CoRegNet

DOI: 10.18129/B9.bioc.CoRegNet    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CoRegNet.

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CoRegNet")

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("CoRegNet")

 

HTML	R Script	Custom Print Methods
PDF		Reference Manual

Details

biocViews	GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, SystemsBiology, Transcription, Visualization
Version	1.20.0
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 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
Links To Me
Build Report

Package Archives

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

Source Package	CoRegNet_1.20.0.tar.gz
Windows Binary	CoRegNet_1.20.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	CoRegNet_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CoRegNet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CoRegNet
Package Short Url	http://bioconductor.org/packages/CoRegNet/
Package Downloads Report	Download Stats