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spatial-transcriptomics-agent

Maintainer FreedomIntelligence · Last updated April 1, 2026

End-to-end spatial transcriptomics analysis: QC, deconvolution, domain detection.

OpenClawNanoClawAnalysisReproductionspatial-transcriptomics-agent🧠 bioos extended suitesingle-cell & spatial agentsend

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-transcriptomics-agent

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Run STAgent to align histology images with expression matrices, perform clustering/SVG detection, and generate literature-backed spatial reports.
  • Analysis of Visium/Xenium or similar ST datasets.
  • Visual reasoning over spatial plots, H&E images, or cluster maps.
  • Automatically generating Scanpy/Squidpy code for new ST workflows.
  • Hypothesis generation about spatial gene expression patterns.

Source Doc

Excerpt From SKILL.md

Core Capabilities

  1. Dynamic code generation: Create/execute Python scripts for QC, clustering, SVG detection.
  2. Visual reasoning: Interpret spatial plots to identify tissue domains and cell neighborhoods.
  3. Literature retrieval: Pull references that contextualize findings.
  4. Report generation: Deliver publication-style writeups with plots and SVG tables.

Workflow

  1. Env setup: conda env create -f environment.yml && conda activate STAgent.
  2. Data prep: Supply expression_path (.h5ad/Spaceranger) + image_path (H&E/IF) and metadata.
  3. Task selection: Choose tasks such as cluster, find_svg, annotate_domains, or composite instructions; run python repo/src/main.py --data_path ... --task "...".
  4. Execute & interpret: Let STAgent generate scripts, run analyses, and interpret results with literature references.
  5. Package outputs: Save UMAP/spatial plots, SVG tables, QC details, and summary markdown.

Guardrails

  • Document coordinate systems and any scaling between imaging and expression coordinates.
  • Avoid definitive cell-type labels without supporting markers.
  • Capture QC parameters for reproducibility.

Use cases

  • Use spatial-transcriptomics-agent for single-cell or spatial omics analysis.
  • Apply spatial-transcriptomics-agent to clustering, integration, or trajectory workflows.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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