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

(downloads) docker_r-geneexpressionfromgeo

versions:

0.9-2,  0.9-1,  0.9-0

depends bioconductor-annotate:

depends bioconductor-biobase:

depends bioconductor-geoquery:

depends r-base:

>=4.3,<4.4.0a0

depends r-biocmanager:

depends r-markdown:

depends r-r.utils:

depends r-xml2:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-geneexpressionfromgeo

and update with::

   mamba update r-geneexpressionfromgeo

To create a new environment, run:

mamba create --name myenvname r-geneexpressionfromgeo

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, 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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