CellTypeAI: cell annotation for scRNA-seq using local generative-AI.

Authors

Rufus H Daw, Harry R Deijnen, Magnus Rattray, John R Grainger

Published in

Bioinformatics (Oxford, England). Volume 42. Issue Supplement_2. Aug 01, 2026.

Abstract

Single-cell RNA sequencing (scRNA-seq) cell annotation techniques rely on the matching of known defining marker genes to a given cell population. However, these methods may lack robustness to dynamic fluctuations in cell marker expression between patients, samples and pathologies. The advent of easy-to-implement predictive technologies, like generative-AI (gen-AI), has facilitated the introduction of computational workflows that improve otherwise inaccurate context-dependent cell type annotation. Here, we introduce CellTypeAI, a streamlined, scalable program developed for tissue context-dependent cell annotation of scRNA-seq datasets using modern gen-AI models, enhanced by retrieval augmented generation methods.
Our implementation builds upon local gen-AI hosting technologies and directly integrates into scRNA-seq analysis pipelines. We show that CellTypeAI provides improved annotation accuracy compared to current conventional annotation methods and nascent cloud-based gen-AI approaches. As CellTypeAI leverages locally-run AI models, it can be applied to sensitive datasets, unlike approaches utilising online gen-AI tools such as ChatGPT, DeepSeek, or Claude. CellTypeAI presents a novel solution for tissue-specific cell type identification, overcoming traditional marker-based limitations via locally-deployed gen-AI models.
The source code is available at: https://github.com/rhdaw/CellTypeAI.

PMID:
42635202
Bibliographic data and abstract were imported from PubMed on 24 Aug 2026.

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