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CoRegNet

CoRegNet : reconstruction and integrated analysis of co-regulatory networks


Bioconductor version: Release (3.18)

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 (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CoRegNet")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneExpression, GeneRegulation, GraphAndNetwork, Network, NetworkEnrichment, NetworkInference, Software, SystemsBiology, Transcription, Visualization
Version 1.40.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends R (>= 2.14), igraph, shiny, arules, methods
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Suggests RColorBrewer, gplots, BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package
Windows Binary CoRegNet_1.40.0.zip (64-bit only)
macOS Binary (x86_64) CoRegNet_1.40.0.tgz
macOS Binary (arm64) CoRegNet_1.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CoRegNet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CoRegNet
Bioc Package Browser https://code.bioconductor.org/browse/CoRegNet/
Package Short Url https://bioconductor.org/packages/CoRegNet/
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