ArticleNucleic acids research2024
standR: spatial transcriptomic analysis for GeoMx DSP data.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed, 65 citations in OpenAlex.
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- Early EGFR Inhibition Triggers Actionable Tumor and Microenvironmental Remodeling in Lung Cancer.Cancer research communications · 2026Article
- Mitigating Fixation Artifacts in Spatial Transcriptomics: Methodological Insights from Human Brain Tissue.Molecular neurobiology · 2026Article
- X-linked SEPTIN6-related congenital neutropenia and B cell deficiency.Journal of human immunity · 2026Article
- Single-cell spatial pharmacobiology identifies conserved stromal barriers to therapeutic antibody delivery in human solid tumors.Nature biotechnology · 2026Article
- Decoding the role of H19 in cholestatic liver injury using snRNA-seq, spatial transcriptomics, and machine learning-based disease prediction.Cell & bioscience · 2026Article
- Brain FGF2 and NCAM1 contribute to FGFR1-dependent progression of estrogen receptor-positive breast cancer brain metastases.Nature communications · 2026Article
- Conventional type-1 DC density is associated with checkpoint inhibitor response across multiple types of cancer.The Journal of clinical investigation · 2026Article
- Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment.Cell reports. Medicine · 2026Article
- Spatial multi-omics characterization of neuroblastoma reveals ferroptosis-associated metabolic features in high-risk tumors.Genome medicine · 2026Article
- Molecular profiling of sacral chordomas through methylation, spatial transcriptomics and multiplexed immunofluorescence.ESMO rare cancers · 2026Article
- Comparative spatial whole transcriptome analysis of matched frozen and formalin-fixed paraffin-embedded colorectal cancer tissues.Biochemistry and biophysics reports · 2026Article
- Spatial proteomics in precision medicine: technologies, bioinformatics, and translational applications.Precision clinical medicine · 2026Review
- TNF-⍺-mediated myeloid-instructed CD14Cell reports. Medicine · 2026Article
- The future of mathematical oncology in the age of AI.NPJ systems biology and applications · 2026Review
- Decoding the Role of H19 in Cholestatic Liver Injury Using snRNA-seq, Spatial Transcriptomics, and Machine Learning-Based Disease Prediction.Research square · 2026Article
- Intratumoral microbiome: the double-edged sword in remodeling cancer immunotherapy.Molecular cancer · 2026Review
- Temporal Stretch-Induced Nuclear Mechanosensing Coordinates Early Chromatin Accessibility and Genome Protection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
To gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cells in situ. State-of-the-art spatial profiling technologies, such as the Nanostring GeoMx Digital Spatial Profiler (DSP), now allow quantitative spatially resolved measurement of the transcriptome in tissues. However, the bioinformatics pipelines currently used to analyse GeoMx data often fail to successfully account for the technical variability within the data and the complexity of experimental designs, thus limiting the accuracy and reliability of the subsequent analysis. Carefully designed quality control workflows, that include in-depth experiment-specific investigations into technical variation and appropriate adjustment for such variation can address this issue. Here, we present standR, an R/Bioconductor package that enables an end-to-end analysis of GeoMx DSP data. With four case studies from previously published experiments, we demonstrate how the standR workflow can enhance the statistical power of GeoMx DSP data analysis and how the application of standR enables scientists to develop in-depth insights into the biology of interest.
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Registered trials
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.