Related Experiment Video
Updated: Feb 6, 2026
07:40
Spatially Compact Arrangement of Larval Zebrafish Sections for Spatial Transcriptomic Analysis
Published on: May 16, 2025
968
VST-DAVis: an R Shiny application and web-browser for spatial transcriptomics data analysis and visualization
Sankarasubramanian Jagadesan1, Chittibabu Guda1,2
1Department of Genetics, Cell Biology and Anatomy, 985805 Nebraska Medical Center, University of Nebraska Medical Center, Omaha, NE 68198-5805, United States.
Bioinformatics Advances
|February 5, 2026
Summary
Visium HD Spatial Transcriptomics Data Analysis and Visualization (VST-DAVIS) is a user-friendly R Shiny application for analyzing spatial transcriptomics data. It offers comprehensive tools for researchers, simplifying complex analyses and visualization for single or multiple samples.
Area of Science:
- Spatial Transcriptomics
- Bioinformatics
- Computational Biology
Background:
- Spatial transcriptomics technologies like 10x Genomics Visium HD generate complex datasets.
- Analyzing these datasets requires specialized bioinformatics expertise and tools.
- Existing tools may lack user-friendliness or comprehensive analytical capabilities.
Purpose of the Study:
- To develop an interactive R Shiny application named VST-DAVIS for intuitive spatial transcriptomics data analysis.
- To provide a user-friendly, end-to-end solution for researchers, including those without programming expertise.
- To support both single and multiple sample analyses for comparative studies.
Main Methods:
- Developed VST-DAVIS as an R Shiny application and web browser.
- Integrated popular R packages (Seurat, Monocle3, CellChat, hdWGCNA) for diverse analytical tasks.
- Designed a streamlined graphical interface for intuitive data handling and visualization.
Main Results:
- VST-DAVIS enables comprehensive spatial transcriptomics analysis from quality control to network reconstruction.
- The application supports various input formats and outputs high-quality graphics.
- It facilitates comparative analyses across multiple samples and biological conditions.
Conclusions:
- VST-DAVIS makes advanced spatial transcriptomics data analysis accessible to a broader research community.
- The tool enhances the usability of Visium HD data for researchers with varying technical skills.
- It provides a robust platform for exploring spatial gene expression, cell communication, and co-expression networks.
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