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Related Experiment Video

Updated: Jun 14, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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SimpleViz: A user-friendly, web-based tool for publication-ready data visualization in bioinformatics.

Byeong Seob Oh1, Juhee Kim2, Minjeong Kwon2

  • 1Multidimensional Genomics Research Center, Kangwon National University, Chuncheon, Republic of Korea.

Molecules and Cells
|May 10, 2025
PubMed
Summary

SimpleViz is a free, web-based tool for creating publication-quality bioinformatics visualizations, including RNA-seq analysis, without coding. This accessible platform empowers researchers to generate complex graphics easily.

Keywords:
Bar/violin/dot plotData visualizationPrincipal component analysis plotVolcano plot

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Visualization

Background:

  • Large-scale biological datasets necessitate effective visualization tools.
  • Current software often presents barriers due to cost or required programming expertise.
  • Accessible bioinformatics visualization is crucial for researchers.

Purpose of the Study:

  • Introduce SimpleViz, a free, web-based platform for creating scientific figures.
  • Enable researchers to generate professional-quality visualizations without coding.
  • Address the accessibility gap in bioinformatics data visualization tools.

Main Methods:

  • Developed a web-based platform using a Shiny interface.
  • Integrated gene-level analysis for RNA-seq data.
  • Included core visualization types: box/violin/dot plots, volcano plots, PCA plots, and heatmaps.

Main Results:

  • SimpleViz facilitates intuitive data upload, visualization generation, and customization.
  • Users can create tailored visuals for publication without programming skills.
  • The platform offers extensive customization and built-in statistical comparisons.

Conclusions:

  • SimpleViz provides an accessible and adaptable solution for bioinformatics visualization.
  • The platform meets the evolving data analysis needs in biomedical research.
  • Continuous improvement based on user feedback is planned.