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DeepBlueR: large-scale epigenomic analysis in R.

ABSTRACT:

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.

Contact

felipe.albrecht@mpi-inf.mpg.de or markus.list@mpi-inf.mpg.de.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Albrecht F

PROVIDER: S-EPMC5870546 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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DeepBlueR: large-scale epigenomic analysis in R.

Albrecht Felipe F List Markus M Bock Christoph C Lengauer Thomas T

Bioinformatics (Oxford, England) 20170701 13

<h4>Motivation</h4>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.<h4>Results</h4>To make public epigenomic data conveniently available for analysis in R, we developed an R/Bioconductor package that connects to the Dee ...[more]

PMID: 28334349

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