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.

Package details

AuthorAristidis G. Vrahatis and Panos Balomenos
Bioconductor views DifferentialExpression GeneExpression GraphAndNetwork ImmunoOncology KEGG Network NetworkEnrichment Normalization Pathways RNASeq SystemsBiology
MaintainerAristidis G. Vrahatis <>, Panos Balomenos <>
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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DEsubs documentation built on Nov. 8, 2020, 8:31 p.m.