{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T20:41:58Z","timestamp":1791232918556,"version":"4.1.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T00:00:00Z","timestamp":1775606400000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001349","name":"National Medical Research Council","doi-asserted-by":"publisher","award":["MOH-001067"],"award-info":[{"award-number":["MOH-001067"]}],"id":[{"id":"10.13039\/501100001349","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001350","name":"Ministry of Health, Singapore","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001350","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Spatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. However, most computational methods for spatial analysis do not explicitly model local tissue context, such as boundaries, neighborhoods, or gradients. Here, we present SpNeigh (https:\/\/github.com\/jinming-cheng\/SpNeigh\/), an R package for spatial neighborhood analysis and spatially aware differential expression modeling. SpNeigh includes tools for boundary detection, spatial neighborhood extraction, distance-based weighting, and gradient-based statistical testing. It supports both region-based differential expression and smooth spatial modeling using spline-based regression, along with a spatial enrichment index that identifies genes enriched near defined spatial features. We demonstrate the utility of SpNeigh across multiple platforms and tissues, including mouse brain, human breast cancer, and human liver, revealing intermediate populations at tissue interfaces, immune microenvironment differences, and spatially zonated gene expression patterns. SpNeigh offers a flexible and interpretable framework for dissecting spatial gene expression dynamics in complex tissues.<\/jats:p>","DOI":"10.1093\/nargab\/lqag039","type":"journal-article","created":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T12:43:13Z","timestamp":1774615393000},"source":"Crossref","is-referenced-by-count":3,"title":["SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3806-4694","authenticated-orcid":false,"given":"Jinming","family":"Cheng","sequence":"first","affiliation":[{"name":"Centre for Biomedical Data Science, Duke-NUS Medical School , Singapore169857 ,","place":["Singapore"]},{"name":"Duke-NUS AI + Medical Sciences Initiative, Duke-NUS Medical School , Singapore169857 ,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0584-2584","authenticated-orcid":false,"given":"Pierce Kah Hoe","family":"Chow","sequence":"additional","affiliation":[{"name":"Surgery Academic-Clinical Program, Duke-NUS Medical School , Singapore169857 ,","place":["Singapore"]},{"name":"Department of Hepato-pancreato-biliary and Transplant Surgery, Singapore General Hospital and National Cancer Centre Singapore , Singapore169610 ,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3610-4883","authenticated-orcid":false,"given":"Nan","family":"Liu","sequence":"additional","affiliation":[{"name":"Centre for Biomedical Data Science, Duke-NUS Medical School , Singapore169857 ,","place":["Singapore"]},{"name":"Duke-NUS AI + Medical Sciences Initiative, Duke-NUS Medical School , Singapore169857 ,","place":["Singapore"]},{"name":"Pre-hospital and Emergency Research Centre, Health Services Research and Population Health, Duke-NUS Medical School , Singapore169857 ,","place":["Singapore"]},{"name":"NUS Artificial Intelligence Institute, National University of Singapore , Singapore119077 ,","place":["Singapore"]},{"name":"Department of Biostatistics and Bioinformatics, Duke University , Durham 27710 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,8]]},"reference":[{"key":"2026041108585914500_B1","doi-asserted-by":"publisher","first-page":"8353","DOI":"10.1038\/s41467-023-43458-x","article-title":"High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis","volume":"14","author":"Janesick","year":"2023","journal-title":"Nat Commun"},{"key":"2026041108585914500_B2","doi-asserted-by":"publisher","first-page":"11046","DOI":"10.1073\/pnas.1612826113","article-title":"High-throughput single-cell 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