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
ExpressionAtlas_1.35.0.zip(r-4.5)ExpressionAtlas_1.35.0.zip(r-4.4)ExpressionAtlas_1.35.0.zip(r-4.3)
ExpressionAtlas_1.35.0.tgz(r-4.4-any)ExpressionAtlas_1.35.0.tgz(r-4.3-any)
ExpressionAtlas_1.35.0.tar.gz(r-4.5-noble)ExpressionAtlas_1.35.0.tar.gz(r-4.4-noble)
ExpressionAtlas_1.35.0.tgz(r-4.4-emscripten)ExpressionAtlas_1.35.0.tgz(r-4.3-emscripten)
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'))

Peer review:

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 2 months agofrom:08329fa171. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 29 2024
R-4.5-winOKDec 31 2024
R-4.5-linuxOKDec 29 2024
R-4.4-winNOTEDec 31 2024
R-4.4-macNOTEDec 29 2024
R-4.3-winNOTEDec 31 2024
R-4.3-macNOTEDec 29 2024

Exports:getAtlasDatagetAtlasExperimentsearchAtlasExperiments

Dependencies:abindaskpassbase64encBiobaseBiocGenericsBiocManagerBiocStylebitopsbookdownbslibcachemclicrayoncurlDelayedArraydigestevaluatefastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhtmltoolshttrIRangesjquerylibjsonliteknitrlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslR6rappdirsRCurlrlangrmarkdownS4ArraysS4VectorssassSparseArraystatmodSummarizedExperimentsystinytexUCSC.utilsxfunXMLxml2XVectoryaml

ExpressionAtlas package vignette

Rendered fromExpressionAtlas.Rmdusingknitr::rmarkdownon Dec 29 2024.

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

Citation

To cite package ‘ExpressionAtlas’ in publications use:

Keays M (2024). ExpressionAtlas: Download datasets from EMBL-EBI Expression Atlas. R package version 1.35.0, https://bioconductor.org/packages/ExpressionAtlas.

Corresponding BibTeX entry:

  @Manual{,
    title = {ExpressionAtlas: Download datasets from EMBL-EBI
      Expression Atlas},
    author = {Maria Keays},
    year = {2024},
    note = {R package version 1.35.0},
    url = {https://bioconductor.org/packages/ExpressionAtlas},
  }