Package: ExpressionAtlas 1.35.0

Pedro Madrigal

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 [cre]

ExpressionAtlas_1.35.0.tar.gz
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ExpressionAtlas_1.35.0.tar.gz(r-4.5-noble)ExpressionAtlas_1.35.0.tar.gz(r-4.4-noble)
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ExpressionAtlas.pdf |ExpressionAtlas.html✨
ExpressionAtlas/json (API)
NEWS

# 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-1.35.0(bioc 3.21)ExpressionAtlas-1.34.0(bioc 3.20)

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

expressiondataexperimentdatasequencingdatamicroarraydataarrayexpress

4.42 score 19 scripts 478 downloads 7 mentions 3 exports 60 dependencies

Last updated 4 months agofrom:08329fa171. Checks:3 OK, 1 WARNING, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 28 2025
R-4.5-winOKJan 28 2025
R-4.5-macWARNINGJan 28 2025
R-4.5-linuxOKJan 28 2025
R-4.4-winNOTEJan 28 2025
R-4.4-macNOTEJan 28 2025
R-4.3-winNOTEJan 28 2025
R-4.3-macNOTEJan 28 2025

Exports:getAtlasDatagetAtlasExperimentsearchAtlasExperiments

Dependencies:abindaskpassbase64encBiobaseBiocGenericsBiocManagerBiocStylebitopsbookdownbslibcachemclicrayoncurlDelayedArraydigestevaluatefastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshttrIRangesjquerylibjsonliteknitrlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslR6rappdirsRCurlrlangrmarkdownS4ArraysS4VectorssassSparseArraystatmodSummarizedExperimentsystinytexUCSC.utilsxfunXMLxml2XVectoryaml

ExpressionAtlas package vignette

Maria Keays

Rendered fromExpressionAtlas.Rmdusingknitr::rmarkdownon Jan 28 2025.

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