# Spatial Cell-Cell Communication - Usage Guide

> This skill covers analyzing cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Identify which cell types are communicating and through which signaling pathways.

- Skill: `tools-only/spatial-cell-cell-communication-usage-guide` (Agent Skill, multi-file: 3 files)
- Install (CLI): `npx skillmds@latest add tools-only/spatial-cell-cell-communication-usage-guide`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tools-only/spatial-cell-cell-communication-usage-guide/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: tools-only (https://skillmd.com/u/tools-only)
- Updated: 2026-09-29
- Page: https://skillmd.com/skills/tools-only/spatial-cell-cell-communication-usage-guide

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# Spatial Cell-Cell Communication - Usage Guide

## Overview

This skill covers analyzing cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Identify which cell types are communicating and through which signaling pathways.

## Prerequisites

```bash
pip install squidpy scanpy pandas networkx matplotlib
```

## Quick Start

Tell your AI agent what you want to do:
- "Run ligand-receptor analysis on my spatial data"
- "Find which cell types are communicating"

## Example Prompts

### Basic Analysis
> "Analyze cell-cell communication in my Visium data"

> "Run ligand-receptor analysis between cell types"

### Specific Interactions
> "Find interactions between T cells and macrophages"

> "Check if CCL2-CCR2 signaling is active"

### Visualization
> "Show a heatmap of cell-cell interactions"

> "Plot the communication network"

## What the Agent Will Do

1. Verify cell type annotations exist
2. Build spatial neighbor graph
3. Run ligand-receptor permutation test
4. Filter significant interactions
5. Visualize results

## Tips

- **Cell type annotations** - Required before running communication analysis
- **Spatial neighbors** - Analysis considers spatial proximity
- **Permutations** - More permutations = more robust p-values but slower
- **Custom databases** - Can use custom ligand-receptor pair lists