ArticleBioinformatics (Oxford, England)2026
hoodscanR: profiling single-cell neighborhoods in spatial transcriptomics data.
Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Spatial transcriptomics identifies immune-stromal niches associated with cancer in adult dermatomyositis.Nature communications · 2026Article
- Spatial Transcriptomics of Adipose Tissue: Technologies, Applications, and Challenges.Journal of obesity & metabolic syndrome · 2025Review
- HISSTA: a human in situ single-cell transcriptome atlas.Bioinformatics (Oxford, England) · 2025Article
- Spatial Transcriptomics Identifies Immune-Stromal Niches Associated with Cancer in Adult Dermatomyositis.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
15 authors.
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Abstract
motivationUnderstanding complex cellular neighborhoods has provided new insights into tissue biology. Accurate neighborhood identification is crucial, yet existing methods often focus on hard assignment and do not generate cell-specific neighborhood profiles at single-cell level.
resultsWe developed hoodscanR, a Bioconductor package identifying and analyzing cellular neighborhoods in spatial data. The central output of hoodscanR is a cell-level neighborhood probability profile, which represents partial membership of each cell across multiple annotation-defined neighborhoods. This probabilistic representation supports downstream analyses including neighborhood visualization, uncertainty assessment, neighborhood-based clustering and neighborhood-aware differential expression. Applying hoodscanR to breast and lung cancer datasets, we showcase its ability to characterize mixed tissue environments and identify transcriptional changes in tumor cells from distinct spatial neighborhoods. AVAILABILITY: The hoodscanR package is publicly available in Bioconductor at https://bioconductor.org/packages/release/bioc/html/hoodscanR.html.
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