Next-Generation (NG) IEDB Tools Documentation

• Overview
  • Background & design philosophy
  • Notable features
    • Minimalistic interface
    • Integration of related tools
    • Pipelines
• Getting Started
  • Input Sequence Formats
    • FASTA
    • Whitespace-separated
    • Named whitespace-separated
    • JSON
  • 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 rows
    • Table states
    • Show/hide columns
    • Downloads
• Available Tools
  • T cell class I
    • MHC-binding and elution predictions
    • Immunogenicity predictions
    • MHC-I processing pathway predictions
  • Cluster
    • Parameter selection
    • Results
  • Mutant Peptide Generator
    • VCF input files
    • Parameter selection
    • Results
  • Pepmatch
    • Parameter selection
    • Results
  • PepX
    • Parameter selection
    • Results
  • Peptide Variant Comparison
    • Input Sequences
    • Parameter selection
    • 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)
  • Notes on the 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
• Troubleshooting
  • What are the input size limits?
  • Why does PepMatch not seem to complete?
  • How do I get more personalized support?
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