| 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: | 1.20.4 |
| Date: | 2021-12-01 |
| Author: | Dongmin Jung, Xijin Ge |
| Maintainer: | Dongmin Jung <dmdmjung@gmail.com> |
| Depends: | biomaRt, fgsea, kernlab, ggplot2, igraph, STRINGdb, yeastExpData |
| Imports: | httr, grDevices, graphics, stats, utils |
| 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: | RELEASE_3_14 |
| git_last_commit: | 403294a |
| git_last_commit_date: | 2021-12-01 |
| Date/Publication: | 2021-12-02 |
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>