ExpressionAtlas: Download datasets from EMBL-EBI Expression Atlas

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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
Date of publication
None
Maintainer
Maria Keays <mkeays@ebi.ac.uk>
License
GPL (>= 3)
Version
1.2.0

View on Bioconductor

Man pages

allExps
A SimpleList containing some dummy Expression Atlas datasets
atlasRes
A DataFrame listing some Expression Atlas experiments
getAtlasData
Download data from multiple Expression Atlas experiments
getAtlasExperiment
Download data for an Expression Atlas experiment
rnaseqExps
A SimpleList containing a dummy RNA-seq Expression Atlas...
searchAtlasExperiments
Search for Expression Atlas experiments

Files in this package

ExpressionAtlas/DESCRIPTION
ExpressionAtlas/NAMESPACE
ExpressionAtlas/NEWS
ExpressionAtlas/R
ExpressionAtlas/R/functions.R
ExpressionAtlas/build
ExpressionAtlas/build/vignette.rds
ExpressionAtlas/data
ExpressionAtlas/data/allExps.rda
ExpressionAtlas/data/atlasRes.rda
ExpressionAtlas/data/rnaseqExps.rda
ExpressionAtlas/inst
ExpressionAtlas/inst/NEWS
ExpressionAtlas/inst/doc
ExpressionAtlas/inst/doc/ExpressionAtlas.R
ExpressionAtlas/inst/doc/ExpressionAtlas.Rmd
ExpressionAtlas/inst/doc/ExpressionAtlas.html
ExpressionAtlas/man
ExpressionAtlas/man/allExps.Rd
ExpressionAtlas/man/atlasRes.Rd
ExpressionAtlas/man/getAtlasData.Rd
ExpressionAtlas/man/getAtlasExperiment.Rd
ExpressionAtlas/man/rnaseqExps.Rd
ExpressionAtlas/man/searchAtlasExperiments.Rd
ExpressionAtlas/tests
ExpressionAtlas/tests/testthat
ExpressionAtlas/tests/testthat.R
ExpressionAtlas/tests/testthat/test_functions.R
ExpressionAtlas/vignettes
ExpressionAtlas/vignettes/ExpressionAtlas.Rmd