ODE modelcrossvalidateODE
Create default options to perform parameter estimation with a genetic algorithm.defaultParametersGA
Create default options to perform parameter estimation with scatter search meta-heuristic.defaultParametersSSm
Returns the objective function to perform parameter estimation.getLBodeContObjFunction
Simulate value signals a CNO list With Logic-Based ODEs.getLBodeDataSim
Get the objective function to evaluate the fitness of a given model structure and set of parameters.getLBodeMINLPObjFunction
Simulate the logic-based ODE modelgetLBodeModelSim
Get a function to simulate a logic based ODE model.getLBodeSimFunction
Find which species in the model are states.getStates
Convert an incidence matrix into an adjacency matrix.incidence2Adjacency
Indices that relate cnolist to modelindices
Search for the best combination of continuous parameters and logic gates.minlpLBodeSSm
A model from CellNoptRmodel
Perform parameter estimation using a genetic algorithm (package genalg) or ssm (if package essm available).parEstimationLBode
Perform parameter estimation using a genetic algorithm (package genalg).parEstimationLBodeGA
Perform parameter estimation using essR.parEstimationLBodeSSm
A pknmodel from CellNoptRpknmodel
Plot data against simulated values.plotLBodeFitness
Simulate the model and plot the obtained with the different experimental conditions.plotLBodeModelSim
runCNORoderunCNORode
converts output of getLBodeModelSim to cnolistsimdata2cnolist
Simulate value signals a CNO list With Logic-Based ODEs.simulate