scgpt

by aipoch5.0k

Install

The skill file stays in the publisher's repository.

Paste the copied command in a terminal. It installs this SKILL.md into that agent.

npx skills add aipoch/open-science --skill scgpt -a cursor -y

Download skill resources/skills/scgpt/SKILL.md on GitHub

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Questions

How do I install scgpt?: Download resources/skills/scgpt/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does scgpt live?: The publisher keeps it at https://github.com/aipoch/open-science.
Which agents can use scgpt?: Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.

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

Requirement	Minimum	Recommended
Python	3.10+	3.11
CUDA	12.1+	12.4+
GPU VRAM	16 GB	24 GB+

Symptom	Fix
`flash_attn is not installed` warning at import	Harmless; pass `use_fast_transformer=False`
`'Vocab' object has no attribute 'vocab'`	Env has an old torchtext shim — update the env
Nearly all genes dropped	Wrong `gene_col`; check `adata.var.columns`
"scgpt not in manifest" / env-detection misses scGPT	The baked env manifest lists the distribution as `scGPT` (and `flash_attn`), pip's canonical casing — normalize manifest keys before lookup: `name.lower().replace('-', '_')`

scgpt

Install

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Questions

scGPT checkpoints are distributed as unlabeled Google Drive directories

(linked from github.com/bowang-lab/scGPT); the repo LICENSE (MIT) covers

the CODE, and no source states a weights license. Per the sourcing rule:

leave `license` absent. Repo root is a README, not a terms page —

info_url. verified 2026-06-30

third_party: - kind: weights name: scGPT provider: Wang Lab (University of Toronto) info_url: https://github.com/bowang-lab/scGPT

scGPT — Single-Cell Foundation Model

Prerequisites

How to run

Loading the vocabulary and checkpoint

Embedding an AnnData

Output format

Remote compute

Gotchas

Troubleshooting

Install

Related skills

Questions

scGPT checkpoints are distributed as unlabeled Google Drive directories

(linked from github.com/bowang-lab/scGPT); the repo LICENSE (MIT) covers

the CODE, and no source states a weights license. Per the sourcing rule:

leave license absent. Repo root is a README, not a terms page —

info_url. verified 2026-06-30

third_party: - kind: weights name: scGPT provider: Wang Lab (University of Toronto) info_url: https://github.com/bowang-lab/scGPT

scGPT — Single-Cell Foundation Model

Prerequisites

How to run

Loading the vocabulary and checkpoint

Embedding an AnnData

Output format

Remote compute

Gotchas

Troubleshooting

leave `license` absent. Repo root is a README, not a terms page —