VST-DAVis is a user-friendly, browser-based R Shiny application designed for researchers without programming expertise to analyze and visualize 10x Genomics Spatial Transcriptomics Visium HD. It supports single and multiple sample analyses as well as group comparisons, offering a range of functionalities for comprehensive data exploration.
VST-DAVis includes nine functional modules:
- Single or Multiple Samples Analysis
- Stats
- Sample Groups and QC Filtering
- Normalization and PCA Analysis
- Clustering
- Marker Identification
- Cell Type Prediction
- Cluster-Based Plots
- Condition-Based Analysis
- Subclustering
- Correlation Network Analysis
- Genome Ontology (GO) Terms
- Pathway Analysis
- GSEA Analysis
- Cell-Cell Communication
- Trajectory and Pseudotime Analysis
- Co-Expression and TF Analysis
- Co-Expression Network Analysis
- Transcription Factor Regulatory Network Analysis
VST-DAVis is deployed online and accessible at:
https://www.gudalab-rtools.net/VST-DAVis
Ensure the following software is installed:
- R (>= 4.5.2): Download R
- RStudio (>= 2025.09.2): Download RStudio
- Bioconductor (>= 3.22)
- Shiny (>= 1.11.1)
Note: VST-DAVis has been tested with these versions. Using older versions of R may cause errors during package installation. Updating to the latest R version is recommended.
Run the following commands in an R session to install required packages:
if (!require("BiocManager")) install.packages("BiocManager", update=FALSE)
if (!require("devtools")) install.packages("devtools", update=FALSE)
# Function to check and install CRAN packagesinstall_cran_packages<-function(packages) {
for (pkginpackages) {
if (!require(pkg, character.only=TRUE)) {
install.packages(pkg, dependencies=TRUE)
}
}
}
# Function to check and install Bioconductor packagesinstall_bioc_packages<-function(packages) {
for (pkginpackages) {
if (!require(pkg, character.only=TRUE)) {
BiocManager::install(pkg, update=FALSE, dependencies=TRUE)
}
}
}
# Function to check and install GitHub packagesinstall_github_packages<-function(packages) {
for (pkgin names(packages)) {
if (!require(pkg, character.only=TRUE)) {
devtools::install_github(packages[[pkg]], upgrade="never", dependencies=TRUE)
}
}
}
# List of CRAN packagescran_packages<- c("shiny", "DT", "shinythemes", "shinyjs", "shinyFiles", "shinyWidgets", "shinycssloaders", "ggplot2", "data.table", "ggpubr", "shinydashboard", "dplyr", "tibble", "HGNChelper", "openai", "metap", "ggrepel", "R.utils", "circlize", "hdf5r", "ggupset", "gridExtra", "ggalluvial", "NMF", "ggraph", "igraph", "cowplot", "pdftools", "xgboost", "Seurat", "arrow", "SeuratObject", "msigdbr", "filelock")
if (!require("msigdbdf"))install.packages("msigdbdf", repos="https://igordot.r-universe.dev")
# List of Bioconductor packagesbioc_packages<- c("sctransform", "celldex", "SingleR", "scRNAseq", "glmGamPoi", "scran", "EnhancedVolcano", "ComplexHeatmap", "clusterProfiler", "org.Hs.eg.db", "org.Mm.eg.db", "org.Mmu.eg.db", "org.Rn.eg.db", "org.Ss.eg.db", "ReactomePA", "fgsea", "enrichplot", "multtest", "WGCNA", "hdWGCNA", "motifmatchr", "TFBSTools", "GenomicRanges", "JASPAR2020", "JASPAR2024", "EnsDb.Hsapiens.v86", "BSgenome.Hsapiens.UCSC.hg38", "BSgenome.Mmusculus.UCSC.mm10")
# List of GitHub packagesgithub_packages<-list(
"GPTCelltype"="Winnie09/GPTCelltype",
"openxlsx"="ycphs/openxlsx",
"presto"="immunogenomics/presto",
"monocle3"="cole-trapnell-lab/monocle3",
"SeuratWrappers"="satijalab/seurat-wrappers",
"SeuratDisk"="mojaveazure/seurat-disk",
"patchwork"="thomasp85/patchwork",
"CellChat"="jinworks/CellChat",
"genesorteR"="mahmoudibrahim/genesorteR",
"hdWGCNA"="smorabit/hdWGCNA"
)
# Install all packages
install_cran_packages(cran_packages)
install_bioc_packages(bioc_packages)
install_github_packages(github_packages)To launch VST-DAVis, follow one of these methods:
- Open an R session in RStudio.
- Execute the following lines of code:
library(shiny)
shiny::runGitHub('VST-DAVis', 'GudaLab')library(shiny)
runApp('/path/to/the/VST-DAVis-master', launch.browser = TRUE)
Replace /path/to/the/VST-DAVis-master with the actual path to the downloaded folder
A detailed user manual is available under the "Manual" tab at: https://www.gudalab-rtools.net/VST-DAVis
To ensure seamless analysis and reproducibility, VST-DAVis includes one reference dataset for each input format. These datasets, sourced from NCBI, have been pre-tested with the tool and allow users to explore its functionalities and understand the analysis workflow effectively.
These datasets are ideal for:
- Demonstrating VST-DAVis functionalities.
- Familiarizing users with the tool's analysis workflow.
- Testing the application in different input formats.
Users can download these datasets directly from the provided links and use them to explore VST-DAVis. Users who download sample files from NCBI or other public repositories need to rename and organize their files to match the Space Ranger output format, which is required by our application.
So We have also included example datasets in both supported formats to guide users:
- H5 + Spatial folder format P1_ON1_A.zip (Organism: Human; GEO accession: GSM5591748)
- Space Ranger Matrix, Feature, Barcode, and Spatial image files format control_e14_2.zip (Organism: Mouse; accession: GSM7804885)
Users can download and extract these example files directly from the GitHub repository or from the upload page of the application. This will help users correctly format their data and ensure full compatibility with our tool.
This application was tested on: Linux (Red Hat and Ubuntu) and Windows (10 and 11)
Jagadesan S, Guda C, VST-DAVis: an R Shiny application and web-browser for spatial transcriptomics data analysis and visualization, Bioinformatics Advances, Volume 6, Issue 1, 2026, vbag007 (https://doi.org/10.1093/bioadv/vbag007).