title: A bedr way of genomic interval processing.
abstract: BACKGROUND
  Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annotation, merging multiple experiments together and subsequently quantifying and visualizing the overlap. The most widely-used tools for these tasks work at the command-line (e.g. BEDTools) and the small number of available R packages are either slow or have distinct semantics and features from command-line interfaces.
  
  
  RESULTS
  To provide a robust R-based interface to standard command-line tools for genomic coordinate manipulation, we created bedr. This open-source R package can use either BEDTools or BEDOPS as a back-end and performs data-manipulation extremely quickly, creating R data structures that can be readily interfaced with existing computational pipelines. It includes data-visualization capabilities and a number of data-access functions that interface with standard databases like UCSC and COSMIC.
  
  
  CONCLUSIONS
  bedr package provides an open source solution to enable genomic interval data manipulation and restructuring in R programming language which is commonly used in bioinformatics, and therefore would be useful to bioinformaticians and genomic researchers.
authors.affiliation: Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.
authors.forename: Syed
authors.initials: S
authors.lastname: Haider
authors.affiliation: Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.
authors.forename: Daryl
authors.initials: D
authors.lastname: Waggott
authors.affiliation: Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.|Departments of Radiation Oncology, Pharmacology & Toxicology, and Medical Biophysics, University of Toronto, Toronto, M5G 2M9 Canada.
authors.forename: Emilie
authors.initials: E
authors.lastname: Lalonde
authors.affiliation: Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.
authors.forename: Clement
authors.initials: C
authors.lastname: Fung
authors.affiliation: Departments of Radiation Oncology, Pharmacology & Toxicology, and Medical Biophysics, University of Toronto, Toronto, M5G 2M9 Canada.|Ontario Cancer Institute and Campbell Family Institute for Cancer Research, Princess Margaret Hospital, University Health Network, Toronto, M5G 2M9 Canada.
authors.forename: Fei-Fei
authors.initials: FF
authors.lastname: Liu
authors.affiliation: Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.|Departments of Radiation Oncology, Pharmacology & Toxicology, and Medical Biophysics, University of Toronto, Toronto, M5G 2M9 Canada.
authors.forename: Paul C
authors.initials: PC
authors.lastname: Boutros
keywords: BED format; Data integration; Genomic intervals; Sequence algebra