Package: ExpressionAtlas 2.5.0

Anil Thanki

ExpressionAtlas: Download datasets from EMBL-EBI Expression Atlas

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.

Authors:Maria Keays [aut], Pedro Madrigal [aut], Anil Thanki [cre]

ExpressionAtlas_2.5.0.tar.gz
ExpressionAtlas_2.5.0.zip(r-4.7)ExpressionAtlas_2.5.0.zip(r-4.6)ExpressionAtlas_2.5.0.zip(r-4.5)
ExpressionAtlas_2.5.0.tgz(r-4.6-any)ExpressionAtlas_2.5.0.tgz(r-4.5-any)
ExpressionAtlas_2.5.0.tar.gz(r-4.7-any)ExpressionAtlas_2.5.0.tar.gz(r-4.6-any)
ExpressionAtlas_2.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ExpressionAtlas/json (API)

# Install 'ExpressionAtlas' in R:

install.packages('ExpressionAtlas', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

allExps - A SimpleList containing some dummy Expression Atlas datasets
atlasRes - A DataFrame listing some Expression Atlas experiments
rnaseqExps - A SimpleList containing a dummy RNA-seq Expression Atlas dataset

On BioConductor:ExpressionAtlas-2.5.0(bioc 3.24)ExpressionAtlas-2.4.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

expressiondata experimentdata sequencingdata microarraydata arrayexpress

4.83 score 24 scripts 7 mentions 3 exports 56 dependencies

Last updated from:5efeaff3e3. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	171
linux-devel-x86_64	OK	298
source / vignettes	OK	218
linux-release-x86_64	OK	354
macos-release-arm64	OK	196
macos-oldrel-arm64	OK	252
windows-devel	OK	210
windows-release	OK	208
windows-oldrel	OK	204
wasm-release	OK	124

Exports:getAtlasData getAtlasExperiment searchAtlasExperiments

Dependencies:abind askpass base64enc Biobase BiocGenerics BiocManager BiocStyle bitops bookdown bslib cachem cli curl DelayedArray digest evaluate fastmap fontawesome fs generics GenomicRanges highr htmltools httr IRanges jquerylib jsonlite knitr lattice lifecycle limma Matrix MatrixGenerics matrixStats memoise mime openssl R6 rappdirs RCurl rlang rmarkdown S4Arrays S4Vectors sass Seqinfo SparseArray statmod SummarizedExperiment sys tinytex xfun XML xml2 XVector yaml

ExpressionAtlas package vignette

Rendered fromExpressionAtlas.Rmdusingknitr::rmarkdown

Last update: 2022-10-21
Started: 2016-02-22

Citation

Development and contributors

Readme and manuals

Help Manual

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