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.

Author
Aristidis G. Vrahatis and Panos Balomenos
Date of publication
Maintainer
Aristidis G. Vrahatis <agvrahatis@upatras.gr> and Panos Balomenos <balomenos@upatras.gr>
License
GPL-3
Version
1.0.1

View on Bioconductor

Man pages

DEsubs
Default run of DEsubs
geneVisualization
Gene level visualization
organismVisualization
Organism level visualization
subpathwayToGraph
Subpathway To Graph
subpathwayTypes
All subpathway types
subpathwayVisualization
Subpathway level visualization

Files in this package

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