AN
数据与复现
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observ…
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数据与复现
SP
spatial-transcriptomics-agent
维护者 FreedomIntelligence · 最近更新 2026年4月1日
End-to-end spatial transcriptomics analysis: QC, deconvolution, domain detection.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/spatial-transcriptomics-agent
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- 运行 STAgent to align histology images ，支持 expression matrices，perform 聚类/SVG detection，、 generate literature-backed spatial reports。
- Analysis of Visium/Xenium 或 similar ST 数据集s。
- Visual reasoning over spatial plots，H&E images，或 cluster maps。
- Automatically generating Scanpy/Squidpy code ，用于 new ST workflows。
- Hypothesis generation about spatial gene expression patterns。
原始文档
SKILL.md 摘录
Core Capabilities
- Dynamic code generation: Create/execute Python scripts for QC, clustering, SVG detection.
- Visual reasoning: Interpret spatial plots to identify tissue domains and cell neighborhoods.
- Literature retrieval: Pull references that contextualize findings.
- Report generation: Deliver publication-style writeups with plots and SVG tables.
Workflow
- Env setup:
conda env create -f environment.yml && conda activate STAgent. - Data prep: Supply
expression_path(.h5ad/Spaceranger) +image_path(H&E/IF) and metadata. - Task selection: Choose tasks such as
cluster,find_svg,annotate_domains, or composite instructions; runpython repo/src/main.py --data_path ... --task "...". - Execute & interpret: Let STAgent generate scripts, run analyses, and interpret results with literature references.
- 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.
适用场景
- Use spatial-transcriptomics-agent ，用于 single-cell 或 spatial omics analysis。
- Apply spatial-transcriptomics-agent to 聚类，integration，或 trajectory workflows。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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