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
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author Gopaulakrishnan, Shweta
Pollack, Samuela
Stubbs, BJ
Pagès, Hervé
Readey, John
Davis, Sean
Waldron, Levi
Morgan, Martin
Carey, Vincent
author_facet Gopaulakrishnan, Shweta
Pollack, Samuela
Stubbs, BJ
Pagès, Hervé
Readey, John
Davis, Sean
Waldron, Levi
Morgan, Martin
Carey, Vincent
author_sort Gopaulakrishnan, Shweta
collection PubMed
description 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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spelling pubmed-63921522019-03-01 restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor Gopaulakrishnan, Shweta Pollack, Samuela Stubbs, BJ Pagès, Hervé Readey, John Davis, Sean Waldron, Levi Morgan, Martin Carey, Vincent F1000Res Software Tool Article 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. F1000 Research Limited 2019-01-07 /pmc/articles/PMC6392152/ /pubmed/30828438 http://dx.doi.org/10.12688/f1000research.17518.1 Text en Copyright: © 2019 Gopaulakrishnan S et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Gopaulakrishnan, Shweta
Pollack, Samuela
Stubbs, BJ
Pagès, Hervé
Readey, John
Davis, Sean
Waldron, Levi
Morgan, Martin
Carey, Vincent
restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
title restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
title_full restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
title_fullStr restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
title_full_unstemmed restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
title_short restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor
title_sort restfulse: a semantically rich interface for cloud-scale genomics with bioconductor
topic Software Tool Article
url 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
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