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.

Documentation

Manual: bedr.pdf
Vignette: bedr

Maintainer: Paul Boutros <Paul.Boutros at oicr.on.ca>

Author(s): Daryl Waggott, Syed Haider, Emilie Lalonde, Clement Fung, Paul C. Boutros

Install package and any missing dependencies by running this line in your R console:

install.packages("bedr")

Depends R (>= 3.0)
Imports testthat(>=0.7.1), VennDiagram(>=1.6.4), data.table(>=1.8.11), R.utils(>=2.0.2), yaml(>=2.1.10), parallel, grid
Suggests knitr(>=1.4)
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Package bedr
Materials
URL
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Version 1.0.3
Published 2016-08-23
License GPL-2
BugReports
SystemRequirements Preferred genomic operations engine: BEDtools, BEDOPS and Tabix.
NeedsCompilation no
Citation
CRAN checks bedr check results
Package source bedr_1.0.3.tar.gz