ErmineJ documentation

This manual is organized into the following topics:

• Tutorials
  • Software Installation Notes
  • Software Startup and Overview
  • Running an Analysis: General steps and ORA
  • Running an Analysis: Resampling
  • Running an Analysis: ROC
  • Running an Analysis: Correlation
  • Tutorial: Precision-Recall scoring
  • Analysis Results
  • Multifunctionality diagnostics
  • Gene set details
    • Changing the Gene URL
  • Saving and Loading Analyses and Projects
  • Manipulating Gene Sets
  • Multifunctionality
  • ErmineJ Tree View
  • Locating Gene Sets
  • Handling repeated genes
  • Multiple Test Correction in ermineJ
  • Tips: Speeding up Resampling
  • Explanation: Computing Gene Set Sizes
  • Explanation: Interpreting Gene Set Scores
  • ermineJ API
  • ermineJ CLI
• Data file formats
  • Input: Gene Scores
  • Input: Gene Expression Profiles
  • Input: Gene Set Descriptions
  • Input: Gene Annotations
  • Converting Excel files
  • Output Format
  • Gene Sets
• Frequently asked questions