{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:13Z","timestamp":1772138053431,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,3,8]],"date-time":"2022-03-08T00:00:00Z","timestamp":1646697600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32-CA233399"],"award-info":[{"award-number":["T32-CA233399"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P30-CA076292"],"award-info":[{"award-number":["P30-CA076292"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R00-CA226679"],"award-info":[{"award-number":["R00-CA226679"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Spatially resolved transcriptomics promises to increase our understanding of the tumor microenvironment and improve cancer prognosis and therapies. Nonetheless, analytical methods to explore associations between the spatial heterogeneity of the tumor and clinical data are not available. Hence, we have developed spatialGE, a software that provides visualizations and quantification of the tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics that can be compared against clinical information, spot-level cell deconvolution and spatially informed clustering, all using a new data object to store data and resulting analyses simultaneously.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The R package and tutorial\/vignette are available at https:\/\/github.com\/FridleyLab\/spatialGE. A script to reproduce the analyses in this manuscript is available in Supplementary information. The Thrane study data included in spatialGE was made available from the public available from the website https:\/\/www.spatialresearch.org\/resources-published-datasets\/doi-10-1158-0008-5472-can-18-0747\/.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac145","type":"journal-article","created":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T15:13:12Z","timestamp":1646665992000},"page":"2645-2647","source":"Crossref","is-referenced-by-count":28,"title":["spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5986-4207","authenticated-orcid":false,"given":"Oscar E","family":"Ospina","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Moffitt Cancer Center , Tampa, FL 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher M","family":"Wilson","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Moffitt Cancer Center , Tampa, FL 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex C","family":"Soupir","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Moffitt Cancer Center , Tampa, FL 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Berglund","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Moffitt Cancer Center , Tampa, FL 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Inna","family":"Smalley","sequence":"additional","affiliation":[{"name":"Department of Tumor Biology, Moffitt Cancer Center , Tampa, FL 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenneth Y","family":"Tsai","sequence":"additional","affiliation":[{"name":"Department of Anatomic Pathology, Moffitt Cancer Center , Tampa, FL 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7739-7956","authenticated-orcid":false,"given":"Brooke L","family":"Fridley","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, Moffitt Cancer Center , Tampa, FL 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,3,8]]},"reference":[{"key":"2023041402570902800_","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/s13059-017-1349-1","article-title":"xCell: digitally portraying the tissue cellular heterogeneity landscape","volume":"18","author":"Aran","year":"2017","journal-title":"Genome Biol"},{"key":"2023041402570902800_","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1186\/s12864-020-06832-3","article-title":"Seamless integration of image and molecular analysis for spatial transcriptomics workflows","volume":"21","author":"Bergenstrahle","year":"2020","journal-title":"BMC Genomics"},{"key":"2023041402570902800_","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1007\/978-0-387-48536-2_6","volume-title":"Model-Based Geostatistics","author":"Diggle","year":"2007"},{"key":"2023041402570902800_","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s13059-021-02286-2","article-title":"Giotto: a toolbox for integrative analysis and visualization of spatial expression data","volume":"22","author":"Dries","year":"2021","journal-title":"Genome Biol"},{"key":"2023041402570902800_","first-page":"115","article-title":"The contiguity ratio and statistical mapping","volume":"5","author":"Geary","year":"1954","journal-title":"Incorp. 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