Scanpy analysis

Agentic re-implementation of the classic PBMC3k Scanpy tutorial: QC, clustering, marker discovery, and cell-type annotation — with cutoffs and labels chosen from the data, not hard-coded from the docs.

Instance: laminlabs/lamindata

Agentic analysis

Step	Transform	Outputs
Preprocess, cluster, annotate	clustering.py · agent run	annotated h5ad · cluster markers · QC violins · UMAP · marker dotplot

The cell-type rationale (QC cutoffs, cluster→type map, caveats) is attached as notes on the annotated AnnData.