Proffer documentation

Proffer is fast and flexible tool for protein inference in bottom-up proteomics experiments.

Getting Started

For help installing and running Proffer, see the Quickstart guide.

Contents

• Quickstart guide
  • Installation
  • Basic Usage
  • Python usage
  • Usage with Fulcrum Pipeline
• Benchmarks
  • Setup
  • Load Benchmarks
  • Visualize
    • End-to-end
    • Core inference functions
    • Graph manipulation
• API Reference
  • proffer
    • Submodules
      • proffer.cli
      • proffer.graph
      • proffer.infer
      • proffer.io
      • proffer.reannotate
      • proffer.spark
    • Functions
    • Package Contents
      • infer()