spatial-transcriptomics-agent

STAgent (Spatial Transcriptomics Agent)

ID: biomedical.genomics.st_agent Version: 1.0.0 Status: Candidate Category: Genomics / Spatial Transcriptomics

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Overview

STAgent is a multimodal LLM-based autonomous agent designed for spatial transcriptomics (ST) data analysis. Unlike standard single-cell analysis, ST requires understanding both gene expression and histological (visual) context. STAgent integrates visual reasoning (H&E images) with code generation to perform tasks like identifying spatially variable genes (SVGs) and cell-cell communication analysis.

Key Capabilities

• Visual Reasoning: Analyzes H&E images to identify tissue regions (tumor vs. stroma).
• Tool Use: Automates Scanpy, Squidpy, and Giotto workflows.
• Reporting: Generates publication-style reports with embedded plots.

Reference

• LiuLab-Bioelectronics-Harvard (GitHub)