SPATA

SPATA analyzes spatial transcriptomic data to characterize spatially resolved gene expression patterns and transient dynamics across tissue regions.

Key Features:

• Spatially Resolved Gene Expression Characterization: Characterizes spatially resolved gene expression to identify localized transcriptional programs within tissue sections.
• Transient Dynamics Analysis: Models transient dynamics along spatial trajectories to elucidate temporal changes in gene expression across tissue regions.
• Integration with Monocle3-Pseudotime: Integrates monocle3-pseudotime analysis to examine transcriptional dynamics in combined spatial and temporal contexts.
• Visualization and Trajectory Drawing: Visualizes gene expression patterns and pathway enrichment and enables drawing of spatial trajectories to model directional changes.
• Segmentation for Comparative Analysis: Segments samples into subregions to enable comparative analysis of regional gene expression and pathway activity.

Scientific Applications:

• Developmental Biology: Investigates spatial and temporal transcriptional programs underlying tissue development.
• Cancer Research: Resolves regional gene expression and pathway activity to study tumor heterogeneity and microenvironmental interactions.
• Regenerative Medicine: Maps spatial gene expression dynamics relevant to tissue repair and cellular differentiation.

Methodology:

Implements modeling of transient dynamics along spatial trajectories, integrates monocle3-pseudotime, computes pathway enrichment, visualizes gene expression and pathway activity, supports drawing of spatial trajectories, and segments samples into subregions.