bedtoolsr
The bedtools suite of programs is a widely used set of various utilities for genomic analysis. BedtoolsR is an R package that provides a convenient wrapper for bedtools functions allowing for the documentation and use of them from within the R programming environment, using standard R data types. It uses the version of bedtools installed on your system, rather than its own version, such that you should be able to use it interchangeably from the command line or within R. It also includes additional functionality including the ability to provide either file paths or R objects as inputs and outputs. Bedtoolsr automatically detects the format of the input/output and handles it accordingly
Download
Bedtoolsr code is specific for different versions of bedtools. While most functions should work regardless of the version of bedtools you are using it is recommended that you download (or build) the version that matches your bedtools installation. Source code, as well as precompliled versions for different versions of bedtools are available in the links below. For installation information see Installation & Usage GitHub (source code for building your own package)
GitHub releases (pre-compiled packages for various versions of bedtools)
Note: package versions use the format [bedtools version]-[bedtoolsr build number for this bedtools version].
Publication
Patwardhan, Mayura; Wenger, Craig D.; Davis, Eric S.; Phanstiel, Douglas H.: "Bedtoolsr: An R package for genomic data analysis and manipulation" (in preparation).