spatial-transcriptomics-analysis-squidpy
Installation
SKILL.md
Squidpy Spatial Analysis
Overview
Graph and point-pattern statistics that describe how cell types (or spot clusters) are arranged in tissue and which genes follow a spatial pattern. Each Core API module answers one question and exports a CSV:
| Question | Module |
|---|---|
| Which cell types sit next to each other more than chance? | 2 Neighbourhood enrichment |
| At what distance do two types co-occur? | 3 Co-occurrence |
| How many contacts between types; which types are central? | 4 Interaction matrix + centrality |
| Is a type clustered, random or dispersed? | 5 Ripley's statistics |
| Which genes are spatially patterned? | 6 Spatial autocorrelation |
| Which LR pairs are specific to a cluster pair? | 7 Ligand-receptor test |