ExpressionAtlas
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ExpressionAtlas.
Download datasets from EMBL-EBI Expression Atlas
Bioconductor version: 3.14
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: Pedro Madrigal <pmadrigal at ebi.ac.uk>
citation("ExpressionAtlas")):
Installation
To install this package, start R (version "4.1") 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 | ||
| NEWS | Text |
Details
| biocViews | ArrayExpress, ExperimentData, ExpressionData, MicroarrayData, SequencingData, Software |
| Version | 1.22.1 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL (>= 3) |
| Depends | R (>= 4.1.1), methods, Biobase, SummarizedExperiment, limma, S4Vectors, xml2 |
| Imports | utils, XML, httr |
| System Requirements | |
| URL |
See More
| Suggests | knitr, testthat, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | spatialHeatmap |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ExpressionAtlas_1.22.1.tar.gz |
| Windows Binary | ExpressionAtlas_1.22.1.zip |
| macOS 10.13 (High Sierra) | ExpressionAtlas_1.22.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ExpressionAtlas |
| Source Repository (Developer Access) | git clone [email protected]:packages/ExpressionAtlas |
| Bioc Package Browser | https://code.bioconductor.org/browse/ExpressionAtlas/ |
| Package Short Url | https://bioconductor.org/packages/ExpressionAtlas/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.14 | Source Archive |