STcompare

STcompare enables comparative spatial transcriptomics analysis by testing for differences in spatial correlation and spatial fold-change across structurally matched tissue locations to identify differentially patterned genes.

Key Features:

• Spatial correlation testing: Tests for differences in spatial correlation across matched tissue locations.
• Spatial fold-change testing: Tests for differences in spatial fold-change across structurally matched locations.
• False positive control: Robustly controls for false positives even in the presence of spatial autocorrelation common in spatial transcriptomics data.
• Compatibility with biological replicates: Confirms high spatial correspondence of gene expression patterns across biological replicate samples.

Scientific Applications:

• Disease versus healthy tissue comparison: Identifies genes that spatially change in expression patterns between conditions, such as diseased versus healthy tissues.
• Acute kidney injury analysis: Identifies genes that spatially change in mouse kidneys with acute kidney injury compared to healthy control, revealing tissue compartment-specific molecular dysregulation.
• Cross-sample spatial pattern validation: Confirms high spatial correspondence of gene expression patterns across biological replicates of mouse brains.
• Distinct insight generation: Provides distinct insights from bulk differential gene expression analysis and spatially variable gene expression analysis as well as other spatial comparison methods.

Methodology:

STcompare uses a statistical framework that tests for differences in spatial correlation and spatial fold-change across structurally matched locations.