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 […]
This version adds support for the OBO file format for the Gene Ontology in addition to XML. In the future OBO is likely to be the recommended file type to use for ErmineJ. We are also taking this opportunity to announce the availability of R support for ErmineJ, with the ErmineR library.
Changes in this version affect the behaviour of the software in a particular gene score situation, where the smallest value is the for the top gene. This is in contrast to the typical inputs which are p-values (for which -log10 transformation is conducted, so large values are ranked highest) or fold-changes or other scores that […]
This update mostly affects the command line interface (CLI), but has some impact on the GUI. This includes removing some rarely-used methods, changing some defaults, and renaming some options. This may break (or change the output of) existing scripts using the CLI which is why we have bumped the version number to 3.1. Changes include: […]
ErmineJ now requires Java 8 Updated external URLs for GO terms Multi-gene-mapping microarray probes listed in Gemma platform annotation files are now ignored by default. This behaviour can be modified through a configuration. Changes for compatibility with the new Gemma RESTful API Mac OS distribution now a DMG file.
This release fixes several problems reported by users as well as including some documentation updates. The “generic” distribution of the software had an error in the configuration causing it to fail to execute. The logging configuration was causing some problems for command line use. In the details screen, if your “raw data” matrix is missing […]
This release fixes several issues: Quicklists did not correctly deal with genes in your hitlist that are unannotated (are not members of any gene groups). Error handling for the “multifunctionality diagnostics” has been improved. Problems with selecting score files and poor interaction with the file validation in the Analysis Wizard (bug 3874) The ermineJ log […]
We are excited to announce a major new release of ErmineJ. There are a number of new features, and overall the software is improved and easier to use. Some highlights: Introduction of diagnostics and corrections for “gene multifunctionality”. See the documentation for details. Introduction of a new gene set scoring method based on precision-recall. See […]
Version 2.1.22 – (November 2010) Fixes a CLI bug that caused gene score file to be required even when using the correlation method. This only affects users of the command line tool. Version 2.1.18 – (July 2009) Changes include: Fix broken links on GO file documentation page. Update our mailing list address. Old subscribers have […]