Journal
GENOME BIOLOGY
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02286-2
Keywords
-
Funding
- NIH [UH3HL145609, R01AG066028]
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Giotto is a comprehensive open-source toolbox for spatial data analysis and visualization, providing end-to-end analysis with a wide range of algorithms for characterizing tissue composition and cellular interactions, as well as integrating single-cell RNAseq data for cell-type enrichment analysis. The visualization module allows interactive visualization of analysis outputs and imaging features, demonstrating its general applicability across diverse datasets and platforms.
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.
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