bio-spatial-transcriptomics-spatial-domains - Spatial Domain Detection in Spatial Transcriptomics
Identify spatial domains and tissue regions using expression and spatial context clustering
Tags
Updated: 2026-03-20Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Build spatial neighbors graph
- Run Leiden clustering
- Combine expression graphs
- Compute silhouette scores
- Smooth domain boundaries
- Compare clustering methods
- Find marker genes
- Annotate domains
- Visualize clustering results
Inputs
- Spatial transcriptomics data
- AnnData object
- Gene expression matrix
- Spatial coordinates
Outputs
- Domain labels
- Cluster assignments
- Visualization plots
- Marker gene lists
- Silhouette scores
Requirements
- Python 3.x
- Squidpy
- Scanpy
- NumPy
- SciPy
- scikit-learn