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 (3.15)

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 <ana.galhoz at helmholtz-muenchen.de>, Denes Turei <turei.denes at gmail.com>, Michael P. Menden <michael.menden at helmholtz-muenchen.de>, Albert Krewinkel <ana.galhoz at helmholtz-muenchen.de>

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

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


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biocViews Annotation, GeneSignaling, GeneTarget, GraphAndNetwork, Network, Pathways, Software, SystemsBiology, Transcriptomics
Version 1.3.0
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
Suggests knitr, testthat, rmarkdown
URL https://github.com/AnaGalhoz37/wppi
BugReports https://github.com/AnaGalhoz37/wppi/issues
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