recipe bioconductor-pfp

Pathway Fingerprint Framework in R

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/PFP.html

License:

GPL-2

Recipe:

/bioconductor-pfp/meta.yaml

An implementation of the pathway fingerprint framework that introduced in paper "Pathway Fingerprint: a novel pathway knowledge and topology based method for biomarker discovery and characterization". This method provides a systematic comparisons between a gene set (such as a list of differentially expressed genes) and well-studied "basic pathway networks" (KEGG pathways), measuring the importance of pathways and genes for the gene set. The package is helpful for researchers to find the biomarkers and its function.

package bioconductor-pfp

(downloads) docker_bioconductor-pfp

versions:

1.7.0-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-clusterprofiler:

>=4.8.0,<4.9.0

depends bioconductor-graph:

>=1.78.0,<1.79.0

depends bioconductor-kegggraph:

>=1.60.0,<1.61.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-igraph:

depends r-magrittr:

depends r-plyr:

depends r-tidyr:

requirements:

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-pfp

and update with::

   mamba update bioconductor-pfp

To create a new environment, run:

mamba create --name myenvname bioconductor-pfp

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-pfp:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda 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-pfp/README.html)