CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis

Abstract Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data analysis are pivotal for advancing biological research, enabling precise characterization of cellular heterogeneity. However, existing analysis approaches require extensive manual programming and tool manipulation, posing significant challenges for researchers. To address this, we introduce CellAgent, an autonomous, LLM-driven approach that performs end-to-end scRNA-seq and spatial transcriptomics data analysis through natural language interactions. CellAgent employs a multi-agent hierarchical decision-making framework, simulating a “deep-thinking” workflow to ensure that each analytical step remains consistent with the overall task objective. To further enhance its capabilities, we developed sc-Omni, a high-performance, expert-curated toolkit that consolidates essential tools for scRNA-seq and spatial transcriptomics analysis. Additionally, we introduce a self-reflective optimization mechanism, enabling automated, iterative refinement of results through specialized evaluation methods, effectively replacing traditional manual assessments. Benchmarking against human experts demonstrates that CellAgent achieves approximately 60% improvement in efficiency across multiple downstream applications. In terms of accuracy, it maintains performance comparable to existing approaches while preserving natural language interactions. By translating natural language interactions into optimized analytical workflows, CellAgent establishes a scalable paradigm for LLM-driven scientific discovery, bridging the gap between experimental biologists and complex data analytics. This framework minimizes reliance on manual coding and exhaustive deliberation, ushering in the era of the “AI Agent for Science.”