{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T03:35:26Z","timestamp":1769052926674,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,7,12]],"date-time":"2023-07-12T00:00:00Z","timestamp":1689120000000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P50HD103555"],"award-info":[{"award-number":["P50HD103555"]}],"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":["U54NS093793"],"award-info":[{"award-number":["U54NS093793"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>In the era where transcriptome profiling moves toward single-cell and spatial resolutions, the traditional co-expression analysis lacks the power to fully utilize such rich information to unravel spatial gene associations. Here, we present a Python package called Spatial Enrichment Analysis of Gene Associations using L-index (SEAGAL) to detect and visualize spatial gene correlations at both single-gene and gene-set levels. Our package takes spatial transcriptomics datasets with gene expression and the aligned spatial coordinates as input. It allows for analyzing and visualizing genes\u2019 spatial correlations and cell types\u2019 colocalization within the precise spatial context. The output could be visualized as volcano plots and heatmaps with a few lines of code, thus providing an easy-yet-comprehensive tool for mining spatial gene associations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The Python package SEAGAL can be installed using pip: https:\/\/pypi.org\/project\/seagal\/. The source code and step-by-step tutorials are available at: https:\/\/github.com\/linhuawang\/SEAGAL.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad431","type":"journal-article","created":{"date-parts":[[2023,7,11]],"date-time":"2023-07-11T20:41:11Z","timestamp":1689108071000},"source":"Crossref","is-referenced-by-count":4,"title":["Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6717-860X","authenticated-orcid":false,"given":"Linhua","family":"Wang","sequence":"first","affiliation":[{"name":"Graduate School of Biomedical Sciences, Program in Quantitative and Computational Biosciences, Baylor College of Medicine , 1 Baylor Plaza , Houston, TX 77030, United States"}]},{"given":"Chaozhong","family":"Liu","sequence":"additional","affiliation":[{"name":"Graduate School of Biomedical Sciences, Program in Quantitative and Computational Biosciences, Baylor College of Medicine , 1 Baylor Plaza , Houston, TX 77030, United States"}]},{"given":"Yang","family":"Gao","sequence":"additional","affiliation":[{"name":"Lester and Sue Smith Breast Center, Baylor College of Medicine , 1 Baylor Plaza , Houston, TX 77030, United States"}]},{"given":"Xiang H -F","family":"Zhang","sequence":"additional","affiliation":[{"name":"Lester and Sue Smith Breast Center, Baylor College of Medicine , 1 Baylor Plaza , Houston, TX 77030, United States"},{"name":"Department of Molecular and Cellular Biology, Baylor College of Medicine , 1 Baylor Plaza , Houston, TX 77030, United States"},{"name":"McNair Medical Institute, Baylor College of Medicine , 1 Baylor Plaza , Houston, TX 77030, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7608-0831","authenticated-orcid":false,"given":"Zhandong","family":"Liu","sequence":"additional","affiliation":[{"name":"Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , 1250 Moursund St , Houston, TX 77030, United States"},{"name":"Department of Pediatrics, Baylor College of Medicine , 1 Baylor Plaza , Houston, TX 77030, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,7,12]]},"reference":[{"key":"2023072302335658500_btad431-B1","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1016\/j.ccell.2022.08.021","article-title":"Spatial transcriptomics","volume":"40","author":"Anderson","year":"2022","journal-title":"Cancer Cell"},{"key":"2023072302335658500_btad431-B2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc Ser B (Methodol)"},{"key":"2023072302335658500_btad431-B3","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1016\/j.immuni.2013.10.003","article-title":"Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer","volume":"39","author":"Bindea","year":"2013","journal-title":"Immunity"},{"key":"2023072302335658500_btad431-B4","doi-asserted-by":"crossref","first-page":"156","DOI":"10.3390\/biom13010156","article-title":"Advances and challenges in spatial transcriptomics for developmental biology","volume":"13","author":"Choe","year":"2023","journal-title":"Biomolecules"},{"key":"2023072302335658500_btad431-B5","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/s41592-020-01040-z","article-title":"Spatially resolved transcriptomics in neuroscience","volume":"18","author":"Close","year":"2021","journal-title":"Nat Methods"},{"key":"2023072302335658500_btad431-B6","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":"2023072302335658500_btad431-B7","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/s41586-019-1186-3","article-title":"Next-generation characterization of the cancer cell line encyclopedia","volume":"569","author":"Ghandi","year":"2019","journal-title":"Nature"},{"key":"2023072302335658500_btad431-B8","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023072302335658500_btad431-B9","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1007\/s101090100064","article-title":"Developing a bivariate spatial association measure: an integration of Pearson's r and Moran's I","volume":"3","author":"Lee","year":"2001","journal-title":"J Geograph Syst"},{"key":"2023072302335658500_btad431-B10","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/s41592-020-01033-y","article-title":"Method of the year: spatially resolved transcriptomics","volume":"18","author":"Marx","year":"2021","journal-title":"Nat Methods"},{"key":"2023072302335658500_btad431-B11","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/s41592-021-01358-2","article-title":"Squidpy: a scalable framework for spatial omics analysis","volume":"19","author":"Palla","year":"2022","journal-title":"Nat Methods"},{"key":"2023072302335658500_btad431-B12","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.4636","article-title":"SpatialDE: identification of spatially variable genes","volume":"15","author":"Svensson","year":"2018","journal-title":"Nat Methods"},{"key":"2023072302335658500_btad431-B13","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad431\/50860583\/btad431.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/7\/btad431\/50938969\/btad431.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/7\/btad431\/50938969\/btad431.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T23:57:19Z","timestamp":1729727839000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad431\/7223197"}},"subtitle":[],"editor":[{"given":"Zhiyong","family":"Lu","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,7,1]]},"references-count":13,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2023,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad431","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,1]]},"published":{"date-parts":[[2023,7,1]]},"article-number":"btad431"}}