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SpatialAgent

Skill FridrichMethod/awesome-skills/skills/spatial-transcriptomics-analysis/SpatialAgent

An agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.From its SKILL.md

Install
npx -y skills add FridrichMethod/awesome-skills --skill SpatialAgent

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SKILL.md

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<!-- # COPYRIGHT NOTICE # This file is part of the "Universal Biomedical Skills" project. # Copyright (c) 2026 MD BABU MIA, PhD <[email protected]> # All Rights Reserved. # # This code is proprietary and confidential. # Unauthorized copying of this file, via any medium is strictly prohibited. # # Provenance: Authenticated by MD BABU MIA -->

SpatialAgent

SpatialAgent focuses on the biological interpretation of spatial transcriptomics data, specifically aiming to propose mechanistic hypotheses about tissue organization and cellular interactions.

When to Use This Skill

  • Mechanistic Interpretation: When you have clusters or spatial domains and need to understand why they are organized that way.
  • Cell-Cell Interaction: To predict and interpret ligand-receptor interactions in a spatial context.
  • Hypothesis Generation: To propose biological mechanisms driving the observed spatial heterogeneity.

Core Capabilities

  1. Tissue Organization Analysis: Decodes the structural logic of tissues (e.g., layers, niches).
  2. Cellular Interaction Prediction: Identifies potential signaling pathways active at domain boundaries.
  3. Hypothesis Proposal: Generates testable biological hypotheses based on spatial data.

Workflow

  1. Input Analysis: Accepts processed ST data (e.g., cluster annotations, DEG lists per spatial domain).
  2. Knowledge Retrieval: Queries biological knowledge bases regarding the observed cell types and genes.
  3. Synthesis: Constructs a narrative explaining the spatial arrangement (e.g., "The proximity of fibroblasts and tumor cells suggests a desmoplastic reaction mediated by TGF-beta signaling...").

Example Usage

User: "Why are the macrophages located at the boundary of the tumor core in this sample?"

Agent Action:

  1. Analyzes the gene expression of macrophages and adjacent tumor cells.
  2. Checks for ligand-receptor pairs (e.g., CSF1-CSF1R).
  3. Proposes: "Macrophages are likely recruited by CSF1 secreted by the tumor cells, forming an immunosuppressive barrier..."
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

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