shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data.
Where this comes from
- Record sourced from PubMed, PMID 40644626.
- Also identified by DOI 10.1093/bioinformatics/btaf401 and PMC identifier 12311272.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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).
Medical subject headings
- Software
- Gene Expression Profiling
- Transcriptome