{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T22:30:01Z","timestamp":1775773801775,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T00:00:00Z","timestamp":1719446400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Sakari Alhopuro foundation","award":["340141"],"award-info":[{"award-number":["340141"]}]},{"name":"Sakari Alhopuro foundation","award":["344698"],"award-info":[{"award-number":["344698"]}]},{"name":"Sakari Alhopuro foundation","award":["345803"],"award-info":[{"award-number":["345803"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The limited resolution of spatial transcriptomics (ST) assays in the past has led to the development of cell type annotation methods that separate the convolved signal based on available external atlas data. In light of the rapidly increasing resolution of the ST assay technologies, we made available and investigated the performance of a deconvolution-free marker-based cell annotation method called scType. In contrast to existing methods, the spatial application of scType does not require computationally strenuous deconvolution, nor large single-cell reference atlases. We show that scType enables ultra-fast and accurate identification of abundant cell types from ST data, especially when a large enough panel of genes is detected. Examples of such assays are Visium and Slide-seq, which currently offer the best trade-off between high resolution and number of genes detected by the assay for cell type annotation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>scType source R and python codes for spatial data are openly available in GitHub (https:\/\/github.com\/kris-nader\/sp-type or https:\/\/github.com\/kris-nader\/sc-type-py). Step-by-step tutorials for R and python spatial data analysis can be found in https:\/\/github.com\/kris-nader\/sp-type and https:\/\/github.com\/kris-nader\/sc-type-py\/blob\/main\/spatial_tutorial.md, respectively.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae426","type":"journal-article","created":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T22:14:25Z","timestamp":1719526465000},"source":"Crossref","is-referenced-by-count":24,"title":["ScType enables fast and accurate cell type identification from spatial transcriptomics data"],"prefix":"10.1093","volume":"40","author":[{"given":"Kristen","family":"Nader","sequence":"first","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki , Helsinki 00290, Finland"},{"name":"iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital , Helsinki 00290, Finland"}]},{"given":"Misra","family":"Tasci","sequence":"additional","affiliation":[{"name":"School of Medicine, Ko\u00e7 University , Istanbul 34450, Turkey"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7780-482X","authenticated-orcid":false,"given":"Aleksandr","family":"Ianevski","sequence":"additional","affiliation":[{"name":"Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki , Helsinki 00290, Finland"},{"name":"iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital , Helsinki 00290, Finland"}]},{"given":"Andrew","family":"Erickson","sequence":"additional","affiliation":[{"name":"iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki and Helsinki University Hospital , Helsinki 00290, Finland"},{"name":"Research Program in Systems Oncology, University of Helsinki , Helsinki 00290, Finland"}]},{"given":"Emmy W","family":"Verschuren","sequence":"additional","affiliation":[{"name":"Institute 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