{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:11:06Z","timestamp":1772165466274,"version":"3.50.1"},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T00:00:00Z","timestamp":1674777600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T00:00:00Z","timestamp":1674777600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background:<\/jats:title>\n                    <jats:p>The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called \u2019spatial transcriptomics\u2019. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results:<\/jats:title>\n                    <jats:p>Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions:<\/jats:title>\n                    <jats:p>Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-023-05150-1","type":"journal-article","created":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T04:04:39Z","timestamp":1674792279000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics"],"prefix":"10.1186","volume":"24","author":[{"given":"Fr\u00e9d\u00e9ric","family":"Pont","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan Pablo","family":"Cerapio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pauline","family":"Gravelle","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laetitia","family":"Ligat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carine","family":"Valle","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emeline","family":"Sarot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marion","family":"Perrier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Lopez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camille","family":"Laurent","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean Jacques","family":"Fourni\u00e9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5278-5952","authenticated-orcid":false,"given":"Marie","family":"Tosolini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,1,27]]},"reference":[{"key":"5150_CR1","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","volume":"36","author":"A Butler","year":"2018","unstructured":"Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36:411\u201320.","journal-title":"Nat Biotechnol"},{"issue":"1","key":"5150_CR2","doi-asserted-by":"publisher","first-page":"1939518","DOI":"10.1080\/2162402X.2021.1939518","volume":"10","author":"J-P Cerapio","year":"2021","unstructured":"Cerapio J-P, Perrier M, Balan\u00e7a C-C, Gravelle P, Pont F, Devaud C, Franchini D-M, F\u00e9liu V, Tosolini M, Valle C, et al. Phased differentiation of $$\\gamma$$$$\\delta$$ t and t cd8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers. Oncoimmunology. 2021;10(1):1939518.","journal-title":"Oncoimmunology"},{"key":"5150_CR3","first-page":"127","volume-title":"Cytobank: providing an analytics platform for community cytometry data analysis and collaboration","author":"TJ Chen","year":"2014","unstructured":"Chen TJ, Kotecha N. Cytobank: providing an analytics platform for community cytometry data analysis and collaboration. Berlin: Springer; 2014. p. 127\u201357."},{"issue":"13","key":"5150_CR4","doi-asserted-by":"publisher","first-page":"3559","DOI":"10.1016\/j.cell.2021.05.010","volume":"184","author":"C-S Cho","year":"2021","unstructured":"Cho C-S, Xi J, Si Y, Park S-R, Hsu J-E, Kim M, Jun G, Kang HM, Lee JH. Microscopic examination of spatial transcriptome using seq-scope. Cell. 2021;184(13):3559\u201372.","journal-title":"Cell"},{"issue":"6581","key":"5150_CR5","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1126\/science.abg7216","volume":"375","author":"Y Deng","year":"2022","unstructured":"Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R. Spatial-cut &tag: spatially resolved chromatin modification profiling at the cellular level. 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