recipe bioconductor-wppi

Weighting protein-protein interactions






Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.

package bioconductor-wppi

(downloads) docker_bioconductor-wppi



depends bioconductor-omnipathr:


depends r-base:


depends r-dplyr:

depends r-igraph:

depends r-logger:

depends r-magrittr:

depends r-matrix:

depends r-progress:

depends r-purrr:

depends r-rcurl:

depends r-rlang:

depends r-tibble:

depends r-tidyr:



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-wppi

and update with::

   mamba update bioconductor-wppi

To create a new environment, run:

mamba create --name myenvname bioconductor-wppi

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<tag>

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

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