recipe r-easydifferentialgenecoexpression

A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, 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/>.

Homepage:

https://github.com/davidechicco/easyDifferentialGeneCoexpression

License:

GPL3 / GPL-3.0-only

Recipe:

/r-easydifferentialgenecoexpression/meta.yaml

package r-easydifferentialgenecoexpression

(downloads) docker_r-easydifferentialgenecoexpression

versions:

1.4-0,  1.0-2,  1.0-1,  1.0-0

depends bioconductor-annotate:

depends bioconductor-biobase:

depends bioconductor-diffcoexp:

depends bioconductor-geoquery:

depends bioconductor-limma:

depends r-base:

>=4.3,<4.4.0a0

depends r-geneexpressionfromgeo:

depends r-jetset:

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 r-easydifferentialgenecoexpression

and update with::

   mamba update r-easydifferentialgenecoexpression

To create a new environment, run:

mamba create --name myenvname r-easydifferentialgenecoexpression

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-easydifferentialgenecoexpression:<tag>

(see `r-easydifferentialgenecoexpression/tags`_ for valid values for ``<tag>``)

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