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Giotto: a toolbox for integrative analysis and visualization of spatial expression data.

ABSTRACT: 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.

SUBMITTER: Dries R

PROVIDER: S-EPMC7938609 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Giotto: a toolbox for integrative analysis and visualization of spatial expression data.

Dries Ruben R Zhu Qian Q Dong Rui R Eng Chee-Huat Linus CL Li Huipeng H Liu Kan K Fu Yuntian Y Zhao Tianxiao T Sarkar Arpan A Bao Feng F George Rani E RE Pierson Nico N Cai Long L Yuan Guo-Cheng GC

Genome biology 20210308 1

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 ...[more]

PMID: 33685491

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