Scanpy analysis .md

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 · Branch: scanpy-k-dense · Agent run: Claude Code

Write-up: analysis report

Agentic analysis

Step

Transform

Outputs

QC

01_qc.py

qc h5ad · QC violins

Cluster

02_cluster.py

clustered h5ad · HVG · PCA · UMAP

Markers

03_markers.py

cluster markers · dotplot · heatmap

Canonical check

04_check_canonical.py

canonical marker panel

Annotate

05_annotate.py

annotated h5ad · composition · UMAP · cell-type dotplot

Final plots

06_final_plots.py

UMAP cell types · UMAP clusters · UMAP markers · cell-type heatmap

The 10 cell-type labels live on the annotated AnnData; methods, results, and figures are in the report.