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plyranges: a grammar of genomic data transformation

Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class foll...

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Detalles Bibliográficos
Autores principales: Lee, Stuart, Cook, Dianne, Lawrence, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320618/
https://www.ncbi.nlm.nih.gov/pubmed/30609939
http://dx.doi.org/10.1186/s13059-018-1597-8
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author Lee, Stuart
Cook, Dianne
Lawrence, Michael
author_facet Lee, Stuart
Cook, Dianne
Lawrence, Michael
author_sort Lee, Stuart
collection PubMed
description Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows “tidy” data principles, we create a grammar of genomic data transformation, defining verbs for performing actions on and between genomic interval data and providing a way of performing common data analysis tasks through a coherent interface to existing Bioconductor infrastructure. We implement this grammar as a Bioconductor/R package called plyranges.
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spelling pubmed-63206182019-01-08 plyranges: a grammar of genomic data transformation Lee, Stuart Cook, Dianne Lawrence, Michael Genome Biol Software Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows “tidy” data principles, we create a grammar of genomic data transformation, defining verbs for performing actions on and between genomic interval data and providing a way of performing common data analysis tasks through a coherent interface to existing Bioconductor infrastructure. We implement this grammar as a Bioconductor/R package called plyranges. BioMed Central 2019-01-04 /pmc/articles/PMC6320618/ /pubmed/30609939 http://dx.doi.org/10.1186/s13059-018-1597-8 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Lee, Stuart
Cook, Dianne
Lawrence, Michael
plyranges: a grammar of genomic data transformation
title plyranges: a grammar of genomic data transformation
title_full plyranges: a grammar of genomic data transformation
title_fullStr plyranges: a grammar of genomic data transformation
title_full_unstemmed plyranges: a grammar of genomic data transformation
title_short plyranges: a grammar of genomic data transformation
title_sort plyranges: a grammar of genomic data transformation
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320618/
https://www.ncbi.nlm.nih.gov/pubmed/30609939
http://dx.doi.org/10.1186/s13059-018-1597-8
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