CellNOptR

This package is for version 3.9 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: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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")
CellNOptR0_1flowchart.pdf PDF
Fig2.pdf PDF
Fig3.pdf PDF
Fig4.pdf PDF
Fig6.pdf PDF
Fig7.pdf PDF
Fig8.pdf PDF
Main vignette:Playing with networks using CellNOptR PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bioinformatics, CellBasedAssays, CellBiology, ImmunoOncology, Proteomics, Software, TimeCourse
Version 1.30.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL-3
Depends R (>= 2.15.0), RBGL, graph, methods, hash, RCurl, Rgraphviz, XML, ggplot2
Imports igraph, stringi, stringr
System Requirements Graphviz version >= 2.2
URL
See More
Suggests data.table, plyr, dplyr, tidyr, readr, RUnit, BiocGenerics
Linking To
Enhances
Depends On Me CNORdt, CNORfeeder, CNORfuzzy, CNORode
Imports Me
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_1.30.0.tar.gz
Windows Binary CellNOptR_1.30.0.zip
Mac OS X 10.11 (El Capitan) CellNOptR_1.30.0.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
Old Source Packages for BioC 3.9 Source Archive