Package Recipe 'bioconductor-padog'

recipe bioconductor-padog

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

Homepage:: https://bioconductor.org/packages/3.20/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:

1.52.0-0, 1.48.0-0, 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,

1.52.0-0, 1.48.0-0, 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:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-hgu133a.db >=3.13.0,<3.14.0
on bioconductor-hgu133plus2.db >=3.13.0,<3.14.0
on bioconductor-keggdzpathwaysgeo >=1.48.0,<1.49.0
on bioconductor-keggrest >=1.50.0,<1.51.0
on bioconductor-limma >=3.66.0,<3.67.0
on r-base >=4.5,<4.6.0a0
on r-dorng
on r-foreach
on r-gsa
on r-nlme

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-padog

to add into an existing workspace instead, run:

pixi add bioconductor-padog

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-padog

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-padog

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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)