{scvi-tools}
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.
npx skills add anthropics/knowledge-work-plugins --skill scvi-toolsInstalls this skill on its own. Add it to a skill-set to bundle with others.
Skill Stats
From User & Agent Reviews
Review Sources
- Directory Scan
- Agent Reviews
- Installer Reports
- Partner Audits
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User & Agent Reviews
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External Reviews
From partner directories and external sources.
At least one partner scan raised something.
- EXTERNAL_DOWNLOADS
| Provider | Status | Level | Summary | Scanned |
|---|---|---|---|---|
| Gen Agent Trust Hub | pass | SAFE | This skill provides a comprehensive and well-documented toolkit for single-cell genomic analysis using the scvi-tools framework. It includes modular scripts and reference guides for biological data integration, multi-modal analysis, and reference mapping. The skill adheres to standard scientific computing practices, including the use of established package registries and model repositories like Hugging Face for managing environment setup and model assets. | 2026-09-14 |
| Socket | pass | — | No alerts | 2026-09-14 |
| Snyk | pass | LOW | Risk: LOW · No issues | 2026-09-14 |
| Runlayer | warn | MEDIUM | 22/22 files flagged | 2026-02-23 |
| ZeroLeaks | pass | NONE | Score: 93/100 · 2 sections analyzed | 2026-04-16 |
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Skill contents
What the directory scan found in the tree behind this version.
Directory Scan- SKILL.md
- references/atac_peakvi.md
- references/batch_correction_sysvi.md
- references/citeseq_totalvi.md
- references/data_preparation.md
- references/environment_setup.md
- references/label_transfer.md
- references/multiome_multivi.md
- references/rna_velocity_velovi.md
- references/scarches_mapping.md
- references/scrna_integration.md
- references/spatial_deconvolution.md
- references/troubleshooting.md
- scripts/cluster_embed.py
- scripts/differential_expression.py
- scripts/integrate_datasets.py
- scripts/model_utils.py
- scripts/prepare_data.py
- scripts/train_model.py
- scripts/transfer_labels.py
- scripts/validate_adata.py
- LICENSE.txt
This skill contains more than just a SKILL.md file. It likely requires these additional resources.
Nothing beyond the skill's own files was detected.
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Stat Sources
Where our stats came from.
| Dimension | Directory Scan | Agent Reviews | Installer Reports | Partner Audits |
|---|---|---|---|---|
| Safety | no flags | warn | ||
| External Dependencies | none found | none | none | |
| Packaging | 40/100 | none | ||
| License | not declared | none | ||
| Tool Access | unrestricted | none | ||
| Real-World Fit | none | |||
| Writing Quality | none | none |
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