Localized reading guide
scvi-toolsPurpose, usage and source
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
Source retrieved:
- Source repository
- anthropics/knowledge-work-plugins
- SKILL.md
bio-research/skills/scvi-tools/SKILL.md- Repository stars
- 34,049
- Repository updated
- 2026-10-30
- Categories
- research
- Last collected
License: License file needs review
Workflow excerpts are reading aids, not executable instructions from Codez. No third-party Skill was run to produce this page.
The purpose and workflow passages below are upstream material, organized and translated for reading. They are distinct from the separately labeled Codez editorial analysis.
What this Skill does
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
How the upstream workflow works
How to Use This Skill
Identify the appropriate workflow from the model/workflow tables below Read the corresponding reference file for detailed steps and code Use scripts in scripts/ to avoid rewriting common code For installation or GPU issues, consult references/environment_setup.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
Upstream passage · L18 ↗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.
Upstream passage · L6 ↗# 1. Validate input data
python scripts/validate_adata.py raw.h5ad --batch-key batch --suggest
# 2. Prepare data (QC, HVG selection)
python scripts/prepare_data.py raw.h5ad prepared.h5ad --batch-key batch --n-hvgs 2000
# 3. Train model
python scripts/train_model.py prepared.h5ad results/ --model scvi --batch-key batch
# 4. Cluster and visualize
python scripts/cluster_embed.py results/adata_trained.h5ad results/ --resolution 0.8
# 5. Differential expression
python scripts/differential_expression.py results/model results/adata_clustered.h5ad results/de.csv --groupby leidenRequirements and setup
Critical Requirements
Raw counts required: scvi-tools models require integer count data HVG selection: Use 2000-4000 highly variable genes
Upstream passage · L106 ↗Limits and quality checks
No separate limits passage was selected from this file. This does not mean the Skill is safe for every input or environment. Review the complete source and validate your own result.
Start with a safe trial
- Check the supported host and the repository installation instructions. Keep the Skill directory and its referenced scripts, assets and documentation together; SKILL.md alone may omit dependencies.
- Give the agent your real input, desired output and acceptance criteria. Invocation syntax and available tools depend on the host; this site does not assume a universal install command.
- Try the source workflow in a disposable project or on a copy. Review operations that change files, remote services or billable resources before allowing them.
- Validate the output against the source quality checks and your own requirements. A successful trigger or a high repository Star count does not establish a correct result.
Read further in the source
Related Skills
Translation and scope
This reading guide selects passages from the pinned upstream SKILL.md. Translation is assisted. It is not a complete manual or a claim of tested compatibility. Read the original and its referenced files before use.
This introduction refers to the pinned version below; current repository activity and collection time are shown separately.
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- Source retrieved
- Source commit
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03a69b32b77db86afe5f87b75db2ae4c92b03b6e9e16e2c5e66cde2d4ad9c5bc