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

Seung J Kim, Matthew J Cecchini, Marco Mura

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Seung J KimInterstitial Lung Disease Lab, London Health Sciences Research Institute, London, ON, N6A 5W9, Canada.ORCID 0000-0001-5263-0758

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

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

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

summaryNanoString'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).

Indexed as

Gene Expression ProfilingSoftwareTranscriptomeAnimalsComputational BiologyHumansMice

Identifiers

PMID40644626

DOI10.1093/bioinformatics/btaf401

PMCPMC12311272

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.