shinyDSP：一个用于交互式分析和可视化NanoString GeoMx全转录组图谱数据的Shiny应用程序。

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

作者信息

Kim Seung J, Cecchini Matthew J, Mura Marco

机构信息

Interstitial Lung Disease Lab, London Health Sciences Research Institute, London, ON, N6A 5W9, Canada.

Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.

出版信息

Bioinformatics. 2025 Jul 1;41(7). doi: 10.1093/bioinformatics/btaf401.

DOI:10.1093/bioinformatics/btaf401

PMID:40644626

Abstract

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).

摘要

NanoString公司的GeoMx数字空间分析平台使研究人员能够阐明人类和小鼠福尔马林固定石蜡包埋组织中不同细胞微环境的空间转录组图谱。迄今为止，尚无免费的、开源的交互式应用程序来促进使用最新测试方法进行数据分析。我们创建了shinyDSP，这是一个R闪亮应用程序，可指导用户对GeoMx DSP数据进行质量控制、标准化和差异基因表达分析。它包括各种用户提供的定制选项，以满足个人审美选择和要求。