xiFDR documentation

Version: 3.0.0a17.dev20+g35fb723

xiFDR is a tool for crosslink mass spectrometry (CLMS) false discovery rate (FDR) estimation and crosslink spectrum match (CSM) aggregation. Usual applications are the extraction of residue links or protein-protein interactions (PPIs) above a desired significance threshold. Further, xiFDR supports boosting of FDR levels to obtain the largest possible number of residue-links or PPIs by finding the optimal FDR thresholds.

Contents:

• Basic usage
  • Installation
  • Input format
  • Running a full multi-level FDR
  • Running a boosted multi-level FDR
• How it works
  • Aggregation levels
  • Aggregation functions
  • FDR groups
  • Validity checks
• API
  • Boosting
  • Multi-Level FDR calculation