Table 3.

Analysis Packages for ST Data

	Programming Language	Clustering	Incorporates Histology	Integration with scRNA-seq	CCI Analysis	Additional Features
Seurat	R	Yes	No	Yes	No	Widely used Supports integration with additional single-cell assays (multimodal data support)
Giotto	R	Yes	No	Yes	Yes	Interactive component
BayesSpace	R	Yes	No	No	No	Resolution enhancement of low-resolution data
Tangram	Python	No	Yes	Yes	No	Multimodal data support
SpaOTsc	Python	No	No	Yes	Yes	Infers spatial distance of cell-cell signaling
SpaGCN	Python	Yes	Yes	No	No	Adjustable parameter for weighting of histology on spatial clustering

For comprehensive overview of data analysis and packages, see Lewis et al. 2021; Longo et al. 2021.