DOI: 10.18129/B9.bioc.getDEE2  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see getDEE2.

Programmatic access to the DEE2 RNA expression dataset

Bioconductor version: 3.16

Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage ( and main publication (

Author: Mark Ziemann [aut, cre], Antony Kaspi [aut]

Maintainer: Mark Ziemann <mark.ziemann at>

Citation (from within R, enter citation("getDEE2")):


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biocViews GeneExpression, Sequencing, Software, Transcriptomics
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 years)
License GPL-3
Depends R (>= 4.0)
Imports stats, utils, SummarizedExperiment, htm2txt
Suggests knitr, testthat, rmarkdown
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