scvi-tools SKILL.md skillA
scvi-tools from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/scvi-tools@v1.4Pins v1.4 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/scvi-tools/SKILL.md- Versions recorded
- 6
- Latest version
- v1.4, committed Oct 1, 2026
- First version recorded
- May 27, 2026
- Size
- 10,233 bytes
- Repository stars
- 56,497
- License
- MIT
Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. Use for generative modeling, reference mapping, multimodal analysis, or model-based uncertainty; use scanpy for standard preprocessing and exploratory analysis.
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
# scvi-tools Targets **scvi-tools 1.5.1**, released September 10, 2026. APIs below were checked against the tagged source and official documentation. The examples are illustrative: the repository tests exercise short CPU synthetic fits for SCVI, SCANVI, TOTALVI, MULTIVI, METHYLVI, PEAKVI and POISSONVI, plus count-preserving preprocessing, DE output contracts, save/load and minification. The tested stack is Python 3.13, Scanpy 1.12.4, AnnData 0.13.4, MuData 0.4.1, PyTorch 2.14.1 and Lightning 2.6.6. Long training, hardware-specific paths and other specialized workflows remain illustrative; these checks do not establish convergence or biological validity. ## Choose the model and its input contract | Task | Class | Required input | | --- | --- | --- | | RNA integration | `scvi.model.SCVI` | Unnormalized RNA counts | | RNA annotation | `scvi.model.SCANVI` | Counts and partial labels | | CITE-seq | `scvi.model.TOTALVI` | RNA and protein counts, aligned cells | | RNA + ATAC integration | `scvi.model.MULTIVI` | Registered MuData with aligned modality representation | | ATAC accessibility | `scvi.model.PEAKVI` | Cells by peaks, binary/count accessibility | …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/scvi-tools@sha256:b22633470d40ddafThe line at the top of this page pins the label v1.4, 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_dbgbogdtyhh4ywdb)
5 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between May 27, 2026 and Oct 1, 2026, about one every 25 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.4 latest | 2026-10-01 | a92663a | 10,233 B | A | view · diff |
| v1.3 | 2026-09-30 | ce9e6e9 | 9,692 B | A | view · diff |
| v1.2 | 2026-09-02 | 1e5eeff | 9,252 B | A | view · diff |
| v1.1 | 2026-07-26 | b085e11 | 8,295 B | A | view · diff |
| git:20260611.1b8fae3 | 2026-06-11 | 1b8fae3 | 8,300 B | A | view · diff |
| v1.0 | 2026-05-27 | 0936740 | 7,254 B | A | view |
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 (10233 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
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_dbgbogdtyhh4ywdb GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/scvi-tools GET https://markdownregistry.com/api/v1/blob/b22633470d40ddaf31451fbbf811941fc89c3174c404ca359f25378691267e73
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.
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