scgpt SKILL.md skillA
scgpt from pengqianhan/ai-human-research-os is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pengqianhan/ai-human-research-os/scgpt@git:20260715.38d79bePins git:20260715.38d79be in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pengqianhan/ai-human-research-os
- Path
research-skills-hub/claude-science-skills/skills/scgpt/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260715.38d79be, committed Jul 15, 2026
- Size
- 5,347 bytes
- Repository stars
- 3
- License
- MIT
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 pengqianhan/ai-human-research-os/scgpt@sha256:7af27c91d22afd7bThe line at the top of this page pins the label git:20260715.38d79be, 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_75pk6lv2pklnbszq)
1 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 1 version of this file, committed on Jul 15, 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 (5347 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
pengqianhan/ai-human-research-os · 3 stars · license MIT · pushed 2026-10-19 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_75pk6lv2pklnbszq GET https://markdownregistry.com/api/v1/resolve?ref=pengqianhan/ai-human-research-os/scgpt GET https://markdownregistry.com/api/v1/blob/7af27c91d22afd7bd465d2d84b5fbe6702792d9233fa81ab75cbfa00818cf55e
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.
More from pengqianhan/ai-human-research-os
Every file in pengqianhan/ai-human-research-os