{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T19:39:25Z","timestamp":1754163565197,"version":"3.41.2"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T00:00:00Z","timestamp":1752192000000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>NanoString\u2019s 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf401","type":"journal-article","created":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T19:08:41Z","timestamp":1752260921000},"source":"Crossref","is-referenced-by-count":0,"title":["shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5263-0758","authenticated-orcid":false,"given":"Seung J","family":"Kim","sequence":"first","affiliation":[{"name":"Interstitial Lung Disease Lab, London Health Sciences Research Institute , London, ON, N6A 5W9,","place":["Canada"]}]},{"given":"Matthew J","family":"Cecchini","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University , London, ON, N6A 5C1,","place":["Canada"]}]},{"given":"Marco","family":"Mura","sequence":"additional","affiliation":[{"name":"Interstitial Lung Disease Lab, London Health Sciences Research Institute , London, ON, N6A 5W9,","place":["Canada"]},{"name":"Department of Medicine, Schulich School of Medicine and Dentistry, Western University , London, ON, N6A 5W9,","place":["Canada"]}]}],"member":"286","published-online":{"date-parts":[[2025,7,11]]},"reference":[{"key":"2025073102363345800_btaf401-B1","doi-asserted-by":"crossref","first-page":"bbaa163","DOI":"10.1093\/bib\/bbaa163","article-title":"An approach for normalization and quality control for NanoString RNA expression data","volume":"22","author":"Bhattacharya","year":"2021","journal-title":"Brief Bioinform"},{"key":"2025073102363345800_btaf401-B2","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1093\/bioinformatics\/btz647","article-title":"NACHO: an R package for quality control of NanoString nCounter data","volume":"36","author":"Canouil","year":"2020","journal-title":"Bioinformatics"},{"key":"2025073102363345800_btaf401-B3","doi-asserted-by":"crossref","first-page":"btac762","DOI":"10.1093\/bioinformatics\/btac762","article-title":"Easy NanoString nCounter data analysis with the 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normalization","volume":"40","author":"Montoto-Louzao","year":"2024","journal-title":"Bioinformatics"},{"key":"2025073102363345800_btaf401-B11","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025073102363345800_btaf401-B12","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1093\/bioinformatics\/bts188","article-title":"NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data","volume":"28","author":"Waggott","year":"2012","journal-title":"Bioinformatics"},{"key":"2025073102363345800_btaf401-B13","first-page":"e151","article-title":"NanoStringDiff: a novel statistical method for differential expression analysis based on NanoString nCounter data","volume":"44","author":"Wang","year":"2016","journal-title":"Nucleic 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