An interesting as well as important task in epigenomic and genomic analysis is to statitistically assess the genomic features related to a particular region. For this purpose randomization methods have been vastly used. These methods take into account complexity of genomes neglecting the statistical model behined it.
Gel et al. (2016) have recently developed an R package which is based on permutation tests which are particularly meant to work with genomic regions. It not only takes into account all randomization methods but is also customizable. Moreover it also assess new functions to evaluate specificity occuring in local regions. regione R is available freely at the following website http://www.bioconductor.org/packages/regioneR
Reference:
Gel B.(2016).regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.Bioinformatics 32(2):289-291