scvi-tools
anthropics/knowledge-work-pluginsOfficial collectionAI & ML engineeringScience & research
scvi-tools is a skill in anthropics/knowledge-work-plugins, last changed 29 Jan 2026. It can run shell commands, reach the network, name web addresses and bundle scripts — read the findings before installing.
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.
At a glance
What it can touch
How much a skill can do, not whether it is risky.
Pattern check
Nothing flagged
That isn't proof the skill is harmless.
Commit 2574e29 · 3 Nov 2026
How the check worksPattern check: nothing flagged
That isn't proof the skill is harmless.
Install
Each tab says whether it installs commit 2574e29, the one we checked, or the latest version.
OpenCode also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Goose also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Windsurf (Devin Desktop) also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Zed also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Roo Code also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Factory Droid also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Junie also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Amp also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
No install command here reaches Kiro. Copy the skill's folder into .kiro/skills/ in your project, or ~/.kiro/skills/ for all your projects. anthropics/knowledge-work-plugins/bio-research/skills/scvi-tools (opens in a new tab)
Antigravity also looks in .agents/skills/, so the Any agent steps reach it with This project. For All projects, see where Antigravity looks.
Cline also looks in .claude/skills/, so the Claude Code steps reach it with This project. For All projects, see where Cline looks.
Claude Code
Pinned to commit 2574e29, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/anthropics/knowledge-work-plugins.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&git -C "$tmp" sparse-checkout set -- bio-research/skills/scvi-tools &&git -C "$tmp" checkout -q 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&mkdir -p .claude/skills &&mkdir .claude/skills/scvi-tools &&cp -R "$tmp"/bio-research/skills/scvi-tools/. .claude/skills/scvi-tools/ &&rm -rf "$tmp"If Claude Code was already running and this created the skills folder, run /reload-skills.
Or install the bio-research plugin it ships in. Installs the latest version, not the one we checked. Installs everything in the plugin, including any hooks, MCP servers and scripts our check doesn't cover.
claude plugin marketplace add anthropics/knowledge-work-plugins --scope project &&claude plugin install bio-research@knowledge-work-plugins --scope projectClaude apps
Pinned to commit 2574e29, the one we checked.
Skills in the Claude apps belong to your account rather than to a project.
Make scvi-tools.zip, with the skill folder at the top level:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/anthropics/knowledge-work-plugins.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&git -C "$tmp" sparse-checkout set -- bio-research/skills/scvi-tools &&git -C "$tmp" checkout -q 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&out="$(mktemp -d)" &&cp -R "$tmp"/bio-research/skills/scvi-tools "$out"/scvi-tools &&(cd "$out" && zip -qr - scvi-tools) > scvi-tools.zip &&rm -rf "$tmp" "$out"In Claude, open Customize > Skills, select +, then + Create skill > Upload a skill, and choose scvi-tools.zip.
On Free, Pro and Max plans, turn on Code execution and file creation (Create and edit files in newer settings) under Settings > Capabilities.
Codex
Pinned to commit 2574e29, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/anthropics/knowledge-work-plugins.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&git -C "$tmp" sparse-checkout set -- bio-research/skills/scvi-tools &&git -C "$tmp" checkout -q 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&mkdir -p .agents/skills &&mkdir .agents/skills/scvi-tools &&cp -R "$tmp"/bio-research/skills/scvi-tools/. .agents/skills/scvi-tools/ &&rm -rf "$tmp"Codex picks up new skills on its own; restart it if this one does not appear.
Cursor
Pinned to commit 2574e29, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/anthropics/knowledge-work-plugins.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&git -C "$tmp" sparse-checkout set -- bio-research/skills/scvi-tools &&git -C "$tmp" checkout -q 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&mkdir -p .cursor/skills &&mkdir .cursor/skills/scvi-tools &&cp -R "$tmp"/bio-research/skills/scvi-tools/. .cursor/skills/scvi-tools/ &&rm -rf "$tmp"Copilot & VS Code
Pinned to commit 2574e29, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/anthropics/knowledge-work-plugins.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&git -C "$tmp" sparse-checkout set -- bio-research/skills/scvi-tools &&git -C "$tmp" checkout -q 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&mkdir -p .github/skills &&mkdir .github/skills/scvi-tools &&cp -R "$tmp"/bio-research/skills/scvi-tools/. .github/skills/scvi-tools/ &&rm -rf "$tmp"In a running Copilot CLI session, run /skills reload.
Or install it with gh skill, which also installs the commit we checked. Needs GitHub CLI 2.90 or later.
gh skill install anthropics/knowledge-work-plugins bio-research/skills/scvi-tools/SKILL.md@2574e29377c7173d0cecffef29a6ecbd7f8ccb5d --agent github-copilot --scope projectGemini CLI
Pinned to commit 2574e29, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/anthropics/knowledge-work-plugins.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&git -C "$tmp" sparse-checkout set -- bio-research/skills/scvi-tools &&git -C "$tmp" checkout -q 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&mkdir -p .gemini/skills &&mkdir .gemini/skills/scvi-tools &&cp -R "$tmp"/bio-research/skills/scvi-tools/. .gemini/skills/scvi-tools/ &&rm -rf "$tmp"In a running session, run /skills reload.
Or use Gemini CLI’s own installer. Installs the latest version, not the one we checked.
gemini skills install https://github.com/anthropics/knowledge-work-plugins.git --path bio-research/skills/scvi-tools --scope workspaceAny agent
Pinned to commit 2574e29, the one we checked.
OpenCode, Goose, Windsurf (Devin Desktop), Zed, Roo Code, Factory Droid, Junie, Amp and Antigravity read .agents/skills in a project.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/anthropics/knowledge-work-plugins.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&git -C "$tmp" sparse-checkout set -- bio-research/skills/scvi-tools &&git -C "$tmp" checkout -q 2574e29377c7173d0cecffef29a6ecbd7f8ccb5d &&mkdir -p .agents/skills &&mkdir .agents/skills/scvi-tools &&cp -R "$tmp"/bio-research/skills/scvi-tools/. .agents/skills/scvi-tools/ &&rm -rf "$tmp"Or use the skills CLI from skills.sh. Installs the latest version, not the one we checked. The skills CLI reports installs to skills.sh unless you set DISABLE_TELEMETRY=1.
npx skills@1.7.4 add anthropics/knowledge-work-plugins --skill scvi-toolsWhat it can touch
From the files and frontmatter at commit 2574e29. This is how much a skill can do, not whether it is risky.
Pattern check
Pattern check: nothing flagged · commit 2574e29 · 3 Nov 2026
We checked every text file in this skill, at commit 2574e29 on 3 Nov 2026, against 45 published patterns such as download-and-run commands, hidden text and credential access. We don't run the skill, we don't read the web pages it points to, and we can't judge everything its instructions might lead an agent to do. In published tests, pattern checks like this one missed most malicious skills. Read the skill before you install it — especially anything it asks you to download or run.
How the check worksReport an incorrect finding
Outside links we did not follow
- https://docs.scvi-tools.org/
- https://docs.scvi-tools.org/en/stable/tutorials/index.html
- https://huggingface.co/scvi-tools
- https://github.com/scverse/scvi-tools/issues
- http://www.apache.org/licenses/
- http://www.apache.org/licenses/LICENSE-2.0
- https://download.pytorch.org/whl/cu118
- https://download.pytorch.org/whl/cu121
- https://download.pytorch.org/whl/cpu
- https://cellxgene.cziscience.com/
Show 1 more
- https://discourse.scverse.org/
Format check
Each agent reads SKILL.md a little differently. We check the file against each one's published rules; we don't run the skill in any agent.
Agent Skills specPasses
The open format from agentskills.io, held to the strictest version of each rule among the agents we check.
- Note
There is no license field, so readers can't tell whether they may reuse the skill. O2
Fix: Add license: with an SPDX name such as MIT or Apache-2.0, or the name of a bundled licence file.
- Note
Reference files over 100 lines with no table of contents at the top: references/atac_peakvi.md (399 lines), references/batch_correction_sysvi.md (418 lines), references/citeseq_totalvi.md (421 lines), references/data_preparation.md (287 lines), references/environment_setup.md (255 lines) and 7 more. B5
Fix: Add a short list of the sections at the top of each.
- Note
Claude CodePasses
Claude Code reads its own extra fields, ignores unknown ones, and still loads a skill whose frontmatter is broken, without its fields.
- Note
Reference files over 100 lines with no table of contents at the top: references/atac_peakvi.md (399 lines), references/batch_correction_sysvi.md (418 lines), references/citeseq_totalvi.md (421 lines), references/data_preparation.md (287 lines), references/environment_setup.md (255 lines) and 7 more. B5
Fix: Add a short list of the sections at the top of each.
- Note
Claude apps & API uploadPasses
Uploading to claude.ai or the Claude API, or packaging with Anthropic's script, accepts only the six spec fields and stops on anything else.
- Note
The description is 719 characters. The claude.ai Help Center says 200 at most, though Anthropic's API docs and validator allow 1,024. D4
Fix: If the claude.ai upload refuses it, trim the description to 200 characters.
- Note
Reference files over 100 lines with no table of contents at the top: references/atac_peakvi.md (399 lines), references/batch_correction_sysvi.md (418 lines), references/citeseq_totalvi.md (421 lines), references/data_preparation.md (287 lines), references/environment_setup.md (255 lines) and 7 more. B5
Fix: Add a short list of the sections at the top of each.
- Note
- OpenAI (Codex & API)Passes
- VS Code & CopilotPasses
SKILL.md
Files
22 files
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