CellNOptR

DOI: 10.18129/B9.bioc.CellNOptR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see CellNOptR.

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

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	CellBasedAssays, CellBiology, ImmunoOncology, Network, Pathways, Proteomics, Software, TimeCourse
Version	1.44.0
In Bioconductor since	BioC 2.9 (R-2.14) (11.5 years)
License	GPL-3
Depends	R (>= 4.0.0), RBGL, graph, methods, RCurl, Rgraphviz, XML, ggplot2, rmarkdown
Imports	igraph, stringi, stringr
LinkingTo
Suggests	data.table, dplyr, tidyr, readr, knitr, RUnit, BiocGenerics
SystemRequirements	Graphviz version >= 2.2
Enhances	doParallel, foreach
URL
Depends On Me	CNORdt, CNORfeeder, CNORfuzzy, CNORode
Imports Me	bnem
Suggests Me	MEIGOR
Links To Me
Build Report

Package Archives

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

Source Package	CellNOptR_1.44.0.tar.gz
Windows Binary	CellNOptR_1.44.0.zip (64-bit only)
macOS Binary (x86_64)	CellNOptR_1.44.0.tgz
macOS Binary (arm64)	CellNOptR_1.44.0.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