Genomics: Introducing CompBioAgent: A New LLM-Powered Tool for Single-Cell RNA-Seq Data Exploration
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We’re thrilled to announce the launch of CompBioAgent, a powerful and user-friendly web-based tool that transforms how researchers engage with single-cell RNA sequencing (scRNA-seq) data. Driven by advanced large language models (LLMs), CompBioAgent enables users to explore and analyze scRNA-seq datasets using natural language—no coding required.For example, users can ask the tool to “Show proportions of each cell type in disease and control states for multiple sclerosis.” |
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This innovative tool is the result of a collaborative effort between researchers at BioInfoRx, Inc., Biogen Inc., and Stanford University. Plans are underway to integrate CompBioAgent into BxGenomics, expanding its reach and impact within the research community. You can read the full preprint on bioRxiv.
Key Features:
- Natural Language Interface: Ask questions like “Show TYK2 expression in Multiple Sclerosis(MS) patients”, and get high-quality plots instantly.
- Smart Query-to-JSON Conversion: Translates your input into structured queries using advanced prompt engineering.
- LLM-Powered Intelligence: Integrates both commercial and open-source LLMs (GPT, Claude, Llama, DeepSeek) to parse biological queries.
- Real-Time Visualization: Plots rendered instantly through Cellxgene VIP, with support for dynamic modifications and high-resolution outputs.
- Broad Dataset Support: Explore publicly available scRNA-seq datasets for diseases like Multiple Sclerosis(MS), Alzheimer’s Disease(AD), Cutaneous Lupus Erythematosus(CLE), Systemic Lupus Erythematosus(SLE), Glaucoma, and Diabetes.
See it in action:
Visit the live demo to try out example queries and experience CompBioAgent firsthand. Explore the full source code on GitHub and see how it can be integrated into your workflow.
Who is it for:
- Biologists & Clinicians looking to interpret scRNA-seq data without writing code
- Bioinformaticians who want to accelerate hypothesis testing
- Educators seeking to make omics data analysis accessible to students
Spread the word:
We believe CompBioAgent has the potential to democratize access to complex single-cell data analysis tools. Please share with your colleagues and collaborators! Follow us for updates as we continue to improve CompBioAgent with more datasets, visualizations, and intelligent features.