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...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Genome Biology Jg. 20; H. 1; S. 4
Hauptverfasser: Lee, Stuart, Cook, Dianne, Lawrence, Michael
Format: Journal Article
Sprache:Englisch
Veröffentlicht: London BioMed Central 04.01.2019
Springer Nature B.V
BMC
Schlagworte:
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-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
Beschreibung
Zusammenfassung: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 .
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
ObjectType-Article-2
ObjectType-Undefined-1
ObjectType-Feature-3
content type line 23
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-018-1597-8