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>

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
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SystemRequirements
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Depends On Me	gsean
Imports Me
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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