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CoRegNet

CoRegNet is an R/Bioconductor package for gene regulatory network inference and analysis.

It uses a a Shiny/Cytoscape.js interface for the analysis of networks.

Install

From R :

source("http://bioconductor.org/biocLite.R")
biocLite("CoRegNet")

Quick user guide

  1. reconsruct a large-scale regulatory network from a gene expression matrix EXP
    GRN = hLICORN(EXP)
  1. Infer transcription factor activity
	influence = regulatorInfluence(GRN,EXP)
  1. Retrieve inferred co-coregulators
	coregs= coregulators(GRN,EXP)
  1. Analyze the network of cooperative regulators using an interactive display
 display(GRN,EXP,influence)

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Version

Version

1.8.2

License

GPL-3

Maintainer

Remy Nicolle

Last Published

February 15th, 2017

Functions in CoRegNet (1.8.2)

summary

Summaries and info coregnet
regulators

Interogate a coregnet object.
discretizeExpressionData

Three-value discretization of gene expression data.
addEvidences

Integration of regulatory evidences.
display

Display a shiny interactive web interface to
coregnet-class

Class coregnet --- Specifying the structure of the network used throughout the package.
coregnet

Initialize a co-regulatory network object.
refine

Refine an inferred regulatory network using external evidence.
Human Data Examples

Human Transcription Factor data and Bladder cancer dataset.
coRegnet-package

coRegnet : inference and interrogation co-regulation networks
coregulators

Extract all co-regulators of a regulatory network.
hLICORN

Hybrid Learning of co-operative regulation network.
regulatorInfluence

Regulator Influence, estimating the sample specific activity of Transcription Factors.
masterRegulator

Identify phenotype related Master Regulators.
HumanTF

List of Human Transcription Factors.