geneExpressionFromGEO: Retrieves Gene Expression Dataset and Gene Symbols from GEO Code

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, GPL80, 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, Springer Protocols, New York City, New York, USA, 2021. In press.

Version: 0.8
Depends: R (≥ 3.1.0)
Imports: BiocManager, xml2, Biobase, annotate, GEOquery, markdown, R.utils
Suggests: knitr, rmarkdown
Published: 2021-11-07
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_0.8.tar.gz
Windows binaries: r-devel: geneExpressionFromGEO_0.8.zip, r-release: geneExpressionFromGEO_0.8.zip, r-oldrel: geneExpressionFromGEO_0.8.zip
macOS binaries: r-release (arm64): geneExpressionFromGEO_0.8.tgz, r-release (x86_64): geneExpressionFromGEO_0.8.tgz, r-oldrel: geneExpressionFromGEO_0.8.tgz
Old sources: geneExpressionFromGEO archive

Reverse dependencies:

Reverse imports: easyDifferentialGeneCoexpression

Linking:

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