ExpressionAtlas

DOI: 10.18129/B9.bioc.ExpressionAtlas    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see ExpressionAtlas.

Download datasets from EMBL-EBI Expression Atlas

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	ExpressionAtlas
PDF		Reference Manual
Text		NEWS

Details

biocViews	ArrayExpress, ExperimentData, ExpressionData, MicroarrayData, SequencingData, Software
Version	1.18.0
In Bioconductor since	BioC 3.3 (R-3.3) (5 years)
License	GPL (>= 3)
Depends	R (>= 3.2.0), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2
Imports	utils, XML, httr
LinkingTo
Suggests	knitr, testthat, rmarkdown
SystemRequirements
Enhances
URL
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_1.18.0.tar.gz
Windows Binary	ExpressionAtlas_1.18.0.zip
macOS 10.13 (High Sierra)	ExpressionAtlas_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ExpressionAtlas
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ExpressionAtlas
Package Short Url	https://bioconductor.org/packages/ExpressionAtlas/
Package Downloads Report	Download Stats