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bioRxiv · 10.1101/327841

plyranges: A grammar of genomic data transformation

Lee, S.·Cook, D.·Lawrence, M.
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Abstract

The Bioconductor project provides many interoperable data abstractions for analyzing high-throughput genomics experiments; however implementing a typical genomic workflow with Bioconductor requires learning these abstractions and understanding them at an integrative level. This places a large cognitive burden on the user, especially for non-programmers. To reduce this burden we have created a grammar of genomic data transformation that operates on a single, central Bioconductor data structure, GRanges, which naturally represents genomic intervals and their associated measurements. The grammar defines verbs for performing actions on and between genomic interval data through a simplified, coherent interface to existing Bioconductor infrastructure, resulting in fluent analysis workflows. We have implemented this grammar as an R/Bioconductor package called plyranges.

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Lee, S., Cook, D., Lawrence, M.. 2018-05-23. plyranges: A grammar of genomic data transformation. https://doi.org/10.1101/327841

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