would you please let me know -- is there any package in R / BioC/ python that has implemented permutation/ randomization tests on genomic regions, in the following way :
-- assuming that we have a set of 1000 specific genomic regions (i.e. promoters, enhancers, insulators), and a quantitative measure (let's say "promoter intensity", or "enhancer intensity")
-- to compare the intensity of these 1000 specific genomic regions with the intensity of the random sets of 1000 genomic regions , and compute a p-value.
thanks a lot,
ps 1: 've asked the question also on BioC mailing list : https://support.bioconductor.org/p/128507/
ps 2: 've been looking over https://bioconductor.org/packages/release/bioc/html/regioneR.html, although it is focused more on simple associations/spatial relations between the sets of genomic regions.