wppi
Weighting protein-protein interactions
Bioconductor version: Release (3.19)
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("wppi")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, GeneSignaling, GeneTarget, GraphAndNetwork, Network, Pathways, Software, SystemsBiology, Transcriptomics |
| Version | 1.12.0 |
| 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 |
See More
| Suggests | knitr, testthat, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | wppi_1.12.0.tar.gz |
| Windows Binary (x86_64) | wppi_1.12.0.zip |
| macOS Binary (x86_64) | wppi_1.12.0.tgz |
| macOS Binary (arm64) | wppi_1.12.0.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 |