DeepBlueR: large-scale epigenomic analysis in R

MOTIVATION: While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. The DeepBlue Epigenomic Data Server provides a powerful interface and API for filtering, transforming, aggregating and downloadin...

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Autores principales: Albrecht, Felipe, List, Markus, Bock, Christoph, Lengauer, Thomas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870546/
https://www.ncbi.nlm.nih.gov/pubmed/28334349
http://dx.doi.org/10.1093/bioinformatics/btx099
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author Albrecht, Felipe
List, Markus
Bock, Christoph
Lengauer, Thomas
author_facet Albrecht, Felipe
List, Markus
Bock, Christoph
Lengauer, Thomas
author_sort Albrecht, Felipe
collection PubMed
description MOTIVATION: While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. The DeepBlue Epigenomic Data Server provides a powerful interface and API for filtering, transforming, aggregating and downloading data from several epigenomic consortia. RESULTS: To make public epigenomic data conveniently available for analysis in R, we developed an R/Bioconductor package that connects to the DeepBlue Epigenomic Data Server, enabling users to quickly gather and transform epigenomic data from selected experiments for analysis in the Bioconductor ecosystem. AVAILABILITY AND IMPLEMENTATION: http://deepblue.mpi-inf.mpg.de/R. REQUIREMENTS: R 3.3, Bioconductor 3.4. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-58705462018-04-05 DeepBlueR: large-scale epigenomic analysis in R Albrecht, Felipe List, Markus Bock, Christoph Lengauer, Thomas Bioinformatics Applications Notes MOTIVATION: While large amounts of epigenomic data are publicly available, their retrieval in a form suitable for downstream analysis is a bottleneck in current research. The DeepBlue Epigenomic Data Server provides a powerful interface and API for filtering, transforming, aggregating and downloading data from several epigenomic consortia. RESULTS: To make public epigenomic data conveniently available for analysis in R, we developed an R/Bioconductor package that connects to the DeepBlue Epigenomic Data Server, enabling users to quickly gather and transform epigenomic data from selected experiments for analysis in the Bioconductor ecosystem. AVAILABILITY AND IMPLEMENTATION: http://deepblue.mpi-inf.mpg.de/R. REQUIREMENTS: R 3.3, Bioconductor 3.4. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-07-01 2017-02-22 /pmc/articles/PMC5870546/ /pubmed/28334349 http://dx.doi.org/10.1093/bioinformatics/btx099 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Albrecht, Felipe
List, Markus
Bock, Christoph
Lengauer, Thomas
DeepBlueR: large-scale epigenomic analysis in R
title DeepBlueR: large-scale epigenomic analysis in R
title_full DeepBlueR: large-scale epigenomic analysis in R
title_fullStr DeepBlueR: large-scale epigenomic analysis in R
title_full_unstemmed DeepBlueR: large-scale epigenomic analysis in R
title_short DeepBlueR: large-scale epigenomic analysis in R
title_sort deepbluer: large-scale epigenomic analysis in r
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870546/
https://www.ncbi.nlm.nih.gov/pubmed/28334349
http://dx.doi.org/10.1093/bioinformatics/btx099
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AT listmarkus deepbluerlargescaleepigenomicanalysisinr
AT bockchristoph deepbluerlargescaleepigenomicanalysisinr
AT lengauerthomas deepbluerlargescaleepigenomicanalysisinr

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