scgpt SKILL.md skillA
scgpt 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/scgpt@git:20260907.1f786cfPins git:20260907.1f786cf 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/scgpt/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260907.1f786cf, committed Sep 7, 2026
- First version recorded
- Jul 14, 2026
- Size
- 5,961 bytes
- Repository stars
- 5,279
- License
- Apache-2.0
Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use the scvi-tools library.
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
# scGPT — Single-Cell Foundation Model
## Prerequisites
| Requirement | Minimum | Recommended |
| ----------- | ------- | ----------- |
| Python | 3.10+ | 3.11 |
| CUDA | 12.1+ | 12.4+ |
| GPU VRAM | 16 GB | 24 GB+ |
## How to run
### Loading the vocabulary and checkpoint
scGPT checkpoints are **raw directories** (`args.json`, `best_model.pt`,
`vocab.json`) — not Hugging Face hub repos. Point at the directory, not an HF
repo id.
```python
from scgpt.tokenizer.gene_tokenizer import GeneVocab
gv = GeneVocab.from_file("/path/to/scgpt-human/vocab.json")
print(len(gv)) # 60697 for the released human checkpoint
```
### Embedding an AnnData
```python
import anndata as ad
from scgpt.tasks import embed_data
adata = ad.read_h5ad("dataset.h5ad") # var must contain a gene-name column
emb = embed_data(
adata,
model_dir="/path/to/scgpt-human",
gene_col="feature_name",
use_fast_transformer=False, # see Gotchas
)
# emb is an AnnData with .obsm["X_scGPT"]
```
## Output format
`embed_data` returns an `AnnData` whose `.obsm["X_scGPT"]` is the per-cell
…Read the whole file at its exact version.
How to install
mdr add aipoch/open-science/scgpt@sha256:a87b3b7f3990ca24The line at the top of this page pins the label git:20260907.1f786cf, 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_my2oniu4345glzo7)
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Versions
The registry has recorded 3 versions of this file, between Jul 14, 2026 and Sep 7, 2026, about one every 28 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260907.1f786cf latest | 2026-09-07 | 1f786cf | 5,961 B | A | view · diff |
| git:20260811.e7618cb | 2026-08-11 | e7618cb | 5,980 B | A | view · diff |
| git:20260714.a2a3282 | 2026-07-14 | a2a3282 | 5,347 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 (5961 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_my2oniu4345glzo7 GET https://markdownregistry.com/api/v1/resolve?ref=aipoch/open-science/scgpt GET https://markdownregistry.com/api/v1/blob/a87b3b7f3990ca24e087feb462201129711dc6684788ff7b789a2874bff95282
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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