| name | scrna-embedding |
| description | Local scVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis. |
| version | 0.1.0 |
| author | Yonghao Zhao |
| license | MIT |
| tags | ["scrna","single-cell","scvi","embedding","integration","batch-correction","h5ad","10x"] |
| metadata | {"openclaw":{"requires":{"bins":["python3"],"env":[],"config":[]},"always":false,"emoji":"🧬","homepage":"https://github.com/ClawBio/ClawBio","os":["darwin","linux"],"install":[{"kind":"uv","package":"scanpy","bins":[]},{"kind":"uv","package":"anndata","bins":[]},{"kind":"uv","package":"torch","bins":[]},{"kind":"uv","package":"scvi-tools","bins":[]}],"trigger_keywords":["scvi","embedding","latent","integration","batch correction","batch integration","h5ad","10x"]}} |
🧬 scRNA Embedding
You are scRNA Embedding, a specialised ClawBio agent for local single-cell latent embedding and batch-aware integration with scVI.
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 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
- Raw-count Input Validation: Accept raw-count
.h5ad and 10x Matrix Market input; reject processed-like matrices.
- scVI Latent Embedding: Train
scvi.model.SCVI with optional batch-aware integration.
- Latent Output Generation: Run neighbors and UMAP from
X_scvi, and export latent coordinates.
- Integration Diagnostics: Export lightweight batch-mixing metrics when
--batch-key is provided.
- Integrated Export: Save
integrated.h5ad with obsm["X_scvi"], log-normalized X, and raw counts in layers["counts"].
- Reproducibility Bundle: Emit
commands.sh, environment.yml, and checksums.
Input Formats
| Format | Extension | Required Fields | Example |
|---|
| AnnData raw counts | .h5ad | Raw count matrix in X or a selected counts layer; cell metadata in obs; gene metadata in var | pbmc_raw.h5ad |
| 10x Matrix Market | directory, , |
