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ExpressionAtlas

Download datasets from EMBL-EBI Expression Atlas


Bioconductor version: Release (3.18)

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 ebi.ac.uk>

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

Installation

To install this package, start R (version "4.3") 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 1.30.0
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
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_1.30.0.tar.gz
Windows Binary ExpressionAtlas_1.30.0.zip
macOS Binary (x86_64) ExpressionAtlas_1.30.0.tgz
macOS Binary (arm64) ExpressionAtlas_1.30.0.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