wppi

DOI: 10.18129/B9.bioc.wppi    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see wppi.

Weighting protein-protein interactions

Bioconductor version: 3.13

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] , Albert Krewinkel [ctb, cph] (pagebreak Lua filter)

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Annotation, GeneSignaling, GeneTarget, GraphAndNetwork, Network, Pathways, Software, SystemsBiology, Transcriptomics
Version	1.0.0
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
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_1.0.0.tar.gz
Windows Binary	wppi_1.0.0.zip
macOS 10.13 (High Sierra)	wppi_1.0.0.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