Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics

被引：5

作者：

Pont, Frederic ^{[1
,2
,3
]}

Cerapio, Juan Pablo ^{[1
,2
,3
]}

Gravelle, Pauline ^{[1
,2
,3
]}

Ligat, Laetitia ^{[1
,2
,3
]}

Valle, Carine ^{[1
,2
,3
]}

Sarot, Emeline ^{[1
,2
,3
]}

Perrier, Marion ^{[1
,2
,3
]}

Lopez, Frederic ^{[1
,2
,3
]}

Laurent, Camille ^{[1
,2
,3
]}

Fournie, Jean Jacques ^{[1
,2
,3
]}

Tosolini, Marie ^{[1
,2
,3
]}

机构：

[1] Univ Toulouse III Paul Sabatier, Univ Toulouse, Ctr Rech Cancerol Toulouse, CRCT,CNRS,INSERM, Toulouse, France

[2] IUCT Oncopole, Toulouse, France

[3] TOUCAN, Lab Excellence Toulouse Canc, Toulouse, France

来源：

BMC BIOINFORMATICS | 2023年 / 24卷 / 01期

关键词：

Spatial transcriptomics; Single-cell; Multimodal analysis; Visualization; Open-source; Freeware; BOP GENE-CLUSTER; PROTEIN; PREDICTION; EXPRESSION; DIVERSITY;

D O I：

10.1186/s12859-023-05150-1

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: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 'spatial transcriptomics'. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce.Results: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.Conclusions:Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.

引用

页数：12

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