restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor

Bioconductor's SummarizedExperiment class unites numerical assay quantifications with sample- and experiment-level metadata.  SummarizedExperiment is the standard Bioconductor class for assays that produce matrix-like data, used by over 200 packages.  We describe the restfulSE package, a deploy...

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Detalles Bibliográficos
Autores principales: Gopaulakrishnan, Shweta, Pollack, Samuela, Stubbs, BJ, Pagès, Hervé, Readey, John, Davis, Sean, Waldron, Levi, Morgan, Martin, Carey, Vincent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2019
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6392152/
https://www.ncbi.nlm.nih.gov/pubmed/30828438
http://dx.doi.org/10.12688/f1000research.17518.1
Descripción
Sumario:Bioconductor's SummarizedExperiment class unites numerical assay quantifications with sample- and experiment-level metadata.  SummarizedExperiment is the standard Bioconductor class for assays that produce matrix-like data, used by over 200 packages.  We describe the restfulSE package, a deployment of  this data model that supports remote storage.  We illustrate use of SummarizedExperiment with remote HDF5 and Google BigQuery back ends, with two applications in cancer genomics.  Our intent is to allow the use of familiar and semantically meaningful programmatic idioms to query genomic data, while abstracting the remote interface from end users and developers.

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