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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 iD ORCID: 0000-0003-2034-601X , Pedro Madrigal [aut] ORCID iD ORCID: 0000-0003-1959-8199 , Anil Thanki [cre] ORCID iD ORCID: 0000-0002-8941-444X

Maintainer: Anil Thanki <anilthanki 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")
ExpressionAtlas HTML R Script
Reference Manual PDF
NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ArrayExpress, ExperimentData, ExpressionData, MicroarrayData, SequencingData, Software
Version 2.1.1
In Bioconductor since BioC 3.3 (R-3.3) (9.5 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_2.1.1.tar.gz
Windows Binary (x86_64) ExpressionAtlas_2.1.0.zip
macOS Binary (x86_64) ExpressionAtlas_2.1.1.tgz
macOS Binary (arm64) ExpressionAtlas_2.1.1.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