DEsubs: DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DEsubs")
AuthorAristidis G. Vrahatis and Panos Balomenos
Bioconductor views DifferentialExpression GeneExpression GraphAndNetwork KEGG Network NetworkEnrichment Normalization Pathways RNASeq SystemsBiology
Date of publication
MaintainerAristidis G. Vrahatis <agvrahatis@upatras.gr> and Panos Balomenos <balomenos@upatras.gr>
LicenseGPL-3
Version1.2.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/DEmeasures.R R/DEsubs.R R/TSPM.R R/networkConstruction.R R/subpathwayAnalysis.R R/utilities.R R/visualizations.R R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/DEsubs.R
inst/doc/DEsubs.Rmd
inst/doc/DEsubs.pdf
inst/extdata
inst/extdata/Data
inst/extdata/Data/Disease_GAD.RData
inst/extdata/Data/Disease_OMIM.RData
inst/extdata/Data/Drug_DrugBank.RData
inst/extdata/Data/GO_bp.RData
inst/extdata/Data/GO_cc.RData
inst/extdata/Data/GO_mf.RData
inst/extdata/Data/KEGG.RData
inst/extdata/Data/TF.RData
inst/extdata/Data/edgeLists.RData
inst/extdata/Data/libraryEntrezToExternalNomenclature.RData
inst/extdata/Data/libraryEntrezToHGNC.RData
inst/extdata/Data/miRNA.RData
inst/extdata/User
inst/extdata/User/toyData.txt
inst/extdata/data.RData
inst/unitTests
inst/unitTests/test_DEsubs.R inst/unitTests/test_geneVisualization.R inst/unitTests/test_organismVisualization.R inst/unitTests/test_subpathwayToGraph.R inst/unitTests/test_subpathwayVisualization.R
man
man/DEsubs.Rd man/geneVisualization.Rd man/organismVisualization.Rd man/subpathwayToGraph.Rd man/subpathwayTypes.Rd man/subpathwayVisualization.Rd
tests
tests/runTests.R
vignettes
vignettes/DEsubs.Rmd
vignettes/citations.bib
vignettes/figures
vignettes/figures/fig1.png
vignettes/figures/fig2.png
vignettes/figures/fig3.png

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