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This is the development version of getDEE2; for the stable release version, see getDEE2.

Programmatic access to the DEE2 RNA expression dataset

Bioconductor version: Development (3.20)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

getDEE2 HTML R Script
Reference Manual PDF


biocViews GeneExpression, Sequencing, Software, Transcriptomics
Version 1.15.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
Imports stats, utils, SummarizedExperiment, htm2txt
System Requirements
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Suggests knitr, testthat, rmarkdown
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Imports Me homosapienDEE2CellScore
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Follow Installation instructions to use this package in your R session.

Source Package getDEE2_1.15.0.tar.gz
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macOS Binary (x86_64) getDEE2_1.15.0.tgz
macOS Binary (arm64) getDEE2_1.15.0.tgz
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