Single-cell downstream analysis quick-reference

This skill sheet distills the OmicVerse single-cell downstream tutorials into an executable checklist. Each module highlights prerequisites, the core API entry points, interpretation checkpoints, resource planning notes, and any optional validation or export steps surfaced in the notebooks.

Defensive Validation Patterns

Before running any downstream module, verify prerequisites:

# Before AUCell: verify embeddings exist
assert 'X_umap' in adata.obsm or 'X_pca' in adata.obsm, \
    "Embedding required. Run ov.pp.umap(adata) or ov.pp.pca(adata) first."

# Before metacell DEG: verify raw counts are preserved
assert adata.raw is not None, "adata.raw required. Set adata.raw = adata.copy() before HVG filtering."