recipe bioconductor-getdee2

Programmatic access to the DEE2 RNA expression dataset






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 (

package bioconductor-getdee2

(downloads) docker_bioconductor-getdee2



depends bioconductor-summarizedexperiment:


depends r-base:


depends r-htm2txt:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-getdee2

and update with::

   mamba update bioconductor-getdee2

To create a new environment, run:

mamba create --name myenvname bioconductor-getdee2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-getdee2/tags`_ for valid values for ``<tag>``)

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