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CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data


Bioconductor version: Release (3.18)

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

Author: Thomas Cokelaer [aut], Federica Eduati [aut], Aidan MacNamara [aut], S Schrier [ctb], Camille Terfve [aut], Enio Gjerga [ctb], Attila Gabor [cre]

Maintainer: Attila Gabor <attila.gabor at uni-heidelberg.de>

Citation (from within R, enter citation("CellNOptR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CellNOptR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CellNOptR")
Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data with CellNOptR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, CellBiology, ImmunoOncology, Network, Pathways, Proteomics, Software, TimeCourse
Version 1.48.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL-3
Depends R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown
Imports igraph, stringi, stringr
System Requirements Graphviz version >= 2.2
URL
See More
Suggests data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics
Linking To
Enhances doParallel, foreach
Depends On Me CNORdt, CNORfeeder, CNORfuzzy, CNORode
Imports Me bnem
Suggests Me MEIGOR
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CellNOptR_1.48.0.tar.gz
Windows Binary CellNOptR_1.48.0.zip
macOS Binary (x86_64) CellNOptR_1.48.0.tgz
macOS Binary (arm64) CellNOptR_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CellNOptR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CellNOptR
Bioc Package Browser https://code.bioconductor.org/browse/CellNOptR/
Package Short Url https://bioconductor.org/packages/CellNOptR/
Package Downloads Report Download Stats