inteRelate: flexible and thorough relating of genomic interval datasets through comparative overlap analysis

Summary Testing spatial relationships between genome-mapped features is both a common source of hypothesis generation and an additional layer of supporting evidence for experimental findings. Many computational tools automate the statistical association procedures used to assess overlap between pairs of genomic features. However, none provides a dedicated workflow that directly compares multiple features by assessing their overlap with a separate, common feature, first testing for overall heterogeneity and then identifying which overlap rates differ. Such comparative overlap analysis could directly facilitate comparisons of features within the same class across disease states, cell types, experimental perturbations, and other biological contexts. Here, we describe inteRelate, a software package that uses genomic interval datasets to test spatial relationships between genome-mapped features through comparative overlap analysis. The package functions as an end-to-end pipeline that is highly tunable and thorough in its statistical association procedures. We use experimental data to demonstrate the automation, accuracy, and insight inteRelate provides. Availability and implementation inteRelate is available at https://github.com/loggy01/interelate and archived at https://zenodo.org/records/21891072. Example uses are available in the online supplement. Additionally, the example datasets and results are available at https://zenodo.org/records/22012767.