ExpressionAtlas
This is the released version of ExpressionAtlas; for the devel version, see ExpressionAtlas.
Download datasets from EMBL-EBI Expression Atlas
Bioconductor version: Release (3.23)
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 [aut]
, Anil Thanki [cre]
Maintainer: Anil Thanki <anilthanki at ebi.ac.uk>
citation("ExpressionAtlas")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.4.0 |
| 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 |
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_2.4.0.tar.gz |
| Windows Binary (x86_64) | ExpressionAtlas_2.4.0.zip |
| macOS Binary (big-sur-x86_64) | ExpressionAtlas_2.4.0.tgz |
| macOS Binary (sonoma-arm64) | ExpressionAtlas_2.4.0.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 |