PPInfer-package {PPInfer} | R Documentation |
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.
The DESCRIPTION file:
Package: | PPInfer |
Type: | Package |
Title: | Inferring functionally related proteins using protein interaction networks |
Description: | 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. |
Version: | 1.19.0 |
Date: | 2019-02-03 |
Author: | Dongmin Jung, Xijin Ge |
Maintainer: | Dongmin Jung <dmdmjung@gmail.com> |
Depends: | biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData |
Suggests: | |
License: | Artistic-2.0 |
biocViews: | Software, StatisticalMethod, Network, GraphAndNetwork, GeneSetEnrichment, NetworkEnrichment, Pathways |
NeedsCompilation: | no |
git_url: | https://git.bioconductor.org/packages/PPInfer |
git_branch: | master |
git_last_commit: | c403456 |
git_last_commit_date: | 2021-05-19 |
Date/Publication: | 2021-09-19 |
Index of help topics:
GSEA.barplot Visualize the gene set enrichment analysis ORA Over-representation Analysis ORA.barplot Visualize the over-representation analysis PPInfer-package Inferring functionally related proteins using protein interaction networks enrich.net Visualize network for the functional enrichment analysis net.infer Inferring functionally related proteins using networks net.infer.ST Inferring functionally related proteins with self training net.kernel Kernel matrix for a graph ppi.infer.human Inferring functionally related proteins using protein networks for human ppi.infer.mouse Inferring functionally related proteins using protein networks for mouse self.train.kernel Self training for a kernel matrix
Further information is available in the following vignettes:
PPInfer | User manual (source, pdf) |
Dongmin Jung, Xijin Ge
Maintainer: Dongmin Jung <dmdmjung@gmail.com>