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Download datasets from EMBL-EBI Expression Atlas

Bioconductor version: Release (3.19)

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.

Author: Maria Keays [aut] , Pedro Madrigal [cre]

Maintainer: Pedro Madrigal <pmadrigal at>

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


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

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


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:

ExpressionAtlas HTML R Script
Reference Manual PDF


biocViews ArrayExpress, ExperimentData, ExpressionData, MicroarrayData, SequencingData, Software
Version 1.32.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>= 3)
Depends R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle
Imports utils, XML, httr
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Follow Installation instructions to use this package in your R session.

Source Package ExpressionAtlas_1.32.0.tar.gz
Windows Binary
macOS Binary (x86_64) ExpressionAtlas_1.32.0.tgz
macOS Binary (arm64) ExpressionAtlas_1.32.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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