CellAtria is an advanced agentic system designed to streamline single-cell research by automating data extraction, metadata retrieval, and analysis workflows. Its architectural framework supports complex tasks through multi-turn dialogues with users, enabling seamless interactions for data acquisition, including parsing manuscripts from URLs and local PDF files. CellAtria overcomes access barriers by retrieving structured datasets from public repositories and provides real-time execution logs for transparency and traceability. It also integrates with a companion pipeline, CellExpress, which processes scRNA-seq data into analysis-ready outputs with minimal user intervention. By autonomously executing workflows, CellAtria enhances efficiency, significantly reducing manual effort while ensuring reproducibility. Its performance has been validated across various cancer types, demonstrating scalability and consistency in processing large datasets. This innovative platform not only bridges literature discovery and dataset integration but also supports a comprehensive, user-friendly approach to single-cell transcriptomics. CellAtria exemplifies the future of automated scientific discovery in genomics research.
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