CellNOptR

DOI: 10.18129/B9.bioc.CellNOptR    

This package is for version 3.10 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: 3.10

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: T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve

Maintainer: A.Gabor <gabor.attila87 at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF		CellNOptR0_1flowchart.pdf
PDF		Fig2.pdf
PDF		Fig3.pdf
PDF		Fig4.pdf
PDF		Fig6.pdf
PDF		Fig7.pdf
PDF		Fig8.pdf
PDF	R Script	Main vignette:Playing with networks using CellNOptR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bioinformatics, CellBasedAssays, CellBiology, ImmunoOncology, Proteomics, Software, TimeCourse
Version	1.32.0
In Bioconductor since	BioC 2.9 (R-2.14) (8.5 years)
License	GPL-3
Depends	R (>= 2.15.0), RBGL, graph, methods, hash, RCurl, Rgraphviz, XML, ggplot2
Imports	igraph, stringi, stringr
LinkingTo
Suggests	data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics
SystemRequirements	Graphviz version >= 2.2
Enhances
URL
Depends On Me	CNORdt, CNORfeeder, CNORfuzzy, CNORode
Imports Me
Suggests Me	MEIGOR
Links To Me
Build Report

Package Archives

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

Source Package	CellNOptR_1.32.0.tar.gz
Windows Binary	CellNOptR_1.32.0.zip
Mac OS X 10.11 (El Capitan)	CellNOptR_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CellNOptR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CellNOptR
Package Short Url	https://bioconductor.org/packages/CellNOptR/
Package Downloads Report	Download Stats