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

Bioinformatics. 2022 Apr 28;38(9):2645-2647. doi: 10.1093/bioinformatics/btac145.


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 A script to reproduce the analyses in this manuscript is available in Supplementary information. The Thrane study data included in spatialGE was made available from the public available from the website

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cluster Analysis
  • Humans
  • Neoplasms* / genetics
  • Software
  • Transcriptome*
  • Tumor Microenvironment