title: DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments.
abstract: 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.
authors.affiliation: Department of Computer Engineering and Informatics.|Department of Medicine, University of Patras, Patras, 26500, GR.
authors.forename: Aristidis G
authors.initials: AG
authors.lastname: Vrahatis
authors.affiliation: Department of Computer Engineering and Informatics.|Department of Medicine, University of Patras, Patras, 26500, GR.
authors.forename: Panos
authors.initials: P
authors.lastname: Balomenos
authors.affiliation: Department of Computer Engineering and Informatics.
authors.forename: Athanasios K
authors.initials: AK
authors.lastname: Tsakalidis
authors.affiliation: Department of Medicine, University of Patras, Patras, 26500, GR.|SINAPSE Institute, Center of Life Sciences, National University of Singapore, Singapore 117456.
authors.forename: Anastasios
authors.initials: A
authors.lastname: Bezerianos
mesh_terms: D006801:Humans; D012313:RNA; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D012313:RNA