scvi-tools

name	scvi-tools
description	Deep learning for single-cell analysis using scvi-tools: data integration, batch correction, multi-modal analysis, reference mapping, and more.
type	reference
version	1.0.0
category	science
last_updated	"2026-02-03T00:00:00.000Z"
source	https://github.com/anthropics/knowledge-work-plugins
related_skills	["single-cell-rna-qc","nextflow-pipelines","clinical-trial-protocol","instrument-data-allotrope","scientific-problem-selection"]
capabilities	[]
requires	[]
see_also	[]
tags	[]
scripts_exempt	true

scvi-tools Deep Learning Skill

This skill provides guidance for deep learning-based single-cell analysis using scvi-tools, the leading framework for probabilistic models in single-cell genomics.

How to Use This Skill

1. Identify the appropriate workflow from the model/workflow tables below
2. Read the corresponding reference file for detailed steps and code
3. Use scripts in scripts/ to avoid rewriting common code
4. For installation or GPU issues, consult references/environment_setup.md
5. For debugging, consult references/troubleshooting.md

When to Use This Skill

• When scvi-tools, scVI, scANVI, or related models are mentioned
• When deep learning-based batch correction or integration is needed
• When working with multi-modal data (CITE-seq, multiome)
• When reference mapping or label transfer is required
• When analyzing ATAC-seq or spatial transcriptomics data
• When learning latent representations of single-cell data

Model Selection Guide

Data Type	Model	Primary Use Case
scRNA-seq	scVI	Unsupervised integration, DE, imputation
scRNA-seq + labels	scANVI	Label transfer, semi-supervised integration
CITE-seq (RNA+protein)	totalVI	Multi-modal integration, protein denoising
scATAC-seq	PeakVI	Chromatin accessibility analysis
Multiome (RNA+ATAC)	MultiVI	Joint modality analysis
Spatial + scRNA reference	DestVI	Cell type deconvolution
RNA velocity	veloVI	Transcriptional dynamics
Cross-technology	sysVI	System-level batch correction

Workflow Reference Files

Workflow	Reference File	Description