CNORode: ODE add-on to CellNOptR

ODE add-on to CellNOptR

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNORode")
AuthorDavid Henriques, Thomas Cokelaer
Bioconductor views Bioinformatics CellBasedAssays CellBiology Proteomics TimeCourse
Date of publicationNone
MaintainerDavid Henriques <davidpcnet@hotmail.com>
LicenseGPL-2
Version1.18.0

View on Bioconductor

Man pages

cnolistCNORodeExample: A cnolist from CellNoptR

CNORode-package: Logic based ODE extension for CellNOptR

createLBodeContPars: Create a list with ODE parameter information needed to...

defaultParametersGA: Create default options to perform parameter estimation with a...

defaultParametersSSm: Create default options to perform parameter estimation with...

getLBodeContObjFunction: Returns the objective function to perform parameter...

getLBodeDataSim: Simulate value signals a CNO list With Logic-Based ODEs.

getLBodeMINLPObjFunction: Get the objective function to evaluate the fitness of a given...

getLBodeModelSim: Simulate the logic-based ODE model

getLBodeSimFunction: Get a function to simulate a logic based ODE model.

getStates: Find which species in the model are states.

incidence2Adjacency: Convert an incidence matrix into an adjacency matrix.

indices: Indices that relate cnolist to model

minlpLBodeSSm: Search for the best combination of continuous parameters and...

model: A model from CellNoptR

parEstimationLBode: Perform parameter estimation using a genetic algorithm...

parEstimationLBodeGA: Perform parameter estimation using a genetic algorithm...

parEstimationLBodeSSm: Perform parameter estimation using essR.

plotLBodeFitness: Plot data against simulated values.

plotLBodeModelSim: Simulate the model and plot the obtained with the different...

simdata2cnolist: converts output of getLBodeModelSim to cnolist

simulate: Simulate value signals a CNO list With Logic-Based ODEs.

Functions

cnolistCNORodeExample Man page
CNORode Man page
createLBodeContPars Man page
defaultParametersGA Man page
defaultParametersSSm Man page
getLBodeContObjFunction Man page
getLBodeDataSim Man page
getLBodeMINLPObjFunction Man page
getLBodeModelSim Man page
getLBodeSimFunction Man page
getStates Man page
incidence2Adjacency Man page
indices Man page
minlpLBodeSSm Man page
model Man page
parEstimationLBode Man page
parEstimationLBodeGA Man page
parEstimationLBodeSSm Man page
plotLBodeFitness Man page
plotLBodeModelSim Man page
simdata2cnolist Man page
simulate Man page

Files

DESCRIPTION
NAMESPACE
R
R/createLBodeContPars.R R/defaultParametersGA.R R/defaultParametersSSm.R R/getLBodeContObjFunction.R R/getLBodeDataSim.R R/getLBodeMINLPObjFunction.R R/getLBodeModelSim.R R/getLBodeSimFunction.R R/getStates.R R/incidence2Adjacency.R R/minlpLBodeSSm.R R/parEstimationLBode.R R/parEstimationLBodeGA.R R/parEstimationLBodeSSm.R R/plotLBodeFitness.R R/plotLBodeModelSim.R R/simdata2cnolist.R R/simulate.R R/zzz.R
build
build/vignette.rds
data
data/ToyCNOlist.RData
data/ToyIndices.RData
data/ToyModel.RData
inst
inst/NEWS.Rd
inst/doc
inst/doc/CNORode-vignette.R
inst/doc/CNORode-vignette.Rnw
inst/doc/CNORode-vignette.pdf
inst/doc/ToyModelMMB_FeedbackAnd.csv
inst/doc/ToyModelMMB_FeedbackAnd.sif
man
man/CNORode-package.Rd man/cnolistCNORodeExample.Rd man/createLBodeContPars.Rd man/defaultParametersGA.Rd man/defaultParametersSSm.Rd man/getLBodeContObjFunction.Rd man/getLBodeDataSim.Rd man/getLBodeMINLPObjFunction.Rd man/getLBodeModelSim.Rd man/getLBodeSimFunction.Rd man/getStates.Rd man/incidence2Adjacency.Rd man/indices.Rd man/minlpLBodeSSm.Rd man/model.Rd man/parEstimationLBode.Rd man/parEstimationLBodeGA.Rd man/parEstimationLBodeSSm.Rd man/plotLBodeFitness.Rd man/plotLBodeModelSim.Rd man/simdata2cnolist.Rd man/simulate.Rd
src
src/CNOStructure.h
src/Makevars
src/Toy_Model_MMB_Feedback_OriginalPars_C_test.h
src/cvodea.c
src/cvodea_io.c
src/cvodes.c
src/cvodes_band.c
src/cvodes_bandpre.c
src/cvodes_bandpre_impl.h
src/cvodes_bbdpre.c
src/cvodes_bbdpre_impl.h
src/cvodes_dense.c
src/cvodes_diag.c
src/cvodes_diag_impl.h
src/cvodes_direct.c
src/cvodes_direct_impl.h
src/cvodes_impl.h
src/cvodes_io.c
src/cvodes_spbcgs.c
src/cvodes_spgmr.c
src/cvodes_spils.c
src/cvodes_spils_impl.h
src/cvodes_sptfqmr.c
src/decimal2binary.c
src/findStates.c
src/fnvector_serial.c
src/fnvector_serial.h
src/getAdjacencyMatrix.c
src/getNumBits.c
src/getNumInputs.c
src/getStateIndex.c
src/getTruthTables.c
src/get_count_bits.c
src/get_input_index.c
src/get_support_truth_tables.c
src/get_truth_tables_index.c
src/hill_function.c
src/include
src/include/cvodes
src/include/cvodes/cvodes.h
src/include/cvodes/cvodes_band.h
src/include/cvodes/cvodes_bandpre.h
src/include/cvodes/cvodes_bbdpre.h
src/include/cvodes/cvodes_dense.h
src/include/cvodes/cvodes_diag.h
src/include/cvodes/cvodes_direct.h
src/include/cvodes/cvodes_lapack.h
src/include/cvodes/cvodes_spbcgs.h
src/include/cvodes/cvodes_spgmr.h
src/include/cvodes/cvodes_spils.h
src/include/cvodes/cvodes_sptfqmr.h
src/include/nvector
src/include/nvector/nvector_serial.h
src/include/sundials
src/include/sundials/sundials_band.h
src/include/sundials/sundials_config.h
src/include/sundials/sundials_dense.h
src/include/sundials/sundials_direct.h
src/include/sundials/sundials_fnvector.h
src/include/sundials/sundials_iterative.h
src/include/sundials/sundials_lapack.h
src/include/sundials/sundials_math.h
src/include/sundials/sundials_nvector.h
src/include/sundials/sundials_spbcgs.h
src/include/sundials/sundials_spgmr.h
src/include/sundials/sundials_sptfqmr.h
src/include/sundials/sundials_types.h
src/linear_transfer_function.c
src/normHill.c
src/nvector_serial.c
src/printAdjMat.c
src/printInterMat.c
src/printNminiTerms.c
src/printTruthTables.c
src/rhsODE.c
src/sim_logic_ode.c
src/simulateODE.c
src/sundials_band.c
src/sundials_dense.c
src/sundials_direct.c
src/sundials_iterative.c
src/sundials_math.c
src/sundials_nvector.c
src/sundials_spbcgs.c
src/sundials_spgmr.c
src/sundials_sptfqmr.c
vignettes
vignettes/CNORode-vignette.Rnw
vignettes/ToyModelMMB_FeedbackAnd.png
vignettes/ToyModelMMB_FeedbackAnd.svg
vignettes/comp_tex.bat
vignettes/data_ToyModelMMB_FeddbackAnd.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.