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  3. SpaOTsc: Inferring spatial and signaling relationships between cells from single cell transcriptomic data

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SpaOTsc: Inferring spatial and signaling relationships between cells from single cell transcriptomic data

What is being modeled?
Spatial locations and spatial cell-cell communications of scRNA-seq data
Description & purpose of resource

SpaOTsc uses optimal transport to 1) project between scRNA-seq data and spatial data, 2) infer spatial cell-cell communications of scRNA-seq data, and 3) identify spatially localized subpopulations.

Spatial scales
cellular
tissue
Temporal scales
1 - 103 s
hours
days
This resource is currently
mature and useful in ongoing research
Link to Resource Credibility Assessment
SpaOTsc: Inferring spatial and signaling relationships between cells from single cell transcriptomic data
Can this resource be associated with other resources? (e.g.: modular models, linked tools and platforms)
Yes
Key publications (e.g. describing or using resource)

Cang, Zixuan, and Qing Nie. "Inferring spatial and signaling relationships between cells from single cell transcriptomic data." Nature communications 11.1 (2020): 1-13.

DOI link to publication describing this resource

10.1038/s41467-020-15968-5

Link to resource
SpaOTsc package
Collaborators
Qing Nie
PI contact information
qnie@uci.edu
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