recipe bioconductor-padog

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

Homepage

https://bioconductor.org/packages/3.11/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

1.30.0-0, 1.28.0-1, 1.26.0-1, 1.24.0-0, 1.22.0-0, 1.20.0-0

Depends

• bioconductor-annotationdbi >=1.50.0,<1.51.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-hgu133a.db >=3.2.0,<3.3.0

• bioconductor-hgu133plus2.db >=3.2.0,<3.3.0

• bioconductor-keggdzpathwaysgeo >=1.26.0,<1.27.0

• bioconductor-keggrest >=1.28.0,<1.29.0

• bioconductor-limma >=3.44.0,<3.45.0

• r-base >=4.0,<4.1.0a0

• r-dorng

• r-foreach

• r-gsa

• r-nlme

Required By

• bioconductor-egsea

• bioconductor-blma

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-padog

and update with:

conda update bioconductor-padog

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-padog:<tag>

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

Link to this page

Render an 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/bioconductor-padog/README.html)