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TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data.

Wei Su1, Jianqiang Sun1, Kentaro Shimizu1,2

  • 1Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.

BMC Research Notes
|March 15, 2019
PubMed
Summary

A new graphical user interface, TCC-GUI, enables non-R users to perform differential expression analysis on RNA-Seq data. This tool offers robust normalization and visualization features, making complex analysis accessible via a web browser.

Keywords:
BioinformaticsDifferential expression analysisRNA-SeqShiny app

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Differential expression (DE) analysis is crucial for RNA-Seq data.
  • The TCC R/Bioconductor package offers robust normalization for DE analysis.
  • A need exists for DE analysis tools accessible to non-R users.

Purpose of the Study:

  • To develop a user-friendly interface for the TCC package.
  • To enable differential expression analysis for non-R users.
  • To provide robust normalization and visualization tools for RNA-Seq data.

Main Methods:

  • Development of a graphical user interface (GUI) using R and Shiny.
  • Encapsulation of TCC package functionalities within the Shiny application.
  • Implementation of exploratory analysis, visualization, and reporting tools.

Main Results:

  • TCC-GUI provides a web-based platform for DE analysis.
  • The interface includes robust normalization, simulation data generation, and exploratory tools like average silhouette score.
  • Visualization tools include volcano plots and heatmaps with hierarchical clustering.

Conclusions:

  • TCC-GUI democratizes differential expression analysis for RNA-Seq data.
  • The tool simplifies complex bioinformatics workflows for non-programmers.
  • Accessible via a web browser, TCC-GUI enhances RNA-Seq data interpretation.