ExpressionAtlas

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ExpressionAtlas.

Download datasets from EMBL-EBI Expression Atlas


Bioconductor version: 3.9

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

Maintainer: Suhaib Mohammed <suhaib at ebi.ac.uk>

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

Installation

To install this package, start R (version "3.6") and enter:


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

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")
ExpressionAtlas HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ArrayExpress, ExperimentData, ExpressionData, MicroarrayData, SequencingData, Software
Version 1.12.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>= 3)
Depends R (>= 3.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2
Imports utils, XML, httr
System Requirements
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Suggests knitr, testthat, rmarkdown
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Package Archives

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

Source Package ExpressionAtlas_1.12.0.tar.gz
Windows Binary ExpressionAtlas_1.12.0.zip
Mac OS X 10.11 (El Capitan) ExpressionAtlas_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ExpressionAtlas
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ExpressionAtlas
Bioc Package Browser https://code.bioconductor.org/browse/ExpressionAtlas/
Package Short Url https://bioconductor.org/packages/ExpressionAtlas/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive