To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CoRegNet")

In most cases, you don't need to download the package archive at all.

CoRegNet

DOI: 10.18129/B9.bioc.CoRegNet    

This is the development version of CoRegNet; for the stable release version, see CoRegNet.

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Bioconductor version: Development (3.6)

This package provides methods to identify active transcriptional programs. Methods and classes are provided to import or infer large scale co-regulatory network from transcriptomic data. The specificity of the encoded networks is to model Transcription Factor cooperation. External regulation evidences (TFBS, ChIP,...) can be integrated to assess the inferred network and refine it if necessary. Transcriptional activity of the regulators in the network can be estimated using an measure of their influence in a given sample. Finally, an interactive UI can be used to navigate through the network of cooperative regulators and to visualize their activity in a specific sample or subgroup sample. The proposed visualization tool can be used to integrate gene expression, transcriptional activity, copy number status, sample classification and a transcriptional network including co-regulation information.

Author: Remy Nicolle, Thibault Venzac and Mohamed Elati

Maintainer: Remy Nicolle <remy.c.nicolle at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CoRegNet")

Documentation

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Details

biocViews GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, SystemsBiology, Transcription, Visualization
Version 1.14.0
In Bioconductor since BioC 3.0 (R-3.1) (3 years)
License GPL-3
Depends R (>= 2.14), igraph, shiny, arules, methods
Imports
LinkingTo
Suggests RColorBrewer, gplots, BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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Source Package CoRegNet_1.14.0.tar.gz
Windows Binary CoRegNet_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) CoRegNet_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CoRegNet
Package Short Url http://bioconductor.org/packages/CoRegNet/
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