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

Wenpin HouZhicheng Ji
Published in: Nature methods (2024)
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.
Keyphrases
  • single cell
  • rna seq
  • high throughput
  • gene expression
  • autism spectrum disorder
  • healthcare
  • copy number
  • deep learning
  • cell therapy
  • mesenchymal stem cells
  • social media
  • transcription factor