scvi-tools

Fit single-cell omics models to produce integrated representations, annotations, multimodal estimates, and posterior differential expression.

When to use it

Use for generative modeling, reference mapping, multimodal analysis, or model-based uncertainty rather than standard preprocessing and exploratory analysis.

Give it single-cell measurements and an analysis request; it registers and trains an appropriate model, evaluates its fit, and saves representations, model data, and reproducibility details in the project.