AN
数据与复现
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observ…
K-Dense-AI/claude-scientific-skills查看
数据与复现
SC
scrna-orchestrator
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Local Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count.h5ad.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/scrna-orchestrator
- 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
- You are scRNA Orchestrator，specialised ClawBio agent ，用于 local single-cell RNA-seq analysis ，支持 Scanpy。
- python skills/scrna-orchestrator/scrna_orchestrator.py \ --input <input.h5ad> --output <report_dir>。
原始文档
SKILL.md 摘录
Why This Exists
Single-cell workflows are easy to misconfigure and hard to reproduce when run ad hoc.
- Without it: Users manually stitch QC, normalization, clustering, and marker/DE steps with inconsistent defaults.
- With it: One command produces a consistent
report.md, figures, tables, and reproducibility bundle. - Why ClawBio: The workflow is local-first, explicit about assumptions (raw counts), and ships machine-readable outputs.
Core Capabilities
- QC and Filtering: Mitochondrial percentage filtering and min genes/cells thresholds.
- Preprocessing: Library-size normalization,
log1p, and HVG selection. - Embedding and Clustering: PCA, neighbors graph, UMAP, Leiden clustering.
- Cluster Markers: Wilcoxon cluster-vs-rest marker detection.
- Optional Group DE (v1): Two-group Wilcoxon DE on any
obscolumn. - Optional Volcano Plot: Generate DE volcano plot with
--de-volcano. - Reporting: Markdown report, CSV/TSV tables, PNG figures, reproducibility files.
Input Formats
| Format | Extension | Required Fields | Example |
|---|---|---|---|
| AnnData raw counts | .h5ad | Raw count matrix in X; cell metadata in obs; gene metadata in var | pbmc_raw.h5ad |
| Demo mode | n/a | none | python clawbio.py run scrna --demo |
Notes:
- Processed/normalized/scaled
.h5adinputs are rejected with an actionable error. pbmc3k_processed-style inputs are out of scope for this skill.
适用场景
- Use scrna-orchestrator ，用于 single-cell 或 spatial omics analysis。
- Apply scrna-orchestrator 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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