Introduction

DEsubs is a network-based systems biology R package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customized framework with a broad range of operation modes at all stages of the subpathway analysis, enabling so a case-specific approach. The operation modes include pathway network construction and processing, subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render DEsubs a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level drug targets and biomarkers for complex diseases.DEsubs is implemented as an R package following Bioconductor guidelines: http://bioconductor.org/packages/DEsubs/ CONTACT: tassos.bezerianos@nus.edu.sgSupplementary information: Supplementary data are available at Bioinformatics online.

Publications

  1. DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments.
    Cite this
    Vrahatis AG, Balomenos P, Tsakalidis AK, Bezerianos A, 2016-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Aristidis G Vrahatis
    Developer

    Department of Medicine, University of Patras

  2. Panos Balomenos
    Developer

    Department of Medicine, University of Patras

  3. Athanasios K Tsakalidis
    Developer

  4. Anastasios Bezerianos
    Investigator

    SINAPSE Institute, Center of Life Sciences

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Summary
AccessionBT001168
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByAnastasios Bezerianos