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.
CITATION STYLE
Dries, R., Zhu, Q., Dong, R., Eng, C. H. L., Li, H., Liu, K., … Yuan, G. C. (2021). Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biology, 22(1). https://doi.org/10.1186/s13059-021-02286-2
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