Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
Boston University School of Medicine, Boston, MA, USA.
Genome Biol. 2021 Mar 8;22(1):78. doi: 10.1186/s13059-021-02286-2.
Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.
空间转录组学和蛋白质组学技术为研究细胞的天然微环境提供了新的机会。在这里，我们介绍了 Giotto，这是一个全面的开源空间数据分析和可视化工具包。分析模块通过实现广泛的算法来全面分析组织成分、空间表达模式和细胞相互作用，提供端到端的分析。此外，还可以整合单细胞 RNAseq 数据进行空间细胞类型富集分析。可视化模块允许用户交互式地可视化分析输出和成像特征。为了展示其通用性，我们将 Giotto 应用于涵盖多种技术和平台的广泛数据集。
