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scvi-tools Single-Cell Probabilistic Modeling Guide

A skill that guides Claude through scvi-tools deep generative models for batch correction, multimodal integration, and uncertainty-aware differential expression in single-cell data.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Maps single-cell tasks to the right model: scRNA-seq (scVI, scANVI, VeloVI), ATAC (PeakVI, PoissonVI, scBasset), multimodal (totalVI, MultiVI, MrVI, DIAGVI), spatial (DestVI, Stereoscope, scVIVA), and specialized modalities.
  • Flags the usual traps: scvi.model vs scvi.external namespaces, raw counts requirement, covariate registration in setup_anndata.
  • Gives a canonical workflow: setup → train → extract latent/normalized values → hand off to scanpy for neighbors/UMAP/leiden.
  • Covers model save/load, probabilistic DE (mode="change", delta), GPU/JAX/MLX backends, and points to per-model reference docs.

Who it's for

  • Single-cell researchers who need probabilistic batch correction or transfer learning beyond a plain scanpy pipeline.
  • Bioinformaticians integrating CITE-seq or multiome datasets, paired or unpaired.
  • Labs doing spatial deconvolution or doublet detection.

Examples

  1. "Integrate multi-donor scRNA-seq and give me a UMAP" → scVI setup/train, then X_scVI for neighbors and leiden.
  2. "Run differential expression between TypeA and TypeB with uncertainty" → model.differential_expression(mode="change", delta=0.25).
  3. "Jointly model CITE-seq protein and RNA" → totalVI, or totalANVI when cell-type labels exist.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/scvi-tools/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on AI Skill Mart.
Copy the skills/scvi-tools folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/scvi-tools/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/scvi-tools ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Create the skills folder: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/scvi-tools ~/.claude/skills/
  4. Verify ~/.claude/skills/scvi-tools/SKILL.md and its references/ directory exist.
  5. Install the library in a Python 3.12+ environment: uv pip install scvi-tools (GPU: uv pip install "scvi-tools[cuda]").
  6. Restart Claude Code and try a prompt like "use scVI to batch-correct this AnnData object".
View source on GitHub ↗License: MIT