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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Bibliographic Details
Published in:Genome Biology Vol. 20; no. 1; p. 4
Main Authors: Lee, Stuart, Cook, Dianne, Lawrence, Michael
Format: Journal Article
Language:English
Published: London BioMed Central 04.01.2019
Springer Nature B.V
BMC
Subjects:
Algebra
Animal Genetics and Genomics
Application programming interface
Batch processing
Bioconductor
Bioinformatics
Biology
Biomedical and Life Sciences
class
cognition
Cognitive ability
Data analysis
Data processing
Datasets
Evolutionary Biology
genome
Genomes
Genomics
Genomics - methods
Grammar
Human Genetics
infrastructure
Interoperability
Language
Life Sciences
Microbial Genetics and Genomics
Plant Genetics and Genomics
Software
Terminology as Topic
Australia
Data analysis
Genomes
Bioconductor
Grammar
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Description
Summary: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-018-1597-8