Tutorials and topics
The following main step-by-step help pages are available:
- Notes on installing the software
- Startup and overview of the main software window
- Running an analysis. General steps, but focusing on the ORA method.
- Running a gene score resampling analysis.
- Running a receiver-operator characteristic analysis (ROC).
- Running a precision-recall analysis.
- Running a correlation analysis.
- Exploring analysis results.
- Multifunctionality diagnostics.
- Viewing results in detail.
- Saving and loading result files.
- Manipulating gene sets.
In addition the following topics are available:
- Information about gene multifunctionality
- More information on the tree view
- How to locate a gene set
- How genes that occur more than once are handled.
- How multiple test correction works in ermineJ
- Speeding up resampling
- An explanation of how gene set sizes are computed
- An explanation of how gene set scores are computed
Users who need more than the graphical interface can provide should look at: