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STcompare: Framework for Spatial Transcriptomic Data Comparison

Source: R/STcompare-package.R
STcompare-package.Rd

Compares the spatial gene expression patterns of two spatial transcriptomics datasets of structurally matched tissues, rasterized onto a shared grid of pixels. For each gene, a spatial correlation test gives a permutation p-value that accounts for the spatial autocorrelation of both patterns (Viladomat et al. (2014) doi:10.1111/biom.12139 ), and a spatial fold-change similarity measures how often the expression at matched locations is within a fold change. The method is described in Clifton et al. (2026) doi:10.1093/bioinformatics/btag644 .

Details

The main function is compareSpatial(): for every gene measured in two samples rasterized onto one grid of pixels, it tests whether the spatial patterns are correlated beyond what their spatial autocorrelation alone would give, and measures how often the expression at matched pixels is within a fold change. The functions of the published analyses (spatialCorrelationGeneExp(), spatialCorrelationGeneExpIterPermutations() and spatialSimilarity()) reproduce them exactly.

References

Clifton K, Jiang V, Peixoto RdS, Singh S, Matsuura R, Rabb H, Fan J (2026). STcompare: comparative spatial transcriptomics data analysis of structurally matched tissues to characterize differentially spatially patterned genes. Bioinformatics 42(9):btag644. doi:10.1093/bioinformatics/btag644

See also

Useful links:

Author

Maintainer: Kalen Clifton kclifto2@jh.edu (ORCID)

Authors: