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, .


Reference manual

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install.packages("geneExpressionFromGEO")

1.3 by Davide Chicco, 10 months ago


https://github.com/davidechicco/geneExpressionFromGEO


Report a bug at https://github.com/davidechicco/geneExpressionFromGEO/issues


Browse source code at https://github.com/cran/geneExpressionFromGEO


Authors: Davide Chicco [aut, cre] (ORCID:


Documentation:   PDF Manual  


GPL-3 license


Imports xml2, Biobase, annotate, GEOquery, utils

Suggests knitr, rmarkdown


See at CRAN