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

ABSTRACT: Cell type annotation is an essential step in single-cell RNA-seq analysis. However, it is a time-consuming process that often requires expertise in collecting canonical marker genes and manually annotating cell types. Automated cell type annotation methods typically require the acquisition of high-quality reference datasets and the development of additional pipelines. We assessed the performance of GPT-4, a highly potent large language model, for cell type annotation, and demonstrated that it can automatically and accurately annotate cell types by utilizing marker gene information generated from standard single-cell RNA-seq analysis pipelines. Evaluated across hundreds of tissue types and cell types, GPT-4 generates cell type annotations exhibiting strong concordance with manual annotation

SUBMITTER: Hou W 

PROVIDER: S-EPMC10153208 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature