GREAT Source Code
We soon will offer for download our 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:
- A tool to calculate computationally-defined gene regulatory domains.
- A tool to calculate the genomic region-based binomial enrichment p-value for ontology terms given the regulatory domains of genes annotated with the term and the input regions associated with the term.
To download and compile the tools, perform the following steps:
- Download the source code tarball
- Unpack the tarball using the command '
tar xzvf greatTools.tar.gz'
- Follow the instructions given in the
The logic for associating regions with genes and calculating enrichments is also completely fully described in our Nature Biotechnology paper.
Our full GREAT application is very specific to our systems, which many hardcoded values and other dependencies on our setup. So, instead of providing a setup-specific application, we provide an implementation of the generally usable core calculation logic which can be used readily to build a version of GREAT that works with your system.
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 these data for download, but as 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.
GREAT Gene Sets
Please refer to Genes for instructions on how to download the gene set used by GREAT.