bio-research-scvi-tools SKILL.md skillA
bio-research-scvi-tools from aicodedecode/awesome-muse-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add aicodedecode/awesome-muse-skills/bio-research-scvi-tools@git:20261010.2c068caPins git:20261010.2c068ca in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- aicodedecode/awesome-muse-skills
- Path
skills-imported/bio-research-scvi-tools/SKILL.md- Versions recorded
- 1
- Latest version
- git:20261010.2c068ca, committed Oct 10, 2026
- Size
- 7,831 bytes
- Repository stars
- 25
- License
- MIT
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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
<!-- Provenance: adapted from anthropics/knowledge-work-plugins (Apache-2.0, (c) Anthropic).
Original skill: https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research/skills/scvi-tools. Changes for Muse AI: Claude/Cowork product refs -> Muse AI; MCP -> connector; CLAUDE.md -> MUSE.md; ${CLAUDE_PLUGIN_ROOT} -> this skill's directory; /plugin:command refs -> skill refs. -->
# 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.
## How to Use This Skill
1. Identify the appropriate workflow from the model/workflow tables below
2. Read the corresponding reference file for detailed steps and code
3. Use scripts in `scripts/` to avoid rewriting common code
4. For installation or GPU issues, consult `references/environment_setup.md`
5. For debugging, consult `references/troubleshooting.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)
…Read the whole file at its exact version.
How to install
mdr add aicodedecode/awesome-muse-skills/bio-research-scvi-tools@sha256:99b66ac5e68d4217The line at the top of this page pins the label git:20261010.2c068ca, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_o2nvj4fpxpyi3coh)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Oct 10, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (7831 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
aicodedecode/awesome-muse-skills · 25 stars · license MIT · pushed 2026-10-10 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_o2nvj4fpxpyi3coh GET https://markdownregistry.com/api/v1/resolve?ref=aicodedecode/awesome-muse-skills/bio-research-scvi-tools GET https://markdownregistry.com/api/v1/blob/99b66ac5e68d421726fabad854cdce167361522814f479e654bb5ff2b51ae1d7
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.