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» Home » Documentation

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

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