Using a system call to bedtools, featuremaps intersects two sets of genomic coordinates where one set set encompasses the other. Each interval can then be scaled to a uniform length and the proportional coverage is calculated. Pretty density plots can then be made.
Package details 


Maintainer  
License  What license is it under? I don't know yet. 
Version  0.0.0.9000 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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