SpatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics.

ABSTRACT:

Summary

Spatially resolved transcriptomics promises to increase our understanding of the tumor microenvironment and improve cancer prognosis and therapies. Nonetheless, analytical methods to explore associations between the spatial heterogeneity of the tumor and clinical data are not available. Hence, we have developed spatialGE, a software that provides visualizations and quantification of the tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics that can be compared against clinical information, spot-level cell deconvolution and spatially informed clustering, all using a new data object to store data and resulting analyses simultaneously.

Availability and implementation

The R package and tutorial/vignette are available at h

SUBMITTER: Ospina OE 

PROVIDER: S-EPMC9890305 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature