CNORdt: Add-on to CellNOptR: Discretized time treatments

This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.

Author
A. MacNamara
Date of publication
None
Maintainer
A. MacNamara <aidan.macnamara@ebi.ac.uk>
License
GPL-2
Version
1.16.0

View on Bioconductor

Man pages

CNOlistPB
Toy data
computeScoreDT
Compute the score of a model/data (time-course) set using a...
convert2array
Converts the output of simulatorDT to a 3D array for other...
cutAndPlotResultsDT
Plot the results of a time-course optimization
gaBinaryDT
Genetic algorithm for optimizing models using multiple...
getFitDT
The optimization function that finds the scaling factor for...
modelPB
modelPB
simulatorDT
Discrete time simulation of a boolean model

Files in this package

CNORdt/ChangeLog.txt
CNORdt/DESCRIPTION
CNORdt/NAMESPACE
CNORdt/R
CNORdt/R/computeScoreDT.R
CNORdt/R/convert2array.R
CNORdt/R/cutAndPlotResultsDT.R
CNORdt/R/gaBinaryDT.R
CNORdt/R/getFitDT.R
CNORdt/R/simulatorDT.R
CNORdt/build
CNORdt/build/vignette.rds
CNORdt/data
CNORdt/data/CNOlistPB.RData
CNORdt/data/modelPB.RData
CNORdt/inst
CNORdt/inst/doc
CNORdt/inst/doc/CNORdt-vignette-example.R
CNORdt/inst/doc/CNORdt-vignette.R
CNORdt/inst/doc/CNORdt-vignette.Rnw
CNORdt/inst/doc/CNORdt-vignette.pdf
CNORdt/inst/extdata
CNORdt/inst/extdata/ToyModelPB.csv
CNORdt/inst/extdata/ToyModelPB.sif
CNORdt/man
CNORdt/man/CNOlistPB.Rd
CNORdt/man/computeScoreDT.Rd
CNORdt/man/convert2array.Rd
CNORdt/man/cutAndPlotResultsDT.Rd
CNORdt/man/gaBinaryDT.Rd
CNORdt/man/getFitDT.Rd
CNORdt/man/modelPB.Rd
CNORdt/man/simulatorDT.Rd
CNORdt/src
CNORdt/src/simulatorDT.c
CNORdt/vignettes
CNORdt/vignettes/CNORdt-vignette-plot.pdf
CNORdt/vignettes/CNORdt-vignette.Rnw