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name: multimodal-and-spatial description: "Route scvi-tools tasks involving multimodal, ATAC, spatial, methylation, velocity, perturbation, contrastive, and external specialized model families." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

multimodal-and-spatial

Use this sub-skill when a user needs scvi-tools guidance for non-basic single-cell models beyond core RNA-only workflows: CITE-seq, RNA+protein, RNA+ATAC, ATAC-only, methylation, spatial mapping/deconvolution, velocity, perturbation/contrastive analysis, or external specialized models.

Route by task

• RNA + protein CITE-seq: use scvi.model.TOTALVI; for semi-supervised labels with protein, use scvi.external.TOTALANVI.
• RNA + ATAC or RNA + ATAC + protein with partial modality overlap: use scvi.model.MULTIVI on MuData; for ATAC-only use scvi.model.PEAKVI.
• Spatial mapping or deconvolution: consider scvi.external.Tangram, scvi.external.RNAStereoscope, and scvi.external.SpatialStereoscope; verify reference labels before choosing Stereoscope.
• Bisulfite/methylation: use scvi.external.METHYLVI or scvi.external.METHYLANVI depending on whether labels are needed.
• Dynamics, perturbation, and contrastive designs: use scvi.external.VELOVI, MRVI, RESOLVI, ContrastiveVI, SysVI, DIAGVI, or Decipher only after matching their required data keys.
• Specialized external models: use CYTOVI, SCAR, SCBASSET, GIMVI, or Tangram when their input assumptions match; expect optional extras for some workflows.

Use the references

• Model selection and APIs: references/model-catalog.md
• Required data keys and setup validation: references/data-requirements.md
• Failure diagnosis and recovery: references/troubleshooting.md

Boundaries

• For ordinary AnnData registration, setup_anndata, count layers, batches, labels, covariates, and MuData basics, route to the data-setup sub-skill first.
• For choosing among core RNA-only models such as SCVI, SCANVI, LinearSCVI, AUTOZI, or SOLO, route to the core-models sub-skill.
• Do not assume optional packages for spatial plotting, genomic sequence models, or external integrations are installed unless imports prove it.