Our implementation of the core calculation logic used by GREAT is now available for download. This package is written in C and includes two tools:
To download and install the tools, perform the following steps:
tar xzvf greatTools.tar.gz'
The logic for associating regions with genes and calculating enrichments is also completely described in our Nature Biotechnology paper.
All of the data included in the GREAT ontologies is publicly available, and we provide links or references for every ontology. We do not currently offer our processed ontology data for download, but all data is available from the original sources. Additionally, the GREAT web tool offers numerous "Export" functions to save all ontology data as it pertains to your sets.