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tRigon: an R package and Shiny App for integrative (path-)omics data analysis.

David L Hölscher1,2, Michael Goedertier1,3, Barbara M Klinkhammer1

  • 1Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany.

BMC Bioinformatics
|March 5, 2024
PubMed
Summary

tRigon is a new toolbox for integrative omics data analysis, simplifying complex pathomics data interpretation. This application enables researchers to perform fast, reproducible, and comprehensive analyses without coding expertise.

Keywords:
Data explorationPathomicsStatisticsUser interface

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Area of Science:

  • Computational pathology
  • Bioinformatics
  • Data science

Background:

  • Pathomics offers automated histopathology analysis but faces challenges with high-dimensional data, variability, and missingness.
  • Quick and comprehensible analysis of pathomics data is crucial for broad implementation.
  • Existing tools may not adequately address the complexities of pathomics data analysis.

Purpose of the Study:

  • To develop a user-friendly application for fast, comprehensive, and reproducible pathomics data analysis.
  • To facilitate exploratory feature analysis for researchers without coding expertise.
  • To support the integration and interpretation of pathomics and other omics datasets.

Main Methods:

  • Development of tRigon (Toolbox foR InteGrative (path-)Omics data aNalysis), a Shiny application.
  • tRigon is available as an R package from CRAN and its source code is on GitLab.
  • The application can be installed locally or accessed online via a web interface.

Main Results:

  • tRigon demonstrates fast computation for datasets of various sizes across different hardware.
  • The application provides a user-friendly interface for exploratory data analysis.
  • Successful execution on low- and high-performance hardware indicates broad applicability.

Conclusions:

  • tRigon empowers researchers without coding skills to conduct their own exploratory analyses.
  • The toolbox supports pathomics and non-pathomics datasets on diverse hardware.
  • tRigon facilitates broader implementation and accessibility of advanced pathomics analysis.