Scgpt

What it does

When your agent uses it

• Producing cell embeddings from an AnnData for clustering/integration
• Fine-tuned cell-type annotation
• Gene-level representation for perturbation/GRN tasks

Example prompts

• “/scgpt”

Requirements

• Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit fb309c3. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  No scripts in the folder and no shell commands in SKILL.md (its code samples are python).

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Scgpt loads about 1.3k tokens when it runs. Until then it costs about 97 tokens; SKILL.md has 337 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~97

When it runs · the whole SKILL.md, loaded when a task matches

~1.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from JimLiu/science-skills at commit fb309c3, republished under its Apache-2.0 licence (© JimLiu). 337 words, ~1,330 tokens.

name

scgpt

description

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.

license

Apache-2.0

category

biomodels

requirements

gpu

metadata.display-name

scGPT

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

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"]

c = host.compute.create(provider)
job = c.submit_job(
    intent="scGPT embed 50k cells — 1×GPU, ~5 min",
    inputs=[
        {"src": "dataset.h5ad", "dst_filename": "dataset.h5ad"},
        {"src": "embed.py", "dst_filename": "embed.py"},
    ],
    command="python3 embed.py",
    environment=...,   # env name from compute_details
    outputs=["embedded.h5ad"],
    timeout_seconds=1800,
)
print(job.job_id)   # cell ends here — kernel never blocks on compute

save_artifacts(payload["featured_files"])   # paths under hpc/<job_id>/

h = host.compute.create(provider)
res = h.attach_job(job_id).result()
h.close()

© JimLiu, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/scgpt of JimLiu/science-skills.

Open the folder on GitHubat commit fb309c3

Used in 4 other repositories

We found 4 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 4 other GitHub owners. This page covers the copy in JimLiu/science-skills, which our catalogue first saw on October 7, 2026.

• aipoch/open-scienceresources/skills/scgpt
• HughYau/AcademicForgeskills/claude-science/scgpt
• BioTender-max/awesome-bio-agent-skillsskills/claude-science/scgpt
• PKU-YuanGroup/OpenAI4Sskills/scgpt