{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T02:29:19Z","timestamp":1776220159535,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T00:00:00Z","timestamp":1697500800000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001729","name":"Swedish Foundation for Strategic Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001729","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020"},{"DOI":"10.13039\/501100002794","name":"Swedish Cancer Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002794","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,10,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Spatially resolved transcriptomics technologies generate gene expression data with retained positional information from a tissue section, often accompanied by a corresponding histological image. Computational tools should make it effortless to incorporate spatial information into data analyses and present analysis results in their histological context. Here, we present semla, an R package for processing, analysis, and visualization of spatially resolved transcriptomics data generated by the Visium platform, that includes interactive web applications for data exploration and tissue annotation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The R package semla is available on GitHub (https:\/\/github.com\/ludvigla\/semla), under the MIT License, and deposited on Zenodo (https:\/\/doi.org\/10.5281\/zenodo.8321645). Documentation and tutorials with detailed descriptions of usage can be found at https:\/\/ludvigla.github.io\/semla\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad626","type":"journal-article","created":{"date-parts":[[2023,10,17]],"date-time":"2023-10-17T11:29:40Z","timestamp":1697542180000},"source":"Crossref","is-referenced-by-count":56,"title":["<i>Semla:<\/i> a versatile toolkit for spatially resolved transcriptomics analysis and visualization"],"prefix":"10.1093","volume":"39","author":[{"given":"Ludvig","family":"Larsson","sequence":"first","affiliation":[{"name":"Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory , Tomtebodav\u00e4gen 23, 171 65 Solna , Stockholm, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3755-718X","authenticated-orcid":false,"given":"Lovisa","family":"Franz\u00e9n","sequence":"additional","affiliation":[{"name":"Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory , Tomtebodav\u00e4gen 23, 171 65 Solna , Stockholm, Sweden"},{"name":"Respiratory & Immunology, Neuroscience, Vaccines & Immune Therapies Safety, Clinical Pharmacology & Safety Sciences, BioPharmaceuticals R&D, AstraZeneca , Pepparedsleden 1, 431 83 M\u00f6lndal , Gothenburg, Sweden"}]},{"given":"Patrik L","family":"St\u00e5hl","sequence":"additional","affiliation":[{"name":"Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory , Tomtebodav\u00e4gen 23, 171 65 Solna , Stockholm, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4313-1601","authenticated-orcid":false,"given":"Joakim","family":"Lundeberg","sequence":"additional","affiliation":[{"name":"Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory , Tomtebodav\u00e4gen 23, 171 65 Solna , Stockholm, 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