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ggVolcanoR: A Shiny app for customizable visualization of differential expression datasets.
Kerry A Mullan1, Liesl M Bramberger1, Prithvi Raj Munday1
1Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.
Computational and Structural Biotechnology Journal
|November 8, 2021
Summary
ggVolcanoR is a new R-based application for creating customizable volcano plots and other data visualizations for transcriptomic and proteomic analyses. It simplifies the process for researchers to understand gene expression data and identify biomarkers.
Area of Science:
- Bioinformatics
- Data Visualization
- Genomics
Background:
- Volcano plots, correlation plots, upset plots, and heatmaps are crucial for analyzing differential gene and protein expression data.
- Customizable data visualization aids in understanding dysregulated expression and identifying biomarkers.
Purpose of the Study:
- To introduce ggVolcanoR, an R-based Shiny application for generating customizable analytical plots.
- To provide a user-friendly interface for visualizing and analyzing differential expression datasets.
Main Methods:
- Development of an R-based Shiny application (ggVolcanoR).
- Implementation of interactive features for customizable plot generation (volcano, correlation, upset, heatmaps).
- Provision of both local executable and web-based versions.
Main Results:
- ggVolcanoR enables enhanced customization and visualization of publication-quality analytical plots.
- The application facilitates the comparison of dysregulated genes/proteins across multiple datasets.
- Users can download filtered dysregulated expression data for downstream pathway analysis.
Conclusions:
- ggVolcanoR offers a practical and accessible solution for researchers analyzing differential expression data.
- The tool supports biomarker identification and pathway analysis through intuitive data visualization.
- ggVolcanoR is available as open-source code and a deployed web server.
Keywords:
Correlation plotData visualizationDifferential expression dataHeatmapProteomicsTranscriptomicsUpset plotVolcano plotMore Related Videos
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