跳到主要内容
知知仓学习社ZHICANG

spatial-transcriptomics-analysis

spatial-transcriptomics-analysis，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57 个文本文件，250 KB
它会碰到什么读凭据读文件写文件
命中总数17 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 STAgent/repo/README.md:93cred-paths
    - modify the `.env` file (src/.env) with your own API keys:
  • 严重 STAgent/repo/README.md:93cred-paths
    - modify the `.env` file (src/.env) with your own API keys:
  • 高 STAgent/repo/src/speech_to_text.py:38cred-envread
    api_key=os.getenv("WHISPER_API_KEY")
  • 高 STAgent/repo/src/speech_to_text.py:109cred-envread
    api_key=os.getenv("OPENAI_API_KEY")
  • 高 STAgent/repo/src/tools.py:39cred-envread
    self.serp_api_key = serp_api_key or os.environ.get("SERP_API_KEY")
  • 高 STAgent/repo/src/unified_app.py:276cred-envread
    if page == "OpenAI" and not os.getenv('OPENAI_API_KEY'):
  • 高 STAgent/repo/src/unified_app.py:283cred-envread
    os.environ["OPENAI_API_KEY"] = api_key
  • 高 STAgent/repo/src/unified_app.py:287cred-envread
    elif page == "Anthropic" and not os.getenv('ANTHROPIC_API_KEY'):
  • 高 STAgent/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-analysis

description: Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression.

keywords:

  • spatial-transcriptomics
  • visium
  • xenium
  • scanpy
  • squidpy

measurable_outcome: Process a Visium dataset, identify spatially variable genes, and generate spatial feature plots within 30 minutes.

license: MIT

metadata:

author: MD BABU MIA, PhD

version: "1.0.0"

compatibility:

  • system: python 3.9+

allowed-tools:

  • run_shell_command
  • read_file
  • write_file

Spatial Transcriptomics Skill

Version: 1.0.0

Author: MD BABU MIA, PhD

Date: February 2026

Overview

This skill provides automated analysis capabilities for Spatial Transcriptomics data, specifically designed for 10x Visium and Xenium platforms. It enables the integration of histological data with gene expression profiles to uncover spatial organization of cell types.

Capabilities

  1. Data Loading: Supports Spaceranger output (h5, images).
  2. QC & Preprocessing: Spatial QC metrics, normalization.
  3. Spatial Variable Features: Identification of spatially variable genes (SVGs) using Moran's I and Geary's C.
  4. Deconvolution: Interface for cell type deconvolution (mapping scRNA-seq to spatial).
  5. Visualization: Interactive spatial plots overlaying gene expression on tissue images.

Usage

from Skills.Genomics.Spatial_Transcriptomics.spatial_analyzer import SpatialAnalyzer

# Initialize
sa = SpatialAnalyzer(data_path="./data/visium_sample1")

# Run Pipeline
sa.load_data()
sa.preprocess()
sa.find_spatial_features()
sa.plot_spatial("INS", save_path="./output/insulin_spatial.png")

Requirements

  • scanpy
  • squidpy
  • anndata
  • matplotlib

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

想直接用这个技能？

本站把开放许可（MIT / Apache 等）的技能按仓库打包整理到网盘，点一下转存到你自己的网盘，不用一个个从 GitHub 拉。许可未声明的技能只给原始仓库链接，不打包。

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/SKILL.md

同一个仓库里的其他技能

看这个仓库的全部 897 个技能