Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem.
Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem.
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Giotto Suite：多尺度且与技术无关的空间多组学分析生态系统。
DOI：
10.1101/2023.11.26.568752
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Dries,Ruben
中科院分区：
文献类型：
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作者：
Chen,JiajiGeorge;Chávez-Fuentes,JoselynCristina;O'Brien,Matthew;Xu,Junxiang;Ruiz,Edward;Wang,Wen;Amin,Iqra;Sarfraz,Irzam;Guckhool,Pratishtha;Sistig,Adriana;Yuan,Guo-Cheng;Dries,Ruben
新兴的空间组学技术继续推进组织结构的分子映射以及基因调控和细胞串扰的研究，这反过来又为广泛的生物过程和疾病提供了新的机制见解。这些技术在多个空间尺度上提供越来越多的信息内容。然而，有效地表示和协调不同的空间数据集，包括以可扩展和灵活的方式组合多种模式或空间尺度，仍然是一项重大挑战。在这里，我们介绍了Giotto Suite，这是一套开源软件包，它是一个完全模块化和集成的空间数据分析工具箱的基础。Giotto Suite的核心是一个嵌入在R软件环境中的创新和技术无关的数据框架，它允许以任何空间分辨率表示和集成几乎任何类型的空间组学数据。此外，Giotto Suite还为数据分析、集成和可视化提供了可扩展的端到端解决方案。Giotto Suite集成了分子、形态学、空间和注释特征信息，为多尺度、多组学数据分析创建了一个响应灵活的工作流程，如本文所示，它应用于几种最先进的空间技术。此外，Giotto Suite建立在可互操作的接口和数据结构基础上，将基因组学和空间数据科学的既定领域连接起来，从而使独立开发人员能够创建定制工程管道。因此，Giotto Suite为空间多组学数据分析创建了一个沉浸式生态系统。
Emerging spatial omics technologies continue to advance the molecular mapping of tissue architecture and the investigation of gene regulation and cellular crosstalk, which in turn provide new mechanistic insights into a wide range of biological processes and diseases. Such technologies provide an increasingly large amount of information content at multiple spatial scales. However, representing and harmonizing diverse spatial datasets efficiently, including combining multiple modalities or spatial scales in a scalable and flexible manner, remains a substantial challenge. Here, we present Giotto Suite, a suite of open-source software packages that underlies a fully modular and integrated spatial data analysis toolbox. At its core, Giotto Suite is centered around an innovative and technology-agnostic data framework embedded in the R software environment, which allows the representation and integration of virtually any type of spatial omics data at any spatial resolution. In addition, Giotto Suite provides both scalable and extensible end-to-end solutions for data analysis, integration, and visualization. Giotto Suite integrates molecular, morphology, spatial, and annotated feature information to create a responsive and flexible workflow for multi-scale, multi-omic data analyses, as demonstrated here by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive ecosystem for spatial multi-omic data analysis.