scvi-tools SKILL.md skillA
scvi-tools from aipoch/open-science is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add aipoch/open-science/scvi-tools@git:20260912.a35c1dbPins git:20260912.a35c1db in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- aipoch/open-science
- Path
resources/skills/scvi-tools/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260912.a35c1db, committed Sep 12, 2026
- First version recorded
- Jul 14, 2026
- Size
- 14,567 bytes
- Repository stars
- 5,279
- License
- Apache-2.0
Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. Reach for this skill to integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster. For spatial deconvolution / mapping use the cell2location, DestVI, or Tangram methods instead.
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 — scVI / scANVI
scvi-tools (Gayoso et al. 2022, github.com/scverse/scvi-tools, BSD-3-Clause)
wraps a family
of deep generative models for single-cell omics. The scRNA-seq core is **scVI**
(unsupervised batch-corrected latent embedding) and **scANVI** (scVI + a
classifier head for semi-supervised cell-type label transfer). Both expect
**raw integer UMI counts** and emit a low-dimensional `X_scVI` / `X_scANVI`
that drops into the scanpy neighbors → leiden → umap pipeline.
## Setup (any agent, no API key)
This is a **pure skill** — `kernel.py` is deterministic Python and _you_ (the
base model) do all the reasoning. There is no `host` runtime and no LLM API.
The helpers are `prepare_scvi_counts` for input validation and `h5ad_safe_obs`
for obs/var frames that `anndata.write_h5ad()` can serialize. Load them once
per session in a Python cell:
```python
exec(open("scvi-tools/kernel.py", encoding="utf-8").read()) # path to this skill's kernel.py
```
Nothing auto-loads it outside Claude Science. Then call the helpers directly.
If a helper raises `NameError`, you haven't exec'd kernel.py.
Dependencies: `pip install scvi-tools scanpy anndata`. Training needs a
…Read the whole file at its exact version.
How to install
mdr add aipoch/open-science/scvi-tools@sha256:27779ca65ae12363The line at the top of this page pins the label git:20260912.a35c1db, 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_rt2a2ug6sp7bioxe)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 3 versions of this file, between Jul 14, 2026 and Sep 12, 2026, about one every 30 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260912.a35c1db latest | 2026-09-12 | a35c1db | 14,567 B | A | view · diff |
| git:20260814.c9a70d8 | 2026-08-14 | c9a70d8 | 13,360 B | A | view · diff |
| git:20260714.a2a3282 | 2026-07-14 | a2a3282 | 9,368 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 (14567 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
aipoch/open-science · 5,279 stars · license Apache-2.0 · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_rt2a2ug6sp7bioxe GET https://markdownregistry.com/api/v1/resolve?ref=aipoch/open-science/scvi-tools GET https://markdownregistry.com/api/v1/blob/27779ca65ae12363dc7e60d40320d2e9d19085c3f8cf7ba016c3a2e4b799bf96
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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