:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'r-geneexpressionfromgeo' .. highlight: bash r-geneexpressionfromgeo ======================= .. conda:recipe:: r-geneexpressionfromgeo :replaces_section_title: :noindex: 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 \. 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\, \. :homepage: https://github.com/davidechicco/geneExpressionFromGEO :license: GPL3 / GPL-3.0-only :recipe: /`r-geneexpressionfromgeo `_/`meta.yaml `_ .. conda:package:: r-geneexpressionfromgeo |downloads_r-geneexpressionfromgeo| |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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `r-geneexpressionfromgeo/tags`_ for valid values for ````) .. |downloads_r-geneexpressionfromgeo| image:: https://img.shields.io/conda/dn/bioconda/r-geneexpressionfromgeo.svg?style=flat :target: https://anaconda.org/bioconda/r-geneexpressionfromgeo :alt: (downloads) .. |docker_r-geneexpressionfromgeo| image:: https://quay.io/repository/biocontainers/r-geneexpressionfromgeo/status :target: https://quay.io/repository/biocontainers/r-geneexpressionfromgeo .. _`r-geneexpressionfromgeo/tags`: https://quay.io/repository/biocontainers/r-geneexpressionfromgeo?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/r-geneexpressionfromgeo/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/r-geneexpressionfromgeo/README.html