ExpressionAtlas

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see ExpressionAtlas.

Download datasets from EMBL-EBI Expression Atlas

Bioconductor version: 3.21

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 [cre] ORCID iD 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")
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 2.0.0

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

URL

Suggests knitr, testthat, rmarkdown

Linking To

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Depends On Me

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Suggests Me spatialHeatmap

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Package Archives

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

Source Package ExpressionAtlas_2.0.0.tar.gz

Windows Binary (x86_64) ExpressionAtlas_2.0.0.zip

macOS Binary (x86_64) ExpressionAtlas_2.0.0.tgz

macOS Binary (arm64) ExpressionAtlas_2.0.0.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/

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