ExpressionAtlas

This is the development version of ExpressionAtlas; for the stable release version, see ExpressionAtlas.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Download datasets from EMBL-EBI Expression Atlas

Bioconductor version: Development (3.24)

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

Maintainer: Anil Thanki <anilthanki at ebi.ac.uk>

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

Maria Keays, Pedro Madrigal. ExpressionAtlas: Download datasets from EMBL-EBI Expression Atlas. doi:10.18129/B9.bioc.ExpressionAtlas, R package version 2.5.0, https://bioconductor.org/packages/ExpressionAtlas.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
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	2.5.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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
Enhances
Depends On Me
Imports Me
Suggests Me	spatialHeatmap
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ExpressionAtlas_2.5.0.tar.gz
Windows Binary (x86_64)	ExpressionAtlas_2.5.0.zip
macOS Binary (big-sur-x86_64)	ExpressionAtlas_2.5.0.tgz
macOS Binary (sonoma-arm64)	ExpressionAtlas_2.5.0.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