Next-Generation (NG) IEDB Tools Documentation

• Overview
  • Design Philosophy
  • Notable Features
    • Minimalistic Interface
    • Integration of Related Tools
    • Pipelines
  • Release Notes
• Getting Started
  • First Prediction
  • Sending Results to Another Tool
  • Input Sequence Formats
    • FASTA
    • Whitespace-Separated
    • Named Whitespace-Separated
    • JSON
    • Phosphorylated Residues
  • Prediction Parameters
    • Peptide Lengths
    • MHC Alleles
    • Prediction Models
  • Running a Prediction
    • Returning to an Analysis
    • Warnings and Errors
    • Changing Parameters After a Prediction
  • Tabular Results
    • Sorting
    • Filtering
    • Table States
    • Show/Hide Columns
    • Downloads

• Available Tools
  • B Cell
    • B Cell - Sequence Input
      • Methods
      • Input Data
      • Parameter Selection
      • Results
    • B Cell - Structure Input
      • Methods
      • Input Data
      • Parameter Selection
      • Results
  • T Cell
    • T cell class I
      • Binding Predictions
      • Immunogenicity Predictions
      • Processing Predictions
    • T cell class II
      • Binding Predictions
      • Immunogenicity Predictions
      • Processing Predictions
    • AXEL-F
      • Methods
      • Input Data
      • Parameter Selection
      • Results
    • Patient Harmonic-mean Best Rank (PHBR)
      • Methods
      • Input Data
      • Parameter Selection
      • Results
    • Peptide Variant Comparison
      • Methods
      • Input Data
      • Parameter Selection
      • Results
    • Population Coverage
      • Methods
      • Input Data
      • Parameter Selection
      • Results
    • RATE
      • Methods
      • Input Data
      • Parameter Selection
      • Results
  • Cluster
    • Methods
    • Input Data
    • Parameter Selection
    • Results
      • Tabular Results
      • Cluster Visualization
      • Interpreting Results
  • Mutated Peptide Generator
    • Methods
    • Input Data
      • Recommended: Strip Unnecessary Annotations
      • Recommended: Decomposition and Normalization
      • Recommended: SNPEff annotation
    • Parameter Selection
    • Results
      • Tabular Results
      • Interpreting Results
  • PEPMatch
    • Methods
    • Input Data
    • Parameter Selection
      • Maximum number of mismatches
      • Proteome
      • Include all matches or best match per peptide
      • Include unmatched peptides
    • Results
      • Interpreting Results
  • PepX
    • Methods
    • Input Data
    • Parameter Selection
    • Results
      • Peptide Table (Gene)
      • Peptide Gene Summary Table
      • Peptide Table (Transcript)
      • Peptide Transcript Summary Table
  • PepSySco
    • Methods
    • Input Data
    • Parameter Selection
    • Results
      • Interpreting Scores
  • Conservancy
    • Methods
    • Input Data
      • Epitope sequences
      • Protein sequences
    • Parameter Selection
      • Analysis type
      • Identity Threshold (%)
      • Duplicate handling
    • Results
      • Interpreting Results

• Pipelines
  • Building a Pipeline
    • Passing Filtered Results to Downstream Tool
  • Pipeline Map
  • Saving/Sharing Pipelines
    • Pipeline Steps with Data (pipeline_id)
    • Pipeline Steps without Data (pipeline_spec_id)
  • Pipeline Lifecycle
  • Example Pipelines
    • One-Step Pipeline
    • Two-Step Pipeline
    • Three-Step Pipeline
• API Usage
  • Typical Workflow
  • Core Endpoints
    • /pipeline POST for Submitting Predictions
    • /pipeline GET for Retrieving Pipeline Details
    • /stage GET for Retrieving Stage Information
    • /results GET for Retrieving Stage Results
  • Swagger Documentation
    • Usage
    • Request with Parameters
• Troubleshooting
  • Why does my prediction consistently fail?
  • What are the input size limits?
  • How do I get more personalized support?
• Privacy Notice
  • Information We Collect
  • How We Use Your Information
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