CoRegNet: CoRegNet : reconstruction and integrated analysis of co-regulatory networks

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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
Date of publication
None
Maintainer
Remy Nicolle <remy.c.nicolle@gmail.com>
License
GPL-3
Version
1.10.0

View on Bioconductor

Man pages

addEvidences
Integration of regulatory evidences.
coregnet
Initialize a co-regulatory network object.
CoRegNet-class
Class coregnet - Specifying the structure of the network used...
coRegnet-package
coRegnet : inference and interrogation co-regulation networks
coregulators
Extract all co-regulators of a regulatory network.
discretizeExpressionData
Three-value discretization of gene expression data.
display
Display a shiny interactive web interface to
hLICORN
Hybrid Learning of co-operative regulation network.
HumanDataExamples
Human Transcription Factor data and Bladder cancer dataset.
HumanTF
List of Human Transcription Factors.
masterRegulator
Identify phenotype related Master Regulators.
refine
Refine an inferred regulatory network using external...
regulatorInfluence
Regulator Influence, estimating the sample specific activity...
regulators
Interogate a coregnet object.
summary
Summaries and info coregnet

Files in this package

CoRegNet/DESCRIPTION
CoRegNet/NAMESPACE
CoRegNet/R
CoRegNet/R/classes.R
CoRegNet/R/coRegnet.R
CoRegNet/R/display.R
CoRegNet/R/evidences.R
CoRegNet/R/masterRegulators.R
CoRegNet/R/netInference.R
CoRegNet/README.md
CoRegNet/build
CoRegNet/build/vignette.rds
CoRegNet/data
CoRegNet/data/CHEA_sub.RData
CoRegNet/data/CIT_BLCA_CNV.RData
CoRegNet/data/CIT_BLCA_EXP.RData
CoRegNet/data/CIT_BLCA_Subgroup.RData
CoRegNet/data/ENCODE_sub.RData
CoRegNet/data/HIPPIE_sub.RData
CoRegNet/data/HumanTF.RData
CoRegNet/data/HumanTF_entrezgene.RData
CoRegNet/data/STRING_sub.RData
CoRegNet/data/datalist
CoRegNet/inst
CoRegNet/inst/CITATION
CoRegNet/inst/doc
CoRegNet/inst/doc/CoRegNet.R
CoRegNet/inst/doc/CoRegNet.Rmd
CoRegNet/inst/doc/CoRegNet.html
CoRegNet/inst/unitTests
CoRegNet/inst/unitTests/test_coregnet.R
CoRegNet/inst/www
CoRegNet/inst/www/css
CoRegNet/inst/www/css/style.css
CoRegNet/inst/www/js
CoRegNet/inst/www/js/cy.js
CoRegNet/inst/www/js/cytoscape.min.js
CoRegNet/inst/www/js/jquery-1.11.1.min.js
CoRegNet/inst/www/js/jquery-slick
CoRegNet/inst/www/js/jquery-slick/css
CoRegNet/inst/www/js/jquery-slick/css/dcslick.css
CoRegNet/inst/www/js/jquery-slick/index.html
CoRegNet/inst/www/js/jquery-slick/js
CoRegNet/inst/www/js/jquery-slick/js/jquery.slick.2.1.js
CoRegNet/man
CoRegNet/man/CoRegNet-class.Rd
CoRegNet/man/HumanDataExamples.Rd
CoRegNet/man/HumanTF.Rd
CoRegNet/man/addEvidences.Rd
CoRegNet/man/coRegnet-package.Rd
CoRegNet/man/coregnet.Rd
CoRegNet/man/coregulators.Rd
CoRegNet/man/discretizeExpressionData.Rd
CoRegNet/man/display.Rd
CoRegNet/man/hLICORN.Rd
CoRegNet/man/masterRegulator.Rd
CoRegNet/man/refine.Rd
CoRegNet/man/regulatorInfluence.Rd
CoRegNet/man/regulators.Rd
CoRegNet/man/summary.Rd
CoRegNet/src
CoRegNet/src/comblicorn.c
CoRegNet/tests
CoRegNet/tests/runTests.R
CoRegNet/vignettes
CoRegNet/vignettes/CoRegNet.Rmd
CoRegNet/vignettes/fig
CoRegNet/vignettes/fig/InfluenceHeatmap.png
CoRegNet/vignettes/fig/PPARGLocalView.png
CoRegNet/vignettes/fig/basal1.png
CoRegNet/vignettes/fig/coregnetWithEvidence.png
CoRegNet/vignettes/fig/luminal1.png
CoRegNet/vignettes/fig/wholeApp.png