recipe bioconductor-expressionatlas

Download datasets from EMBL-EBI Expression Atlas



GPL (>= 3)



This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.

package bioconductor-expressionatlas

(downloads) docker_bioconductor-expressionatlas



depends bioconductor-biobase:


depends bioconductor-biocstyle:


depends bioconductor-limma:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-httr:

depends r-jsonlite:

depends r-rcurl:

depends r-xml:

depends r-xml2:



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-expressionatlas

and update with::

   mamba update bioconductor-expressionatlas

To create a new environment, run:

mamba create --name myenvname bioconductor-expressionatlas

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-expressionatlas/tags`_ for valid values for ``<tag>``)

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