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

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
Date of publicationNone
MaintainerRemy Nicolle <remy.c.nicolle@gmail.com>
LicenseGPL-3
Version1.10.0

View on Bioconductor

Functions

activators Man page
activators,coregnet-method Man page
addCooperativeEvidences Man page
addCooperativeEvidences,coregnet-method Man page
addEvidences Man page
addEvidences,coregnet-method Man page
as.data.frame,coregnet-method Man page
as.list,coregnet-method Man page
CHEA_sub Man page
CIT_BLCA_CNV Man page
CIT_BLCA_EXP Man page
CIT_BLCA_Subgroup Man page
coerce,coregnet-method Man page
coerce,coregnet-method,data.frame Man page
coerce,coregnet-method,list Man page
coregnet Man page
coRegnet Man page
coregnet-class Man page
coRegnet-package Man page
coregnetToDataframe Man page
coregnetToDataframe,coregnet-method Man page
coregnetToList Man page
coregnetToList.coregnet Man page
coregnetToList.CoRegNet Man page
coregnetToList,coregnet-method Man page
coregulators Man page
coregulators,coregnet-method Man page
dim,coregnet-method Man page
discretizeExpressionData Man page
display Man page
ENCODE_sub Man page
HIPPIE_sub Man page
hLICORN Man page
HumanTF Man page
HumanTF_entrezgene Man page
length,coregnet-method Man page
masterRegulator Man page
masterRegulator,coregnet-method Man page
print,coregnet-method Man page
refine Man page
refine,coregnet-method Man page
regulatorInfluence Man page
regulatorInfluence,coregnet-method Man page
regulators Man page
regulators,coregnet-method Man page
repressors Man page
repressors,coregnet-method Man page
show,coregnet-method Man page
STRING_sub Man page
summary Man page
summary,coregnet-method Man page
targets Man page
targets,coregnet-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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