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spatial-transcriptomics

ToolUniverse workflow — Spatial Transcriptomics

skills/spatial-transcriptomics/SKILL.md

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---
name: tooluniverse-spatial-transcriptomics
description: Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms. Performs spatial clustering, domain identification, cell-cell proximity analysis, spatial gene expression patterns, tissue architecture mapping, and integration with single-cell data. Use when analyzing spatial transcriptomics datasets, studying tissue organization, identifying spatial expression patterns, mapping cell-cell interactions in tissue context, characterizing tumor microenvironment spatial structure, or integrating spatial and single-cell RNA-seq data for comprehensive tissue analysis.
---

# Spatial Transcriptomics Analysis

Comprehensive analysis of spatially-resolved transcriptomics data to understand gene expression patterns in tissue architecture context. Combines expression profiling with spatial coordinates to reveal tissue organization, cell-cell interactions, and spatially variable genes.

## When to Use This Skill

**Triggers**:
- User has spatial transcriptomics data (Visium, MERFISH, seqFISH, etc.)
- Questions about tissue architecture or spatial organization