scgpt

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
origin	openai4s
category	biomodels
requirements	["gpu"]
capabilities	{"network":{"mode":"none","domains":[]}}
metadata	{"display-name":"scGPT","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

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.

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

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 embedding (n_cells × emb_dim, 512 by default). Downstream: feed to scanpy.pp.neighbors / scanpy.tl.umap.

Remote compute

Needs ≥24 GB VRAM and the released human checkpoint (~200 MB: args.json, best_model.pt, vocab.json). Read compute_details({provider, mode:'read'}) for an environment with and a pre-cached checkpoint directory, then: