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.

Install

KitScout test notes

Not tested by KitScout yet. When our harness runs it, pros, cons and the tasks we tried appear here, with the date and evidence.

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