recipe bioconductor-geoquery

Get data from NCBI Gene Expression Omnibus (GEO)

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/GEOquery.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-geoquery/meta.yaml

Links:

biotools: geoquery

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

package bioconductor-geoquery

versions:

2.74.0-0,  2.70.0-0,  2.68.0-0,  2.66.0-0,  2.62.0-0,  2.60.0-0,  2.58.0-1,  2.58.0-0,  2.56.0-1, 

2.74.0-0,  2.70.0-0,  2.68.0-0,  2.66.0-0,  2.62.0-0,  2.60.0-0,  2.58.0-1,  2.58.0-0,  2.56.0-1,  2.56.0-0,  2.54.0-0,  2.52.0-1,  2.50.5-0,  2.50.0-0,  2.48.0-0,  2.46.3-0,  2.46.0-0,  2.42.0-0,  2.38.4-0,  2.36.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-curl:

depends r-data.table:

depends r-dplyr:

depends r-httr2:

depends r-magrittr:

depends r-r.utils:

depends r-readr:

>=1.3.1

depends r-rentrez:

depends r-rvest:

depends r-stringr:

depends r-tidyr:

depends r-xml2:

requirements:

additional platforms:

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 bioconductor-geoquery

and update with::

   mamba update bioconductor-geoquery

To create a new environment, run:

mamba create --name myenvname bioconductor-geoquery

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/bioconductor-geoquery:<tag>

(see `bioconductor-geoquery/tags`_ for valid values for ``<tag>``)

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