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 1.0.6


  • updated support for tabix version >1.1. tabix deprecated option -B is now replaced with -R

bedr 1.0.5


  • fixed incorrect ordering of chromosome table returned by get.chr.length() - [rolled back]

bedr 1.0.4


  • Added rmarkdown in Suggests section
  • Parameterised test.region.similarity() with gaps.file and repeats.file to support custom files
  • Fixed bug when bedtools 'coverage' output is post-processed in bedr
  • Fixed is.valid.seq() to comply with inputs and outputs as described in docs
  • Exposed utility function bed2index() via NAMESPACE to support its direct usage

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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1.0.7 by Paul C. Boutros, 2 years ago

Browse source code at

Authors: Syed Haider [aut] , Daryl Waggott [aut] , Emilie Lalonde [ctb] , Clement Fung [ctb] , Paul C. Boutros [aut, cre, cph]

Documentation:   PDF Manual  

GPL-2 license

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

Suggests knitr, rmarkdown

System requirements: Preferred genomic operations engine: 'BEDTools', 'BEDOPS' and 'Tabix (>= 1.3)'.

Imported by chicane.

See at CRAN