Version 3.2 (April 2021)

Limits GO files to OBO format. Support for RDF-XML has been dropped as the format we supported was deprecated by the GO consortium. If you need to run analyses using the old XML format you will have to use an older version of ErmineJ. Fixes a reported issue with OBO file parsing. Miscellaneous minor updates […]
Powerful, flexible and simple gene set analysis.

ErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing something interesting" in an experiment that generates long lists of candidates. The software is designed to be used by biologists with little or no informatics background (but if you do, you might be interested in the CLI or the R support).

ErmineJ is free software developed by the Pavlidis lab at the University of British Columbia.

ErmineJ can be downloaded here, or run ErmineJ right now using WebStart. The source is also available on GitHub.

Major features include: For more information see the user manual. If you like ErmineJ, you should check out GOtrack. Explore Gene Ontology and GO annotation history and how changes over time impacts application and interpretation.