scvi-contrastivevi

What problem does it solve?

ContrastiveVI enables analysis of perturbation experiments by separating salient (perturbation-specific) variation from background (shared) variation in single-cell data.

Core Features & Use Cases

• Identify target vs background effects in Perturb-seq and related experiments.
• Train models with dual latent spaces to visualize perturbation effects and adjust for confounders.
• Use differential expression analysis focused on perturbation-specific signals.

Quick Start

Identify target and background cells, set up an AnnData object with counts, initialize ContrastiveVI, train with n_latent and n_salient, and extract latent representations for downstream analysis.