Package: CNORdt 1.55.0

A. MacNamara

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.

Authors:A. MacNamara

CNORdt_1.55.0.tar.gz
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CNORdt_1.55.0.tgz(r-4.6-x86_64)CNORdt_1.55.0.tgz(r-4.6-arm64)CNORdt_1.55.0.tgz(r-4.5-x86_64)CNORdt_1.55.0.tgz(r-4.5-arm64)
CNORdt_1.55.0.tar.gz(r-4.7-arm64)CNORdt_1.55.0.tar.gz(r-4.7-x86_64)CNORdt_1.55.0.tar.gz(r-4.6-arm64)CNORdt_1.55.0.tar.gz(r-4.6-x86_64)
CNORdt_1.55.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CNORdt/json (API)

# Install 'CNORdt' in R:

install.packages('CNORdt', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

CNOlistPB - Toy data
modelPB - ModelPB

On BioConductor:CNORdt-1.55.0(bioc 3.24)CNORdt-1.54.0(bioc 3.23)

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

immunooncology cellbasedassays cellbiology proteomics timecourse

4.00 score 25 scripts 2 mentions 6 exports 56 dependencies

Last updated from:b36db97fe5. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	160
linux-devel-arm64	NOTE	227
linux-devel-x86_64	NOTE	256
source / vignettes	OK	249
linux-release-arm64	NOTE	232
linux-release-x86_64	NOTE	265
macos-release-arm64	NOTE	127
macos-release-x86_64	NOTE	269
macos-oldrel-arm64	NOTE	192
macos-oldrel-x86_64	NOTE	260
windows-devel	NOTE	175
windows-release	NOTE	176
windows-oldrel	NOTE	175
wasm-release	OK	153

Exports:computeScoreDT convert2array cutAndPlotResultsDT gaBinaryDT getFitDT simulatorDT

Dependencies:abind base64enc BH BiocGenerics bitops bslib cachem CellNOptR cli cpp11 digest evaluate farver fastmap fontawesome fs generics ggplot2 glue graph gtable highr htmltools igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr Matrix memoise mime pkgconfig R6 rappdirs RBGL RColorBrewer RCurl Rgraphviz rlang rmarkdown S7 sass scales stringi stringr tinytex vctrs viridisLite withr xfun XML yaml

Using multiple time points to train logic models to data

Rendered fromCNORdt-vignette.Rnwusingutils::Sweave

Last update: 2018-08-30
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

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