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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 |
DOI: | 10.32614/CRAN.package.geneExpressionFromGEO |
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 |
Reference manual: | geneExpressionFromGEO.pdf |
Vignettes: |
geneExpressionFromGEOvignette |
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 imports: | easyDifferentialGeneCoexpression, healthyControlsPresenceChecker |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.