pVACtools 4.0.4 documentation
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Table of Contents

  • pVACseq
  • pVACbind
    • Features
    • Prerequisites
    • Getting Started
    • Usage
    • Output Files
    • Filtering Commands
    • Additional Commands
    • Optional Downstream Analysis Tools
  • pVACfuse
  • pVACvector
  • pVACview
  • Installation
  • Tools Used By pVACtools
  • Frequently Asked Questions
  • Release Notes
  • License
  • Citations
  • How To Contribute
  • Contact
  • Mailing List

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pVACbind logo

pVACbindΒΆ

This component of the pVACtools is used to predict neoantigens for the peptides in a FASTA file.

  • Features
  • Prerequisites
  • Getting Started
  • Usage
  • Output Files
    • Filters applied to the filtered.tsv file
      • Prediction Algorithms Supporting Percentile Information
      • Prediction Algorithms Supporting Elution Scores
    • all_epitopes.tsv and filtered.tsv Report Columns
    • all_epitopes.aggregated.tsv Report Columns
      • The pVACbind Aggregate Report Tiers
        • Tiering Parameters
        • Tiers
        • Criteria Details
    • aggregated.tsv.reference_matches Report Columns
  • Filtering Commands
    • Binding Filter
    • Top Score Filter
  • Additional Commands
    • Download Example Data
    • List Valid Alleles
    • List Allele-Specific Cutoffs
  • Optional Downstream Analysis Tools
    • Generate Aggregated Report
    • Calculate Reference Proteome Similarity
    • NetChop Predict Cleavage Sites
    • NetMHCStab Predict Stability
    • Identify Problematic Amino Acids
  • pVACtools 4.0.4 documentation
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