Modules

GenomeRunner is installed as a grsnp module. There are four submodules in the package:

1. dbcreator_ucsc and dbcreator_encodeDCC - modules for creating organism-specific genome annotation databases
2. optimizer - a module to speed up GenomeRunner by pre-calculating background overlap statistics
3. server - a module for the web interface
4. hypergeom4 - a command-line module for the enrichment/epigenomic similarity analyses

The interplay among the modules is shown on the figure

Before running GenomeRunner, the first step is to create a database of genomic annotations using the dbcreator module. Optionally, optimize the database using the optimizer module. Then, run GenomeRunner web server using the server module. To run GenomeRunner from command line, use the hypergeom4 module.