geneExpressionFromGEO: Easily Downloads a Gene Expression Dataset from a GEO Code and Retrieves the Gene Symbols of Its Probesets

A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.

Version: 0.9
Depends: R (≥ 3.1.0)
Imports: BiocManager, xml2, Biobase, annotate, GEOquery, markdown, R.utils
Suggests: knitr, rmarkdown
Published: 2021-12-16
Author: Davide Chicco ORCID iD [aut, cre]
Maintainer: Davide Chicco <davidechicco at davidechicco.it>
BugReports: https://github.com/davidechicco/geneExpressionFromGEO/issues
License: GPL-3
URL: https://github.com/davidechicco/geneExpressionFromGEO
NeedsCompilation: no
CRAN checks: geneExpressionFromGEO results

Documentation:

Reference manual: geneExpressionFromGEO.pdf
Vignettes: geneExpressionFromGEOvignette

Downloads:

Package source: geneExpressionFromGEO_0.9.tar.gz
Windows binaries: r-devel: geneExpressionFromGEO_0.9.zip, r-release: geneExpressionFromGEO_0.9.zip, r-oldrel: geneExpressionFromGEO_0.9.zip
macOS binaries: r-release (arm64): geneExpressionFromGEO_0.9.tgz, r-release (x86_64): geneExpressionFromGEO_0.9.tgz, r-oldrel: geneExpressionFromGEO_0.9.tgz
Old sources: geneExpressionFromGEO archive

Reverse dependencies:

Reverse imports: easyDifferentialGeneCoexpression

Linking:

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