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 [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
In views:	Omics
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-oldrel (arm64): geneExpressionFromGEO_0.9.tgz, r-release (x86_64): geneExpressionFromGEO_0.9.tgz, r-oldrel (x86_64): geneExpressionFromGEO_0.9.tgz
Old sources:	geneExpressionFromGEO archive

Reverse dependencies:

Reverse imports:

easyDifferentialGeneCoexpression, healthyControlsPresenceChecker

Linking:

Please use the canonical form https://CRAN.R-project.org/package=geneExpressionFromGEO to link to this page.