scvi-tools Single-Cell Modeling Skill

What it does

scvi-tools is a PyTorch/Lightning framework of probabilistic models for single-cell genomics. This skill gives Claude a curated map of the library:

• Model selection by modality: scRNA-seq (scVI, scANVI, AUTOZI, VeloVI, contrastiveVI), ATAC-seq (PeakVI, PoissonVI, scBasset), multimodal (totalVI, totalANVI, MultiVI, MrVI, DIAGVI), spatial (DestVI, Stereoscope, Tangram, scVIVA), specialized (MethylVI, CytoVI, Solo, CellAssign)
• Namespace clarity: core models under scvi.model, everything else under scvi.external — prevents a very common import mistake
• Canonical workflow: setup_anndata → train → get_latent_representation / get_normalized_expression → scanpy neighbors/UMAP/Leiden
• Uncertainty-aware DE: differential_expression(mode="change", delta=...)
• Best practices: raw counts only, gene filtering, covariate registration, model persistence, GPU acceleration
• Pointers to deeper references/ files per model family and to theoretical foundations

Who it's for

• Computational biologists and grad students working with single-cell RNA/ATAC data
• Teams integrating many batches or studies where basic scanpy correction falls short
• Anyone modeling CITE-seq, multiome, or spatial data probabilistically
• Overkill if you only need a standard scanpy QC-to-clustering pipeline

Example uses

1. "Batch-correct this multi-donor scRNA-seq object with scVI and give me a UMAP" → produces filtering, setup_anndata with batch/categorical/continuous covariates, training, X_scVI, and downstream scanpy calls
2. "I have CITE-seq protein + RNA — which model?" → recommends totalVI (or totalANVI when labels exist) with working code
3. "Run differential expression between two cell types with uncertainty" → uses mode="change" with a delta effect-size threshold and explains how to read the output

Install the skill I found on Claude Skill Mart.
Copy the skills/scvi-tools folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/scvi-tools/.
When it's done, tell me in one line what this skill can do.