PPInfer

DOI: 10.18129/B9.bioc.PPInfer    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see PPInfer.

Inferring functionally related proteins using protein interaction networks

Bioconductor version: 3.15

Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.

Author: Dongmin Jung, Xijin Ge

Maintainer: Dongmin Jung <dmdmjung at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("PPInfer")

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("PPInfer")

 

PDF R Script User manual
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod
Version 1.22.0
In Bioconductor since BioC 3.5 (R-3.4) (5.5 years)
License Artistic-2.0
Depends biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData
Imports httr, grDevices, graphics, stats, utils
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me gsean
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package PPInfer_1.22.0.tar.gz
Windows Binary PPInfer_1.22.0.zip
macOS Binary (x86_64) PPInfer_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PPInfer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PPInfer
Package Short Url https://bioconductor.org/packages/PPInfer/
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: