⚙️ To get started, let’s find cells by typing into the CellWhisperer chat box. For example ‘Show me structural cells with immune functions’. CellWhisperer scores each transcriptome by how well it matches this textual query and colors by query match (red: high, blue: low) (2/11)

🔍 We investigate one of the identified cell clusters by selecting the cells & prompting CellWhisperer with ‘Describe these cells in detail’. This interactive workflow is enabled by seamless integration of the CellWhisperer AI chat box into a version of CELLxGENE Explorer (3/11)

🔬 You can easily query large transcriptome datasets for your favorite biological process using CellWhisperer. Just open Tabula Sapiens (cellwhisperer.cemm.at/tabulasapiens/) or GEO (cellwhisperer.cemm.at/geo/) in CellWhisperer & type your query into the chat box – for example “infection” (4/11)

🆕 The CellWhisperer paper (doi.org/10.1038/s415...) includes several new analyses beyond our 2024 bioRxiv preprint (biorxiv.org/content/10.1...). For example, we used CellWhisperer for an AI-guided analysis of human organ development (5/11)

🚀 We also validated CellWhisperer’s chat-based analysis with conventional bioinformatics. CellWhisperer was >4x faster (and 10x cooler 😊). Our recommendation: Use CellWhisperer for dataset exploration – but statistics is still important to ensure rigor & reproducibility (6/11)

🪄 How does CellWhisperer work behind the scenes? We trained a multimodal AI that links transcriptomes and text, enabling free-text search and annotation of RNA profiles. And we connected this model to an LLM that we fine-tuned into a chat assistant for transcriptome data (7/11)

📚 We trained on >1 million bulk & pseudo-bulk transcriptomes with textual annotations that we AI-curated from GEO & @CELLxGENE Census. Our training data is open source and useful for developing multimodal biomedical AI models and future bioinformatics research assistants. (8/11)

Ready to talk to cells? 📖 Read the paper: doi.org/10.1038/s415... 🧬 Try the web app with public datasets: cellwhisperer.bocklab.org 🖥️ Analyze your own datasets: github.com/epigen/cellw... (9/11)

🧬 CellWhisperer introduces a chat-based way to explore scRNA-seq data. By enabling natural language analysis, it bridges biologists and bioinformaticians—paving the way for AI-driven bioinformatics assistants. (10/11)