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Bedtoolsr: An R package for genomic data analysis and manipulation.

ABSTRACT: The sequencing of the human genome and subsequent advances in DNA sequencing technology have created a need for computational tools to analyze and manipulate genomic data sets. The bedtools software suite and the R programming language have emerged as indispensable tools for this purpose but have lacked integration. Here we describe bedtoolsr, an R package that provides simple and intuitive access to all bedtools functions from within the R programming environment. We provide several usability enhancements, support compatibility with past and future versions of bedtools, and include unit tests to ensure stability. bedtoolsr provides a user-focused, harmonious integration of the bedtools software suite with the R programming language that should be of great use to the genomics community.

SUBMITTER: Patwardhan MN

PROVIDER: S-EPMC6941791 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Bedtoolsr: An R package for genomic data analysis and manipulation.

Patwardhan Mayura N MN Wenger Craig D CD Davis Eric S ES Phanstiel Douglas H DH

Journal of open source software 20191206 44

The sequencing of the human genome and subsequent advances in DNA sequencing technology have created a need for computational tools to analyze and manipulate genomic data sets. The bedtools software suite and the R programming language have emerged as indispensable tools for this purpose but have lacked integration. Here we describe bedtoolsr, an R package that provides simple and intuitive access to all bedtools functions from within the R programming environment. We provide several usability e ...[more]

PMID: 31903447

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