PPInfer
Inferring functionally related proteins using protein interaction networks
Bioconductor version: Release (3.20)
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("PPInfer")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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_1.32.0.tar.gz |
| Windows Binary (x86_64) | PPInfer_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | PPInfer_1.32.0.tgz |
| macOS Binary (arm64) | PPInfer_1.31.0.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 |