Decoupler MCP Server

The Decoupler MCP server bridges the gap between advanced single‑cell RNA sequencing (scRNA‑Seq) workflows and conversational AI assistants. By exposing decoupler’s rich analytical toolkit through the Model Context Protocol, it lets developers and researchers invoke complex bioinformatics operations—such as pathway activity inference, transcription factor enrichment, clustering, differential expression, and a suite of visualizations—using simple natural‑language queries. This removes the need to manually script each step, enabling rapid hypothesis generation and iterative exploration directly within familiar AI client interfaces.

At its core, the server offers a modular architecture: an IO module handles reading and writing scRNA‑Seq datasets; a tool module provides core analysis functions like clustering and differential expression; a plotting module generates visual summaries such as violin plots, UMAPs, and t‑SNE embeddings; and a pathway activity module leverages decoupler’s ensemble methods to infer biological processes from expression data. Each capability is wrapped as an MCP resource, allowing the assistant to request specific actions and receive structured results without exposing underlying code complexity.

Developers integrating Decoupler MCP into their AI workflows gain several practical advantages. First, the natural‑language interface accelerates prototyping: a researcher can simply ask “Show me the top differentially expressed genes between cluster A and B” and receive both a ranked list and a violin plot. Second, the server’s compatibility with popular MCP‑enabled clients—such as Cherry Studio, Cline plugins, and Agno agent frameworks—means it can be dropped into existing pipelines with minimal friction. Third, because decoupler’s inference methods are ensemble‑based and well‑validated in the literature, users obtain robust biological insights that would otherwise require manual tuning of multiple tools.

Typical use cases include exploratory data analysis in academic labs, rapid turnaround in clinical genomics settings, and the development of AI‑driven bioinformatics assistants that guide users through complex scRNA‑Seq workflows. By encapsulating heavy computational tasks behind a simple protocol, Decoupler MCP empowers scientists to focus on interpretation rather than infrastructure, ultimately speeding discovery and lowering the barrier to entry for non‑programmatic users.