Individual skill

scgpt

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.

resources/skills/scgpt/SKILL.md

Source commit 357d1a980056e191f380d0e01ec4fbc7cf529d1b

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Observed behavior

Network or broad shell

Last checked

Nov 9, 2026

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