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ExpressionAtlas

Download datasets from EMBL-EBI Expression Atlas

Bioconductor version: Release (3.17)

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 1.28.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 years)
License GPL (>= 3)
Depends R (>= 4.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2, RCurl, jsonlite, BiocStyle
Imports utils, XML, httr
Linking To
Suggests knitr, testthat, rmarkdown
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me spatialHeatmap
Links To Me
Build Report  

Package Archives

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

Source Package ExpressionAtlas_1.28.0.tar.gz
Windows Binary ExpressionAtlas_1.28.0.zip
macOS Binary (x86_64) ExpressionAtlas_1.28.0.tgz
macOS Binary (arm64) ExpressionAtlas_1.28.0.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