DeepBlueR: large-scale epigenomic analysis in R


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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.deSupplementary information:Supplementary data are available at Bioinformatics online.

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