CoRegNet: CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Version 1.12.0

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.

AuthorRemy Nicolle, Thibault Venzac and Mohamed Elati
Bioconductor views GeneExpression GeneRegulation GraphAndNetwork Network NetworkEnrichment NetworkInference SystemsBiology Transcription Visualization
Date of publicationNone
MaintainerRemy Nicolle <remy.c.nicolle@gmail.com>
LicenseGPL-3
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CoRegNet")

Getting started

README.md
CoRegNet: Reconstruction and integrated analysis of Co-Regulatory Networks

Popular man pages

coregnet: Initialize a co-regulatory network object.
discretizeExpressionData: Three-value discretization of gene expression data.
display: Display a shiny interactive web interface to
HumanTF: List of Human Transcription Factors.
masterRegulator: Identify phenotype related Master Regulators.
regulatorInfluence: Regulator Influence, estimating the sample specific activity...
summary: Summaries and info coregnet
See all...

All man pages Function index File listing

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

Functions

CHEA_sub Man page
CIT_BLCA_CNV Man page
CIT_BLCA_EXP Man page
CIT_BLCA_Subgroup Man page
ENCODE_sub Man page
HIPPIE_sub Man page
HumanTF Man page
HumanTF_entrezgene Man page
STRING_sub Man page
activators Man page
activators,coregnet-method Man page
adaptiveCoregSupport Source code
addCooperativeEvidences Man page
addCooperativeEvidences,coregnet-method Man page
addEvidences Man page
addEvidences,coregnet-method Man page
addOneCoRegulatoryEvidence Source code
addOneRegulatoryEvidence Source code
addRegulationEvidence Source code
addRegulatorCooperativityEvidence Source code
as.data.frame,coregnet-method Man page
as.list,coregnet-method Man page
automaticParameters Source code
coRegnet Man page
coRegnet-package Man page
coerce,coregnet-method Man page
coerce,coregnet-method,data.frame Man page
coerce,coregnet-method,list Man page
coregnet Man page Source code
coregnet-class Man page
coregnetToDataframe Man page
coregnetToDataframe,coregnet-method Man page
coregnetToList Man page
coregnetToList,coregnet-method Man page
coregnetToList.CoRegNet Man page
coregnetToList.coregnet Man page
coregulators Man page
coregulators,coregnet-method Man page
descriptionUpdate Source code
dim,coregnet-method Man page
directedNetworkEnrichment Source code
discretizeExpressionData Man page Source code
display Man page Source code
distfun Source code
eand Source code
fishersMethod Source code
fitGRN Source code
getEntry Source code
hLICORN Man page Source code
hclustfun Source code
heatplot Source code
legendPlot Source code
length,coregnet-method Man page
list.enriched Source code
masterRegulator Man page Source code
masterRegulator,coregnet-method Man page
meanSupport Source code
merge.pvalues Source code
netintersect Source code
networkLegendPlot Source code
nvlist Source code
oneGeneHLICORN Source code
parallelRegulationEvidence Source code
parallelRegulatorCooperativityEvidence Source code
print,coregnet-method Man page
printNetwork Source code
quicknonuniqgrnsTOSIGRNS Source code
reactiveAdjacencyMatrix Source code
redoLayout Source code
refine Man page
refine,coregnet-method Man page
regulationEvidence Source code
regulatorCooperativityEvidence Source code
regulatorInfluence Man page
regulatorInfluence,coregnet-method Man page
regulators Man page
regulators,coregnet-method Man page
repressors Man page
repressors,coregnet-method Man page
selectNode Source code
set.overlap Source code
show,coregnet-method Man page
subsigrns Source code
summary Man page
summary,coregnet-method Man page
targets Man page
targets,coregnet-method Man page
testCyto Source code
tfPlot Source code
traits Source code
undirectedNetworkEnrichment Source code
uniqueEvidenceDataFrameByPvalue Source code
updateData Source code
val2col Source code

Files

DESCRIPTION
NAMESPACE
R
R/classes.R
R/coRegnet.R
R/display.R
R/evidences.R
R/masterRegulators.R
R/netInference.R
README.md
build
build/vignette.rds
data
data/CHEA_sub.RData
data/CIT_BLCA_CNV.RData
data/CIT_BLCA_EXP.RData
data/CIT_BLCA_Subgroup.RData
data/ENCODE_sub.RData
data/HIPPIE_sub.RData
data/HumanTF.RData
data/HumanTF_entrezgene.RData
data/STRING_sub.RData
data/datalist
inst
inst/CITATION
inst/doc
inst/doc/CoRegNet.R
inst/doc/CoRegNet.Rmd
inst/doc/CoRegNet.html
inst/unitTests
inst/unitTests/test_coregnet.R
inst/www
inst/www/css
inst/www/css/style.css
inst/www/js
inst/www/js/cy.js
inst/www/js/cytoscape.min.js
inst/www/js/jquery-1.11.1.min.js
inst/www/js/jquery-slick
inst/www/js/jquery-slick/css
inst/www/js/jquery-slick/css/dcslick.css
inst/www/js/jquery-slick/index.html
inst/www/js/jquery-slick/js
inst/www/js/jquery-slick/js/jquery.slick.2.1.js
man
man/CoRegNet-class.Rd
man/HumanDataExamples.Rd
man/HumanTF.Rd
man/addEvidences.Rd
man/coRegnet-package.Rd
man/coregnet.Rd
man/coregulators.Rd
man/discretizeExpressionData.Rd
man/display.Rd
man/hLICORN.Rd
man/masterRegulator.Rd
man/refine.Rd
man/regulatorInfluence.Rd
man/regulators.Rd
man/summary.Rd
src
src/comblicorn.c
tests
tests/runTests.R
vignettes
vignettes/CoRegNet.Rmd
vignettes/fig
vignettes/fig/InfluenceHeatmap.png
vignettes/fig/PPARGLocalView.png
vignettes/fig/basal1.png
vignettes/fig/coregnetWithEvidence.png
vignettes/fig/luminal1.png
vignettes/fig/wholeApp.png
CoRegNet documentation built on May 20, 2017, 9:46 p.m.

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