# shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data

## TL;DR

shinyDSP is an interactive R Shiny app for analyzing and visualizing NanoString GeoMx spatial transcriptomics data.

## Contribution

It introduces a free, open-source, interactive tool for GeoMx data analysis with customizable options.

## Key findings

- shinyDSP supports quality control, normalization, and differential gene expression analysis.
- The app is available on Bioconductor and GitHub with an MIT license.
- It offers user customization for aesthetic and analytical preferences.

## Abstract

NanoString’s GeoMx Digital Spatial Profiling platform enables researchers to elucidate spatial transcriptomic profiles of distinct cellular microenvironments in human and mouse formalin fixed paraffin embedded tissue. To date, there is no free, open source, interactive application to facilitate data analysis with the latest tested methods. We created shinyDSP, a R shiny application that guides users to perform quality control, normalization, and differential gene expression analysis of GeoMx DSP data. It includes various user-provided customization options to meet individual aesthetic choices and requirements.

The release and development versions of shinyDSP are available on Bioconductor under the MIT license (https://www.bioconductor.org/packages/release/bioc/html/shinyDSP.html) and Github (https://github.com/kimsjune/shinyDSP).