recipe bioconductor-healthycontrolspresencechecker

Dowloads A Gene Expression Dataset From GEO And Checks If It Contains Data Of Healthy Controls Or Not

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/healthyControlsPresenceChecker.html

License:

GPL-3

Recipe:

/bioconductor-healthycontrolspresencechecker/meta.yaml

A function that reads in the GEO accession code of a gene expression dataset, retrieves its data from GEO, and checks if data of healthy controls are present in the dataset. It returns true if healthy controls data are found, and false otherwise. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

package bioconductor-healthycontrolspresencechecker

(downloads) docker_bioconductor-healthycontrolspresencechecker

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-geoquery:

>=2.70.0,<2.71.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

depends r-geneexpressionfromgeo:

depends r-magrittr:

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-healthycontrolspresencechecker

and update with::

   mamba update bioconductor-healthycontrolspresencechecker

To create a new environment, run:

mamba create --name myenvname bioconductor-healthycontrolspresencechecker

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-healthycontrolspresencechecker:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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