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

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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

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