Package: CNORdt 1.49.0

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

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CNORdt.pdf |CNORdt.html✨
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-1.49.0(bioc 3.21)CNORdt-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 timecourse

3.78 score 15 scripts 217 downloads 2 mentions 6 exports 64 dependencies

Last updated 3 months agofrom:7924ad24f0. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Dec 29 2024
R-4.5-win-x86_64	NOTE	Dec 29 2024
R-4.5-linux-x86_64	NOTE	Dec 29 2024
R-4.4-win-x86_64	NOTE	Dec 29 2024
R-4.4-mac-x86_64	NOTE	Dec 29 2024
R-4.4-mac-aarch64	NOTE	Dec 29 2024
R-4.3-win-x86_64	NOTE	Dec 29 2024
R-4.3-mac-x86_64	NOTE	Dec 29 2024
R-4.3-mac-aarch64	NOTE	Dec 29 2024

Exports:computeScoreDT convert2array cutAndPlotResultsDT gaBinaryDT getFitDT simulatorDT

Dependencies:abind base64enc BH BiocGenerics bitops bslib cachem CellNOptR cli colorspace cpp11 digest evaluate fansi farver fastmap fontawesome fs 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

Using multiple time points to train logic models to data

Rendered fromCNORdt-vignette.Rnwusingutils::Sweaveon Dec 29 2024.

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