scvi-tools — scVI / scANVI

scvi-tools (Gayoso et al. 2022, github.com/scverse/scvi-tools, BSD-3-Clause) wraps a family of deep generative models for single-cell omics. The scRNA-seq core is scVI (unsupervised batch-corrected latent embedding) and scANVI (scVI + a classifier head for semi-supervised cell-type label transfer). Both expect raw integer UMI counts and emit a low-dimensional X_scVI / X_scANVI that drops into the scanpy neighbors → leiden → umap pipeline.

Setup (any agent, no API key)

This is a pure skill — kernel.py is deterministic Python and you (the base model) do all the reasoning. There is no host runtime and no LLM API. The only helper here is h5ad_safe_obs, which coerces an obs/var frame so anndata.write_h5ad() succeeds. Load it once per session in a Python cell: