SpatialDE

SpatialDE identifies genes with spatially variable expression in tissue samples using data from high-throughput multiplexed imaging and spatial RNA-sequencing to reveal spatial patterns of gene regulation.

Key Features:

• Statistical Testing for Spatial Patterns: Employs a statistical test to detect and characterize genes with significant spatial expression variation across tissue coordinates.
• Automatic Expression Histology: Uses spatial gene-clustering to generate expression-based tissue histologies by grouping genes with similar spatial expression patterns.

Scientific Applications:

• Developmental biology: Maps spatial expression gradients to study organogenesis and tissue patterning.
• Oncology: Identifies genes differentially expressed across tumor versus normal tissue regions, aiding discovery of biomarkers or therapeutic targets.
• Regenerative medicine: Characterizes spatial organization of gene expression relevant to tissue repair and regeneration.

Methodology:

Analyzes multiplexed imaging and spatial RNA-sequencing datasets, quantifies spatial variation in gene expression, applies a statistical test to assess deviation from random distribution, and performs spatial gene-clustering to produce automatic expression histology.