Genomic Region Processing using Tools Such as BEDtools, BEDOPS and Tabix

Genomic regions processing using open-source command line tools such as BEDtools, BEDOPS and Tabix. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.


bedr 1.0.3


  • Standardised function name; renamed snm() to bedr.snm.region()
  • Listed SystemRequirements to the package metadata
  • Added support for Human hg38 genome assembly

bedr 1.0.2


  • Fixed compatibility with data.table >= v1.9.6 for data.table::fread() call

bedr 1.0.1


  • Fixed sort --version command as Solaris does not support --version which is GNU specific

bedr 1.0.0


  • Added bedr's first release

Reference manual

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1.0.3 by Paul Boutros, a year ago

Browse source code at

Authors: Daryl Waggott, Syed Haider, Emilie Lalonde, Clement Fung, Paul C. Boutros

Documentation:   PDF Manual  

GPL-2 license

Imports testthat, VennDiagram, data.table, R.utils, yaml, parallel, grid

Suggests knitr

System requirements: Preferred genomic operations engine: BEDtools, BEDOPS and Tabix.

See at CRAN