PPInfer
Inferring functionally related proteins using protein interaction networks
Bioconductor version: 3.24 · Package version: 1.39.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PPInfer")Details
| Maintainer | Dongmin Jung <dmdmjung@gmail.com> |
| Author | Dongmin Jung, Xijin Ge |
| License | Artistic-2.0 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, StatisticalMethod |
| Package Short Url | https://bioconductor.org/packages/PPInfer/ |
Citation
From within R, enter citation("PPInfer"):
Dongmin Jung, Xijin Ge. PPInfer: Inferring functionally related proteins using protein interaction networks. doi:10.18129/B9.bioc.PPInfer, R package version 1.39.0, https://bioconductor.org/packages/PPInfer.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | PPInfer_1.39.0.tar.gz |
| Windows binary (x86_64) | PPInfer_1.39.0.zip |
| macOS binary (arm64) | PPInfer_1.39.0.tgz |
| macOS binary (x86_64) | PPInfer_1.39.0.tgz |
Dependencies
Depends: biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData
Imports: httr, grDevices, graphics, stats, utils
Reverse dependencies
Depends On Me (1): gsean