Chen Jiaji George, Chávez-Fuentes Joselyn Cristina, O'Brien Matthew, Xu Junxiang, Ruiz Edward, Wang Wen, Amin Iqra, Sarfraz Irzam, Guckhool Pratishtha, Sistig Adriana, Yuan Guo-Cheng, Dries Ruben
Section of Hematology and Medical Oncology, Boston University School of Medicine and Boston Medical Center, Boston, MA 02118, USA.
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
bioRxiv. 2023 Nov 27:2023.11.26.568752. doi: 10.1101/2023.11.26.568752.
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.
新兴的空间组学技术不断推动组织结构的分子图谱绘制以及基因调控和细胞间相互作用的研究，进而为广泛的生物过程和疾病提供新的机制性见解。此类技术在多个空间尺度上提供了越来越多的信息内容。然而，高效地表示和整合多样的空间数据集，包括以可扩展且灵活的方式组合多种模态或空间尺度，仍然是一项重大挑战。在此，我们展示了Giotto Suite，这是一套开源软件包，构成了一个完全模块化且集成的空间数据分析工具箱的基础。Giotto Suite的核心是围绕一个嵌入R软件环境的创新且与技术无关的数据框架构建的，该框架允许以任何空间分辨率表示和整合几乎任何类型的空间组学数据。此外，Giotto Suite为数据分析、整合和可视化提供了可扩展且可延伸的端到端解决方案。Giotto Suite整合了分子、形态、空间和带注释的特征信息，以创建一个响应式且灵活的多尺度、多组学数据分析工作流程，本文通过应用于几种最先进的空间技术对此进行了展示。此外，Giotto Suite基于可互操作的接口和数据结构构建，这些接口和数据结构架起了基因组学和空间数据科学这两个既定领域之间的桥梁，从而使独立开发者能够创建定制设计的管道。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。
