recipe bioconductor-padog

Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/PADOG.html

License:

GPL (>= 2)

Recipe:

/bioconductor-padog/meta.yaml

Links:

biotools: padog, doi: 10.1186/1471-2105-13-136

This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.

package bioconductor-padog

versions:

1.44.0-0,  1.42.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-1, 

1.44.0-0,  1.42.0-0,  1.40.0-0,  1.36.0-0,  1.34.0-0,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.26.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0

depends bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-hgu133a.db:

>=3.13.0,<3.14.0

depends bioconductor-hgu133plus2.db:

>=3.13.0,<3.14.0

depends bioconductor-keggdzpathwaysgeo:

>=1.40.0,<1.41.0

depends bioconductor-keggrest:

>=1.42.0,<1.43.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dorng:

depends r-foreach:

depends r-gsa:

depends r-nlme:

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-padog

and update with::

   mamba update bioconductor-padog

To create a new environment, run:

mamba create --name myenvname bioconductor-padog

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-padog:<tag>

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

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