Welcome to the new bioconductor.org!

PPInfer

Inferring functionally related proteins using protein interaction networks


Bioconductor version: Release (3.18)

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 "4.3") 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")
User manual PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod
Version 1.28.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData
Imports httr, grDevices, graphics, stats, utils
System Requirements
URL
See More
Suggests
Linking To
Enhances
Depends On Me gsean
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 PPInfer_1.28.0.tar.gz
Windows Binary PPInfer_1.28.0.zip
macOS Binary (x86_64) PPInfer_1.28.0.tgz
macOS Binary (arm64) PPInfer_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PPInfer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PPInfer
Bioc Package Browser https://code.bioconductor.org/browse/PPInfer/
Package Short Url https://bioconductor.org/packages/PPInfer/
Package Downloads Report Download Stats