scvi-tools

Overview

scvi-tools is a comprehensive Python framework for probabilistic models in single-cell genomics. Built on PyTorch and PyTorch Lightning, it provides deep generative models using variational inference for analyzing diverse single-cell data modalities.

When to Use This Skill

Use this skill when:

• Analyzing single-cell RNA-seq data (dimensionality reduction, batch correction, integration)

• Working with single-cell ATAC-seq or chromatin accessibility data

• Integrating multimodal data (CITE-seq, multiome, paired/unpaired datasets)

• Analyzing spatial transcriptomics data (deconvolution, spatial mapping)

• Performing differential expression analysis on single-cell data

• Conducting cell type annotation or transfer learning tasks

• Working with specialized single-cell modalities (methylation, cytometry, RNA velocity)

• Building custom probabilistic models for single-cell analysis

Core Capabilities

scvi-tools provides models organized by data modality:

1. Single-Cell RNA-seq Analysis

Core models for expression analysis, batch correction, and integration. See references/models-scrna-seq.md for:

• scVI: Unsupervised dimensionality reduction and batch correction

• scANVI: Semi-supervised cell type annotation and integration

• AUTOZI: Zero-inflation detection and modeling

• VeloVI: RNA velocity analysis

• contrastiveVI: Perturbation effect isolation

2. Chromatin Accessibility (ATAC-seq)

Models for analyzing single-cell chromatin data. See references/models-atac-seq.md for:

• PeakVI: Peak-based ATAC-seq analysis and integration

• PoissonVI: Quantitative fragment count modeling

• scBasset: Deep learning approach with motif analysis

3. Multimodal & Multi-omics Integration

Joint analysis of multiple data types. See references/models-multimodal.md for:

• totalVI: CITE-seq protein and RNA joint modeling

• MultiVI: Paired and unpaired multi-omic integration

• MrVI: Multi-resolution cross-sample analysis

4. Spatial Transcriptomics

Spatially-resolved transcriptomics analysis. See references/models-spatial.md for:

• DestVI: Multi-resolution spatial deconvolution

• Stereoscope: Cell type deconvolution

• Tangram: Spatial mapping and integration

• scVIVA: Cell-environment relationship analysis

5. Specialized Modalities

Additional specialized analysis tools. See references/models-specialized.md for:

• MethylVI/MethylANVI: Single-cell methylation analysis

• CytoVI: Flow/mass cytometry batch correction

• Solo: Doublet detection

• CellAssign: Marker-based cell type annotation

Typical Workflow

All scvi-tools models follow a consistent API pattern:

1. Load and preprocess data (AnnData format)

import scvi import scanpy as sc

adata = scvi.data.heart_cell_atlas_subsampled() sc.pp.filter_genes(adata, min_counts=3) sc.pp.highly_variable_genes(adata, n_top_genes=1200)

2. Register data with model (specify layers, covariates)

scvi.model.SCVI.setup_anndata( adata, layer="counts", # Use raw counts, not log-normalized batch_key="batch", categorical_covariate_keys=["donor"], continuous_covariate_keys=["percent_mito"] )

3. Create and train model

model = scvi.model.SCVI(adata) model.train()

4. Extract latent representations and normalized values

latent = model.get_latent_representation() normalized = model.get_normalized_expression(library_size=1e4)

5. Store in AnnData for downstream analysis

adata.obsm["X_scVI"] = latent adata.layers["scvi_normalized"] = normalized

6. Downstream analysis with scanpy

sc.pp.neighbors(adata, use_rep="X_scVI") sc.tl.umap(adata) sc.tl.leiden(adata)

Key Design Principles:

• Raw counts required: Models expect unnormalized count data for optimal performance

• Unified API: Consistent interface across all models (setup → train → extract)

• AnnData-centric: Seamless integration with the scanpy ecosystem

• GPU acceleration: Automatic utilization of available GPUs

• Batch correction: Handle technical variation through covariate registration

Common Analysis Tasks

Differential Expression

Probabilistic DE analysis using the learned generative models:

de_results = model.differential_expression( groupby="cell_type", group1="TypeA", group2="TypeB", mode="change", # Use composite hypothesis testing delta=0.25 # Minimum effect size threshold )

See references/differential-expression.md for detailed methodology and interpretation.

Model Persistence

Save and load trained models:

Save model

model.save("./model_directory", overwrite=True)

Load model

model = scvi.model.SCVI.load("./model_directory", adata=adata)

Batch Correction and Integration

Integrate datasets across batches or studies:

Register batch information

scvi.model.SCVI.setup_anndata(adata, batch_key="study")

Model automatically learns batch-corrected representations

model = scvi.model.SCVI(adata) model.train() latent = model.get_latent_representation() # Batch-corrected

Theoretical Foundations

scvi-tools is built on:

• Variational inference: Approximate posterior distributions for scalable Bayesian inference

• Deep generative models: VAE architectures that learn complex data distributions

• Amortized inference: Shared neural networks for efficient learning across cells

• Probabilistic modeling: Principled uncertainty quantification and statistical testing

See references/theoretical-foundations.md for detailed background on the mathematical framework.

Additional Resources

• Workflows: references/workflows.md contains common workflows, best practices, hyperparameter tuning, and GPU optimization

• Model References: Detailed documentation for each model category in the references/ directory

• Official Documentation: https://docs.scvi-tools.org/en/stable/

• Tutorials: https://docs.scvi-tools.org/en/stable/tutorials/index.html

• API Reference: https://docs.scvi-tools.org/en/stable/api/index.html

Installation

uv pip install scvi-tools

For GPU support

uv pip install scvi-tools[cuda]

Best Practices

• Use raw counts: Always provide unnormalized count data to models

• Filter genes: Remove low-count genes before analysis (e.g., min_counts=3 )

• Register covariates: Include known technical factors (batch, donor, etc.) in setup_anndata

• Feature selection: Use highly variable genes for improved performance

• Model saving: Always save trained models to avoid retraining

• GPU usage: Enable GPU acceleration for large datasets (accelerator="gpu" )

• Scanpy integration: Store outputs in AnnData objects for downstream analysis