scrna-orchestrator
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional dataset-level plus within-cluster contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
npx skills add BioTender-max/awesome-bio-agent-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, marker analysis, and latent downstream interpretation with inconsistent defaults. - **With it**: One command produces a consistent `report.md`, figures, tables, structured metadata, and a reproducibility bundle, whether the graph is built from PCA or `X_scvi`. - **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. **Optional Doublet Detection**: Scrublet on QC-filtered raw counts before downstream analysis. 3. **Preprocessing**: Library-size normalization, `log1p`, and HVG selection. 4. **Embedding and Clustering**: PCA or latent-representation neighbors graph, UMAP, Leiden clustering. 5. **Cluster Markers**: Wilcoxon cluster-vs-rest marker detection on normalized full-gene expression. 6. **Op
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Status
- Citations
Standard usage python skills/scrna-orchestrator/scrna_orchestrator.py \ Direct matrix.mtx(.gz) path Demo mode Optional doublet detection Optional CellTypist annotation Optional dataset-level pairwise contrasts Optional dataset-level + within-cluster contrasts together Optional latent downstream mode Via ClawBio runner
What does the scrna-orchestrator skill do?
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional dataset-level plus within-cluster contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.