CompBioAgent: an LLM-powered agent for single-cell RNA-seq data exploration

Abstract

AO_SCPLOWBSTRACTC_SCPLOWAdvancements in high-throughput biological technologies, particularly single-cell RNA sequencing (scRNA-seq), have generated vast amounts of complex data that offer valuable insights into gene expression, cellular behavior, and disease mechanisms. However, the analysis of such data often requires specialized computational skills and expertise, which can pose a barrier to many researchers. To address this challenge, we developed CompBioAgent, a user-friendly web application designed to democratize access to bioinformatics resources, powered by Large Language Models (LLMs). By integrating with the CellDepot, CompBioAgent allows users to easily query and explore gene expression data related to various diseases, cell types, and experimental conditions. Moreover, the tool employs Cellxgene Visualization In Plugin (Cellxgene VIP) platform to generate a range of intuitive visualizations, including violin plots, UMAP embeddings, heatmaps, etc. With its natural language interface, CompBioAgent automatically converts scientific queries into structured data requests and returns the plot of interest, enabling seamless exploration of biological data without the need for programming expertise. Such integration enhances the ability of researchers to visualize complex biological insights and identify key patterns, making high-level data analysis more accessible and efficient. A demo website and a list of examples are available at https://celldepot.bxgenomics.com/compbioagent, and the source code is released at https://github.com/interactivereport/compbioagent.