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shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome
Seung J Kim1, Marco Mura2, Marco Mura1,3
1Interstitial Lung Disease Lab, London Health Sciences Research Institute, London, ON, N6A 5W9, Canada.
Summary:
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.
Availability And Implementation:
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).
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