GAT - Genomic association tester
The genomic association tester (GAT) tests for association between sets of genomic intervals.
GAT tests if two sets of genomic intervals are associated more than expected by chance. Assocation typically means nucleotide overlap, but other measures such as the distance between elements or the number of overlapping segments can be used.
The tests are performed by simulation within a genomic context. The simulation part takes care of segment length distribution. The genomic context takes into account chromosomal location and optionally isochores.
Gat is available as an easy-installable package on the Python Package Index.
The code can be found at github.