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OpenMS 3.1.0dev documentation
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OpenMS 3.1.0dev documentation

Introduction

  • What is OpenMS?
  • Background
  • Entry Points to OpenMS

OpenMS Applications and Tools

  • Installation
    • GNU/Linux
    • macOS
    • Windows
  • OpenMS Graphical User Interfaces
  • TOPP Tools
    • Introduction to TOPP
    • Types of TOPP Tools
  • Command Line Interface
  • TOPPView: Visualize with OpenMS
    • Views in TOPPView
    • Display Modes and View Options in TOPPView
    • Data Analysis in TOPPView
    • Data Editing in TOPPView
    • TOPPView Hotkeys

Run Workflows with OpenMS Tools

  • Recommended Workflow Systems
  • OpenMS in KNIME
    • Installation of KNIME and its OpenMS plugin
    • Ready-made OpenMS KNIME workflows
    • OpenMS KNIME User Tutorial
  • OpenMS in Nextflow
    • Installation of nextflow and nf-core
    • Ready-made OpenMS nextflow workflows
    • Tutorial
  • OpenMS on Galaxy
  • OpenMS on TOPPAS

Tutorials and Quick Start Guides

  • User Quickstart Guide
  • OpenMS User Tutorial
  • Worked Examples: Different OpenMS Methods to Achieve the Same Outcome

Develop with OpenMS

  • Developer Quickstart Guide
  • OpenMS C++ Core Library
  • OpenMS API Reference
  • pyOpenMS
  • Build From Source
  • External Code using OpenMS

Contribute to OpenMS

  • Contributor’s Quick Start Guide
  • OpenMS Git Workflow
  • Write and Label GitHub Issues
  • Adding New Tool to The TOPP suite
  • Pull Request Checklist
  • Reporting Bugs and Issues
  • Advanced
    • Developer Guidelines For Adding New Dependent Libraries
    • Custom Compilation of OpenMS
    • Build Custom KNIME Plugin

Downloads

  • OpenMS Installers
  • Workflows
  • Other Resources

Quick Reference

  • Contributor FAQ
  • Developer FAQ
  • Contact Us
  • OpenMS Glossary
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TOPP Tools#

The following sections introduce TOPP, some general concepts and more specific information regarding each tool.

  • Introduction to TOPP
  • Types of TOPP Tools
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Introduction to TOPP
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OpenMS Graphical User Interfaces
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