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wppi

Weighting protein-protein interactions


Bioconductor version: Release (3.18)

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.

Author: Ana Galhoz [cre, aut] , Denes Turei [aut] , Michael P. Menden [aut] , Albert Krewinkel [ctb, cph] (pagebreak Lua filter)

Maintainer: Ana Galhoz <ana.galhoz at helmholtz-muenchen.de>

Citation (from within R, enter citation("wppi")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("wppi")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("wppi")
WPPI workflow HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, GeneSignaling, GeneTarget, GraphAndNetwork, Network, Pathways, Software, SystemsBiology, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports dplyr, igraph, logger, methods, magrittr, Matrix, OmnipathR(>= 2.99.8), progress, purrr, rlang, RCurl, stats, tibble, tidyr
System Requirements
URL https://github.com/AnaGalhoz37/wppi
Bug Reports https://github.com/AnaGalhoz37/wppi/issues
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Suggests knitr, testthat, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package wppi_1.10.0.tar.gz
Windows Binary wppi_1.10.0.zip
macOS Binary (x86_64) wppi_1.10.0.tgz
macOS Binary (arm64) wppi_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/wppi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/wppi
Bioc Package Browser https://code.bioconductor.org/browse/wppi/
Package Short Url https://bioconductor.org/packages/wppi/
Package Downloads Report Download Stats