Package: CNORode 1.49.0

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'))

Datasets:

cnodata - A cnodata from CellNoptR
cnolist - A cnolist from CellNoptR
cnolistCNORodeExample - A cnolist from CellNoptR
indices - Indices that relate cnolist to model
model - A model from CellNoptR
pknmodel - A pknmodel from CellNoptR
pknmodel - A pknmodel from CellNoptR

On BioConductor:CNORode-1.49.0(bioc 3.21)CNORode-1.48.0(bioc 3.20)

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

immunooncology cellbasedassays cellbiology proteomics bioinformatics timecourse

6.22 score 1 packages 37 scripts 250 downloads 5 mentions 19 exports 64 dependencies

Last updated 2 months agofrom:851f0510c3. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 18 2024
R-4.5-win-x86_64	WARNING	Dec 18 2024
R-4.5-linux-x86_64	WARNING	Dec 18 2024
R-4.4-win-x86_64	WARNING	Dec 18 2024
R-4.4-mac-x86_64	WARNING	Dec 18 2024
R-4.4-mac-aarch64	WARNING	Dec 18 2024
R-4.3-win-x86_64	WARNING	Dec 18 2024
R-4.3-mac-x86_64	WARNING	Dec 18 2024
R-4.3-mac-aarch64	WARNING	Dec 18 2024

Exports:createLBodeContPars defaultParametersGA defaultParametersSSm getLBodeContObjFunction getLBodeDataSim getLBodeMINLPObjFunction getLBodeModelSim getLBodeSimFunction getStates incidence2Adjacency minlpLBodeSSm parEstimationLBode parEstimationLBodeGA parEstimationLBodeSSm plotLBodeFitness plotLBodeModelSim runCNORode simdata2cnolist simulate

Dependencies:base64enc BH BiocGenerics bitops bslib cachem CellNOptR cli colorspace cpp11 digest evaluate fansi farver fastmap fontawesome fs genalg generics ggplot2 glue graph gtable highr htmltools igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig R6 rappdirs RBGL RColorBrewer RCurl Rgraphviz rlang rmarkdown sass scales stringi stringr tibble tinytex utf8 vctrs viridisLite withr xfun XML yaml

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 Dec 18 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A cnodata from CellNoptR	cnodata
A cnolist from CellNoptR	cnolist
A cnolist from CellNoptR	cnolistCNORodeExample
Logic based ODE extension for CellNOptR	CNORode
Create a list with ODE parameter information needed to perform parameter estimation	createLBodeContPars
Crossvalidate ODE model	crossvalidateODE
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 model	getLBodeModelSim
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 model	indices
Search for the best combination of continuous parameters and logic gates.	minlpLBodeSSm
A model from CellNoptR	model
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 CellNoptR	pknmodel
Plot data against simulated values.	plotLBodeFitness
Simulate the model and plot the obtained with the different experimental conditions.	plotLBodeModelSim
runCNORode	runCNORode
converts output of getLBodeModelSim to cnolist	simdata2cnolist
Simulate value signals a CNO list With Logic-Based ODEs.	simulate