recipe r-geneexpressionfromgeo

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>.

Homepage:

https://github.com/davidechicco/geneExpressionFromGEO

License:

GPL3 / GPL-3.0-only

Recipe:

/r-geneexpressionfromgeo/meta.yaml

package r-geneexpressionfromgeo

Versions:

0.9-1,  0.9-0

Depends:

• bioconductor-annotate

• bioconductor-biobase

• bioconductor-geoquery

• r-base >=4.2,<4.3.0a0

• r-biocmanager

• r-markdown

• r-r.utils

• r-xml2

Required By:

• bioconductor-healthycontrolspresencechecker

• r-easydifferentialgenecoexpression

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install r-geneexpressionfromgeo

and update with:

conda update r-geneexpressionfromgeo

or use the docker container:

docker pull quay.io/biocontainers/r-geneexpressionfromgeo:<tag>

(see r-geneexpressionfromgeo/tags for valid values for <tag>)

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