A bedr way of genomic interval processing. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Haider, Syed; Waggott, Daryl; Lalonde, Emilie; Fung, Clement; Liu, Fei-Fei; Boutros, Paul
• Is Part Of: Source code for biology and medicine. Volume 11:Issue 1(2016)
• Page Start: 1
• Page End: 7
• Publication Date: 2016-12
• Subjects: Genomic intervals -- BED format -- Sequence algebra -- Data integration; Biology -- Data processing -- Periodicals; Medicine -- Data processing -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1186/s13029-016-0059-5
• Languages: English
• ISSNs: 1751-0473

Abstract

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.