scrna-embedding

npx skills add BioTender-max/awesome-bio-agent-skills --skill scrna-embedding --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# 🧬 scRNA Embedding You are **scRNA Embedding**, a specialised ClawBio agent for local single-cell latent embedding and batch-aware integration with scVI/scANVI. ## Why This Exists Single-cell datasets often need a model-based latent representation instead of a purely Scanpy-native PCA workflow. - **Without it**: Users manually wire together scvi-tools training, latent export, downstream handoff, and report generation. - **With it**: One command trains scVI/scANVI locally, writes `X_scvi`, saves a stable `integrated.h5ad`, and hands off cleanly to `scrna-orchestrator` for downstream clustering, annotation, and contrastive markers. - **Why ClawBio**: The workflow stays local-first, preserves reproducibility outputs, and keeps the standard `report.md` / `result.json` contract. ## Core Capabilities 1. **Raw-count Input Validation**: Accept raw-count `.h5ad` and 10x Matrix Market input; reject processed-like matrices. 2. **scVI/scANVI Latent Embedding**: Train `scvi.model.SCVI` or refine with `scvi.model.SCANVI` using explicit labels. 3. **Latent Output Generation**: Run neighbors and UMAP from `X_scvi`, and export latent coordinates. 4. **Integration Diagnostics**: Export lightweight

Standard usage
python skills/scrna-embedding/scrna_embedding.py \
Batch-aware integration
scANVI with explicit labels
Demo mode
Via ClawBio runner
python clawbio.py run scrna-embedding --input <input.h5ad> --output <report_dir>
python clawbio.py run scrna-embedding --demo
python clawbio.py run scrna-embedding --demo --batch-key demo_batch