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SAAVretrieval manualY.-M. Kang2018-03-20T09:33:18+00:00
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  • 0. Contents
  • 1. Introduction
    • – 1.1 Overview
    • – 1.2 Citation
    • – 1.3 Get Assistance
  • 2. Data Source
  • 3. Preparation of input files
  • – 3.1 SAAV peptide search
  • – 3.2 Input file format
    • — 3.2.1 SAAV peptide list
    • — 3.2.2 SAAV-calling format
  • 4. Usage
  • – 4.1 Test data
    • — 4.1.1 Input file for SAAVidentifier
    • — 4.1.2 Input files for SAAVannotator and SAAVvisualizer
    • — 4.1.3 Input file for SNVretriever
    • — 4.1.4 Input file for SAAVretriever
  • – 4.2 Proteogenomic interpretation pipeline
  • – 4.3 Web interface
    • — 4.3.1 SAAVidentifier module
    • — 4.3.2 SAAVannotator module
    • — 4.3.3 SNVretriever module
    • — 4.3.4 SAAVretriever module
    • — 4.3.5 SAAVvisualizer module
  • – 4.4 Python stand-alone program
    • — 4.4.1 Installation of the SAAVpedia Python package
    • — 4.4.2 Use of the Proteogenomic Interpretation Pipeline
  • – 4.5 REST API
  • 5. User manual
  • – 5.1 Web interface panel
    • — 5.1.1 SAAV sequence database download
    • — 5.1.2 SAAVidentifier
    • — 5.1.3 SAAVannotator
    • — 5.1.4 SNV/SAAVretriever
    • — 5.1.5 SAAVvisualizer
  • – 5.2 Python stand-alone program
    • — 5.2.1 SAAVidentifier.py
    • — 5.2.2 SAAVannotator.py
    • — 5.2.3 SNVretriever.py
    • — 5.2.4 SAAVretriever.py
  • – 5.3 REST API
    • — 5.3.1 SAAVidentifier
    • — 5.3.2 SAAVannotator
    • — 5.3.3 SNVretriever
    • — 5.3.4 SAAVretriever
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