PathLinker Cytoscape App User Manual

Table of Contents

• 1. PathLinker Cytoscape
  • 1.1. Description
  • 1.2. Overview
  • 1.3. Running the App
  • 1.4. Inputs
    • 1.4.1. Network
    • 1.4.2. Sources/Targets
    • 1.4.3. Algorithm
    • 1.4.4. Edge weights
  • 1.5. Outputs
  • 1.6. Example
    • 1.6.1. Load Network
    • 1.6.2. Sources and Targets
    • 1.6.3. Edge weight options
    • 1.6.4. Results
    • 1.6.5. Edge penalty
    • 1.6.6. Include tied paths
  • 1.7. Errors and Warnings
    • 1.7.1. Sources or Targets not in network
    • 1.7.2. Invalid input for parameters
    • 1.7.3. Not all edges have weight
  • 1.8. Cytoscape Automation / cyREST API
  • 1.9. How to Cite PathLinker
  • 1.10. Contact Information