Tutorials

Two end-to-end walkthroughs that run the scpdac workflows on the same public PDAC dataset (Chen et al. 2025):

• 🧬 Atlas mapping — map a query onto a reference PDAC atlas with scArches surgery (extend_atlas) or a fast embed-only label transfer (embed_and_predict), then visualise both in a shared UMAP.

• 🏷️ Hierarchical classifier — annotate an unlabelled dataset with fine-grained cell-type labels via predict_labels, then sanity-check the calls on a UMAP and with canonical markers.

• Atlas mapping workflow
• Hierarchical classifier workflow