bioRxiv: Claude Code plugin Findings Workflow targets reproducible, provenance-tracked LLM-assisted analysis

[bioRxiv] Riffle, Zelter and MacCoss present the Findings Workflow, a free, open-source Claude Code plugin designed to retain the flexibility of conversational LLM-assisted analysis while placing it within a structured, verifiable and reproducible environment, according to the preprint. The authors said the workflow uses staged, gated progression to ensure the science, metadata and data are understood and tested data loaders are built before downstream analysis begins. Specialized subagents perform statistical analysis, programming, visualization, research, reporting and validation, with independent review incorporated throughout, they said. The plugin also provides vetted analysis templates, conventions and methodological guidance. Scientists remain actively involved, exploring data and directing analysis through natural-language conversation, while the workflow supplies structure, verification and persistent state, according to the authors. Findings are recorded automatically together with the data, code, methods, figures and provenance needed to reproduce them. The authors demonstrate the workflow with a worked example reproducing central findings from a published plasma extracellular vesicle proteomics dataset examining Alzheimer's disease (Mag-Net). The preprint has not been peer-reviewed.