Research · Skill
scvi-tools Deep Learning Skill
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.
- Ships scripts Phở cannot run yet
What the skill covers
The sections of its instructions, in order.
- 01 How to Use This Skill
- 02 When to Use This Skill
- 03 Model Selection Guide
- 04 Workflow Reference Files
- 05 CLI Scripts
- Pipeline Scripts
- Example Workflow
- Python Utilities
- 06 Critical Requirements
- 07 Quick Decision Tree
- 08 Key Resources
Reference files
20 files Phở can open while it uses the skill.
- 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
- +4 more
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Frequently asked questions
What does scvi-tools Deep Learning Skill do?
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.
Is scvi-tools Deep Learning Skill free to use?
Yes. scvi-tools Deep Learning Skill is published by Anthropic under the Apache 2.0 licence, and you can use it with a free Phở account.
How do I use scvi-tools Deep Learning Skill in Phở?
Press Open in Phở, then Try to apply it to your next message, or add the Bio research set so Phở loads it whenever a request matches.
Does scvi-tools Deep Learning Skill need other tools?
No. It works in a normal Phở chat with what you type or upload. It also ships scripts, which Phở chat cannot run yet; Phở follows its written steps.
Copied unchanged from anthropics/knowledge-work-plugins at commit d900840 and credited to Anthropic, who is not affiliated with Phở. The full instructions and licence text ship with the skill inside Phở.