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Bioconductor - ExpressionAtlas (development version)

ExpressionAtlas

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

Download datasets from EMBL-EBI Expression Atlas

Bioconductor version: Development (3.22)

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] ORCID: 0000-0003-2034-601X , Pedro Madrigal [cre] ORCID: 0000-0003-1959-8199

Maintainer: Pedro Madrigal <pmadrigal at ebi.ac.uk>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ExpressionAtlas")

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

Documentation

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

browseVignettes("ExpressionAtlas")
Details biocViews ArrayExpress, ExperimentData, ExpressionData, MicroarrayData, SequencingData, Software Version 2.1.0 In Bioconductor since BioC 3.3 (R-3.3) (9 years) License GPL (>= 3) Depends R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle Imports utils, XML, httr System Requirements URL See More Package Archives

Follow Installation instructions to use this package in your R session.

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