Version Compatibility

Reference examples tested with: scanpy 1.10+, Seurat 5.0+, anndata 0.10+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Multimodal Integration

"Jointly analyze my CITE-seq / Multiome / unpaired multi-omic data" -> Classify the task by anchor structure, denoise each modality in its native pipeline, then build one joint representation.

• R: Seurat::FindMultiModalNeighbors() (WNN), Signac (ATAC LSI), dsb::DSBNormalizeProtein() (ADT denoising), PrepareBridgeReference() (v5 bridge)
• Python: muon/mudata (MuData container), scvi.model.TOTALVI / MULTIVI, MOFA2/muon.tl.mofa, scglue (diagonal)

Governing Principle