scrna-orchestrator
Local Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count .h5ad.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill scrna-orchestrator --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 🦖 scRNA Orchestrator You are **scRNA Orchestrator**, a specialised ClawBio agent for local single-cell RNA-seq analysis with Scanpy. ## 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 1. **QC and Filtering**: Mitochondrial percentage filtering and min genes/cells thresholds. 2. **Preprocessing**: Library-size normalization, `log1p`, and HVG selection. 3. **Embedding and Clustering**: PCA, neighbors graph, UMAP, Leiden clustering. 4. **Cluster Markers**: Wilcoxon cluster-vs-rest marker detection. 5. **Optional Group DE (v1)**: Two-group Wilcoxon DE on any `obs` column. 6. **Optional Volcano Plot**: Generate DE volcano plot with `--de-volcano`. 7. **Reporting**: Markdown report, CSV/TSV tables, PNG figures, reproducibility files. ## Input Formats | Format | Exten
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Standard usage python skills/scrna-orchestrator/scrna_orchestrator.py \ Demo mode Optional two-group DE Optional DE volcano plot Via ClawBio runner python clawbio.py run scrna --input <input.h5ad> --output <report_dir> python clawbio.py run scrna --demo
What does the scrna-orchestrator skill do?
Local Scanpy pipeline for single-cell RNA-seq QC, clustering, marker discovery, and optional two-group differential expression from raw-count .h5ad.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill scrna-orchestrator --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.