OMICX: An AI-powered web platform for integrative analysis of multi-condition single-cell transcriptomics data

Here, we introduce OMICX, an interactive, code-free web platform powered by a large language model (LLM) assistant, OMICX-Agent. This intelligent agent enables users to conduct comprehensive single-cell data analyses through natural language conversations, making advanced bioinformatics accessible to all. OMICX-Agent guides users through standard scRNA-seq processing workflows, multi-sample and multi-condition analyses, and integrative studies combining single-cell data with bulk RNA-seq or GWAS summary statistics. We demonstrate OMICX's versatility across three real-world case studies, showcasing its applications in an integrative analysis of scRNA-seq and GWAS summary data; an integrative analysis of scRNA-seq and bulk RNA-seq data; complex multi-condition scRNA-seq data analysis. Designed with usability and reproducibility in mind, OMICX empowers researchers to extract biological insights with ease and confidence. The platform is freely available at https://sqsun.github.io/software.html . • OMICX provides an LLM assistant enabling interactive, code-free single-cell data analysis through natural language conversations. • OMICX supports complex experimental designs including case-control comparisons and temporal differential expression analysis via specialized statistical modules. • OMICX supports integrative analysis of scRNA-seq with bulk RNA-seq and GWAS summary statistics for comprehensive biological insights.