VST-DAVis
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.
VST-DAVis is deployed at: https://www.gudalab-rtools.net/VST-DAVis
VST-DAVis GitHub: https://github.com/GudaLab/VST-DAVis
scAED
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.
scAED is deployed at: https://www.gudalab-rtools.net/scAED
scAED GitHub: https://github.com/GudaLab/scAED
Citation: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/10.1093/bib/bbaf6461
ScRDAVis
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.
ScRDAVis is deployed at: https://www.gudalab-rtools.net/ScRDAVis
ScRDAVis GitHub: https://github.com/GudaLab/ScRDAVis
Citation: 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/10.1371/journal.pcbi.1013721
MetaDAVis
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.
MetaDAVis is deployed at: https://www.gudalab-rtools.net/MetaDAVis
MetaDAVis GitHub: https://github.com/GudaLab/MetaDAVis
Citation: Jagadesan S, Guda C (2025) MetaDAVis: An R shiny application for metagenomic data analysis and visualization. PLoS ONE 20(4): e0319949. https://doi.org/10.1371/journal.pone.0319949