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STAgent

STAgent，来自 FreedomIntelligence/OpenClaw-Medical-Skills 的 agent 技能。

读凭据读文件写文件严重 2 · 高危 7FreedomIntelligence/OpenClaw-Medical-Skills

它会碰到什么

扫了多少19 个文本文件，131 KB
它会碰到什么读凭据读文件写文件
命中总数15 处
命中统计严重 2 · 高 7 · 中 6 · 低 0
逐条看命中（9 条严重或高危）
  • 严重 repo/README.md:93cred-paths
    - modify the `.env` file (src/.env) with your own API keys:
  • 严重 repo/README.md:93cred-paths
    - modify the `.env` file (src/.env) with your own API keys:
  • 高 repo/src/speech_to_text.py:38cred-envread
    api_key=os.getenv("WHISPER_API_KEY")
  • 高 repo/src/speech_to_text.py:109cred-envread
    api_key=os.getenv("OPENAI_API_KEY")
  • 高 repo/src/tools.py:39cred-envread
    self.serp_api_key = serp_api_key or os.environ.get("SERP_API_KEY")
  • 高 repo/src/unified_app.py:276cred-envread
    if page == "OpenAI" and not os.getenv('OPENAI_API_KEY'):
  • 高 repo/src/unified_app.py:283cred-envread
    os.environ["OPENAI_API_KEY"] = api_key
  • 高 repo/src/unified_app.py:287cred-envread
    elif page == "Anthropic" and not os.getenv('ANTHROPIC_API_KEY'):
  • 高 repo/src/unified_app.py:290cred-envread
    os.environ["ANTHROPIC_API_KEY"] = api_key

这一栏是扫描器报的事实，不是结论。命中多不等于有毒（安全工具、规则库、示例脚本本来就会包含危险写法），命中少也不等于干净。它和你手上的凭据、文件、网络有什么关系，需要你自己看。

技能内容

<!--

COPYRIGHT NOTICE

This file is part of the "Universal Biomedical Skills" project.

Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>

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

-->

name: spatial-transcriptomics-agent

description: Spatial analyst

keywords:

  • spatial
  • h5ad
  • H&E
  • clustering
  • SVG

measurable_outcome: For each sample, deliver ≥1 spatial domain map + SVG list + narrative interpretation within 30 minutes.

license: MIT

metadata:

author: LiuLab

version: "1.0.0"

compatibility:

  • system: Python 3.9+

allowed-tools:

  • run_shell_command
  • read_file
  • web_fetch

Spatial Transcriptomics Agent

Run STAgent to align histology images with expression matrices, perform clustering/SVG detection, and generate literature-backed spatial reports.

When to Use

  • 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.

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.

Example Usage

User: "Analyze this breast cancer ST dataset, find immune infiltrates."
Agent: loads data, runs `sqidpy.gr.spatial_neighbors`, computes Leiden clusters, plots marker genes (CD3D, CD19), and summarizes which clusters map to tumor core vs. stromal/immune zones.

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.

References

  • Source repo: https://github.com/LiuLab-Bioelectronics-Harvard/STAgent
  • See local README.md for detailed instructions.

<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

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去原始仓库

它属于哪个仓库

仓库FreedomIntelligence/OpenClaw-Medical-Skills
星标★ 3,010
本站分层T1
该仓技能数897
原文件路径skills/spatial-transcriptomics-analysis/STAgent/SKILL.md

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