Web applications and databases from the Guda Lab for single-cell, spatial, gene-regulation and metagenomic data.
Every tool runs in your web browser on our Shiny server, so there is nothing to install.
R Shiny app
Single Cell Ambient RNA Removal and Visualization (SCARR-Vis) is a browser-based and user-friendly R Shiny application designed for researchers without programming proficiency to analyze and visualize the results. SCARR-Vis removes ambient RNA from 10x Genomics single-cell data using SoupX, DecontX, scCDC, or FastCAR and lets you compare pre vs post cleanup across QC, clustering, UMAP, heatmaps, and per-cell tables.
R Shiny app
Single-cell RNA Data Analysis and Visualization (ScRDAVis) is a browser-based and user-friendly R Shiny application designed for researchers without programming proficiency to analyze and visualize single-cell RNA (scRNA) results. It supports single and multiple sample analyses as well as group comparisons with advanced functional analysis: integrated tools such as CellChat for cell-cell communication, Monocle3 for trajectory and pseudotime inference, clusterProfiler for pathway and GO analysis, and hdWGCNA for co-expression and transcription factor analysis.
R Shiny app
Visium HD Spatial Transcriptomics Data Analysis and Visualization (VST-DAVis) is a browser-based and user-friendly R Shiny application designed for researchers without programming proficiency to analyze and visualize 10x Genomics Spatial Transcriptomics Visium HD. It supports single and multiple sample analyses as well as group comparisons with advanced functional analysis: integrated tools such as CellChat for cell-cell communication, Monocle3 for trajectory and pseudotime inference, clusterProfiler for pathway and GO analysis, and hdWGCNA for co-expression and transcription factor analysis.
Genome browser
The Single-Cell Genomic Regulatory Atlas and Map (scGRAM) is an interactive genome browser for exploring transcription factor binding landscapes across single cells. Built on the hg38 human reference genome, it enables researchers to visualize and compare regulatory elements at single-cell resolution.
Database
We have developed the first active enhancer database at single-cell resolution for both normal and disease conditions, named the Single Cell Active Enhancer Database (scAED). This database offers a streamlined listing of enhancers for each cell type. This was achieved through sequence reads from snMultiome or snATAC-seq, utilizing specialized tools, custom scripts, and suitable parameters. The scAED database is conveniently implemented as an R Shiny web application, ensuring an interactive and user-friendly experience. scAED also provides active enhancers in both healthy and diseased cells, potentially serving as a platform for identifying candidate enhancers that contribute to cell and organ dysfunction. We will include more organs in time.
R Shiny app
Interactive Metagenome Data Analysis and Visualization (MetaDAVis) application analyzes 16S and whole metagenome sequence results at various levels (kingdom to species). It is a browser-based and user-friendly R Shiny application for researchers to analyze and visualize without programming proficiency.
If one of these tools helps your research, please cite the paper that describes it.
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/
Veerappa A, Patel JC, Shakyawar S, Jagadesan S, Guda C. scAED: a framework for mapping the enhancer state at single-cell resolution. Brief Bioinform. 2025;26(6):bbaf646. https://doi.org/
Jagadesan S, Guda C (2025) ScRDAVis: An R shiny application for single-cell transcriptome data analysis and visualization. PLoS Comput Biol 21(11): e1013721. https://doi.org/
Jagadesan S, Guda C (2025) MetaDAVis: An R shiny application for metagenomic data analysis and visualization. PLoS ONE 20(4): e0319949. https://doi.org/