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Updated: Jun 17, 2026

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GeneSEA Explorer: An R Shiny Tool for Differential Gene Expression Analysis With Shannon's Entropy Aggregation.

Ana Margarida Gonçalves1,2,3, Pedro Macedo1, Patrício Costa2,3,4

  • 1Center for Research and Development in Mathematics and Applications (CIDMA), Department of Mathematics, University of Aveiro, Aveiro, Portugal.

Biotechnology and Bioengineering
|June 15, 2026
PubMed
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This summary is machine-generated.

RNA sequencing (RNA-seq) analysis faces challenges with gene expression variability due to different normalization methods. GeneSEA Explorer offers a user-friendly tool to compare methods and identify stable differentially expressed genes (DEGs) using Shannon entropy.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Transcriptomics

Background:

  • RNA sequencing (RNA-seq) is crucial for differential gene expression (DGE) analysis.
  • Normalization method choice significantly impacts DGE results, complicating DEG list stability.
  • Existing R packages often require programming skills, limiting comparative normalization analyses.

Purpose of the Study:

  • To introduce GeneSEA Explorer, a Shiny application for DGE and functional enrichment analysis.
  • To enable comparison of various normalization methods within RNA-seq data analysis.
  • To provide a user-friendly tool for exploring and analyzing DGE results.

Main Methods:

  • Development of a novel R Shiny application, GeneSEA Explorer.
  • Integration of multiple normalization methods for DGE analysis.
Keywords:
BioinformaticsDEGDGE AnalysisNormalizationR Shiny ApplicationRNA SequencingShannon Entropy

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  • Application of Shannon entropy for aggregating DGE results and selecting reliable DEGs.

    • Main Results:

    • GeneSEA Explorer facilitates interactive exploration and visualization of DGE results.
    • The tool allows for direct comparison of DEG lists generated by different normalization methods.
    • Shannon entropy provides a novel approach for robust DEG identification.

    Conclusions:

    • GeneSEA Explorer simplifies DGE analysis and addresses normalization method variability.
    • The application enhances data interpretation and supports robust research conclusions.
    • This bioinformatics tool makes advanced RNA-seq analysis more accessible to researchers.