flippr

Contents:

  • Getting Started
    • Quick start
    • Configuration
    • API & examples
    • Install
  • Quickstart
    • Installation
    • Basic example
    • Replicate argument
  • FragPipe v24 DDA and DIA Tutorial
    • Inputs FLiPPR expects
    • Sample naming
    • Install FLiPPR
    • DDA workflow
      • 1. Configure FragPipe v24.0
      • 2. Choose a DDA LFQ workflow
      • 3. Configure database and search settings
      • 4. Enable MS1 label-free quantification
      • 5. Run FragPipe and inspect output
      • 6. Run FLiPPR on DDA LiP data
      • 7. Run FLiPPR with DDA TrP normalization
    • DIA workflow
      • 1. Choose a DIA workflow in FragPipe
      • 2. Load files and verify data types
      • 3. Configure spectral library and DIA-NN quantification
      • 4. Run FragPipe and inspect output
      • 5. Run FLiPPR on DIA LiP data
      • 6. Run FLiPPR with DIA TrP normalization
    • Working with multiple comparisons
    • Exporting results
    • Important FLiPPR parameters
    • Quality checks
    • Troubleshooting
      • FileNotFoundError when creating Study
      • ColumnNotFoundError during study.run()
      • No rows after filtering
      • Unexpected TrP normalization values
    • References
  • Examples & Use Cases
    • Simple fold-change (LiP only)
    • Fold-change with TrP normalization
    • Multiple-dose experiment
  • API Reference
    • Study
    • Process & Result
    • Combine helpers
    • Notes
  • rcParams and configuration
  • How to cite FLiPPR
flippr
  • Search

© Copyright 2025, Edgar Manriquez-Sandoval - Fried Lab - Johns Hopkins University.

Built with Sphinx using a theme provided by Read the Docs.