wppi

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

Weighting protein-protein interactions

Bioconductor version: Development (3.21)

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] (ORCID: ), Denes Turei [aut] (ORCID: ), Michael P. Menden [aut] (ORCID: ), 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 "4.5") and enter:


if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, GeneSignaling, GeneTarget, GraphAndNetwork, Network, Pathways, Software, SystemsBiology, Transcriptomics
Version	1.15.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 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

Suggests	knitr, testthat, rmarkdown
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

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

Source Package	wppi_1.15.0.tar.gz
Windows Binary (x86_64)	wppi_1.15.0.zip
macOS Binary (x86_64)	wppi_1.15.0.tgz
macOS Binary (arm64)	wppi_1.15.0.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