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Charlie Bayne edited this page Mar 28, 2026 · 1 revision

Help

The Help tab provides documentation, setup guidance, and answers to frequently asked questions.

Quick Start

A three-step summary of the recommended workflow:

  1. Upload your conduit.rds file on the About tab
  2. Explore and filter your data using the View Metadata and Filter Data tabs
  3. Analyze your data using the Analysis tab

AI Assistant Setup

Step-by-step instructions for obtaining API keys from each supported provider (Anthropic, OpenAI, Google Gemini) and configuring them in the AI tab. See the AI Assistant wiki page for full details.

Conduit Ecosystem

Cards linking to the three tools in the Conduit ecosystem:

  • Conduit-Ascent: The Snakemake workflow for raw data processing
  • ConduitR: The underlying R package with analysis functions
  • Conduit-Summit: This app

FAQ

Expandable FAQ panels covering common questions:

Why are there three separate tools? Each tool serves a different purpose: Conduit-Ascent handles computationally intensive processing on HPC infrastructure; ConduitR provides R functions for users who prefer scripted analysis; Conduit-Summit provides a no-code interactive interface for data exploration and visualization.

What input files does Conduit-Summit accept? Only .rds files produced by Conduit-Ascent. The file must contain a valid Conduit object as defined in the conduitR package.

How do I get a .rds file? Run the Conduit-Ascent Snakemake workflow on your raw DIA mass spectrometry data. The conduit.rds file is the final output of that workflow.

Is my data sent anywhere when I use the AI assistant? When using cloud providers (Anthropic, OpenAI, Gemini), summaries of your data structure are sent to the provider's API. Raw data is not transmitted. Use the local Ollama option to keep all data on your machine.

Do I need R experience to use Conduit-Summit? No. Conduit-Summit is designed for non-coders. However, understanding the basics of linear models will help you use the Statistics tab more effectively.

What does each analysis tab do? See the individual wiki pages for each tab, or refer to the descriptions in the Analysis tab itself.

Bug Reporting

Found a bug or have a feature request? Please open an issue on the Conduit-Summit GitHub repository.

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