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Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis

Wenpin Hou, Zhicheng Ji

Nature Methods · 2024 · CC BY

doi:10.1101/2023.04.16.537094

Abstract

Here we demonstrate that the large language model GPT-4 can accurately annotate cell types using marker gene information in single-cell RNA sequencing analysis. When evaluated across hundreds of tissue and cell types, GPT-4 generates cell type annotations exhibiting strong concordance with manual annotations. This capability can considerably reduce the effort and expertise required for cell type annotation. Additionally, we have developed an R software package GPTCelltype for GPT-4’s automated cell type annotation.

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