In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

OLD Giotto Suite website

Please use the new website www.giottosuite.com.

Multi-level Spatial Biology Exploration

Giotto Suite is the new and updated version of Giotto.
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Giotto Suite is being developed as a suite of software tools, including data structures and methods, for the comprehensive analysis and visualization of spatial multi-omics data at all scales and multiple resolutions. It extends and improves our previous R package Giotto. The underlying framework is generalizable to virtually all current and emerging spatial technologies which may differ in resolution(subcellular, single cell or multiple cells), spatial dimension (2D vs 3D), molecular modality (protein, RNA, DNA, …), and throughput (number of cells and analytes). This will ensure that our spatial analysis solutions remain compatible with all current and future developed spatial technologies and platforms. It will also aid in the further integration with other external analysis pipelines and tools.

See NEWS for more details.

Workflow

Wide Compatibility

	Visium
	Seq-Scope
	CyCIF
	IMC
	seqFISH
	MERSCOPE
	CosMx
	. . .

Spatial Data	Image Data	Single-Cell Data
Array-based	Raw (e.g. tiff)	Expression matrix
Spatial Data	Mask files
Subcellular	Polygon shapes

Data Structure

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Analysis

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More technical information can be found in the detailed workflow section.

References

• Dries, R., Zhu, Q. et al. Giotto, a toolbox for integrative analysis and visualization of spatial expression data. Genome Biology (2021). \doi{https://doi.org/10.1186/s13059-021-02286-2}

• Dries, R., Chen, J., Rossi, N. del, Khan, M.M., Sistig, A., Yuan, G.-C., 2021. Advances in spatial transcriptomic data analysis. Genome Res. 31, 1706–1718

• Del Rossi, N., Chen, J. et al. Analyzing Spatial Transcriptomics Data Using Giotto. Current Protocols (2022).

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drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.