wppi

DOI: 10.18129/B9.bioc.wppi    

This is the development version of wppi; for the stable release version, see wppi.

Weighting protein-protein interactions

Bioconductor version: Development (3.14)

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 "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

HTML R Script WPPI workflow
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews Annotation, GeneSignaling, GeneTarget, GraphAndNetwork, Network, Pathways, Software, SystemsBiology, Transcriptomics
Version 1.1.3
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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
LinkingTo
Suggests knitr, testthat, rmarkdown
SystemRequirements
Enhances
URL https://github.com/AnaGalhoz37/wppi
BugReports https://github.com/AnaGalhoz37/wppi/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package wppi_1.1.3.tar.gz
Windows Binary wppi_1.1.3.zip
macOS 10.13 (High Sierra) wppi_1.1.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/wppi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/wppi
Package Short Url https://bioconductor.org/packages/wppi/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: