PathNet
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see PathNet.
An R package for pathway analysis using topological information
Bioconductor version: 3.9
PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.
Author: Bhaskar Dutta <bhaskar.dutta at gmail.com>, Anders Wallqvist <awallqvist at bhsai.org>, and Jaques Reifman <jreifman at bhsai.org>
Maintainer: Jason B. Smith <jsmith at bhsai.org>
citation("PathNet")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("PathNet")
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("PathNet")| PathNet | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, KEGG, MultipleComparison, Network, NetworkEnrichment, Pathways, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | GPL-3 |
| Depends | R (>= 1.14.0) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | PathNetData, RUnit, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | PathNet_1.23.0.tar.gz |
| Windows Binary | PathNet_1.23.0.zip |
| Mac OS X 10.11 (El Capitan) | PathNet_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PathNet |
| Source Repository (Developer Access) | git clone [email protected]:packages/PathNet |
| Bioc Package Browser | https://code.bioconductor.org/browse/PathNet/ |
| Package Short Url | https://bioconductor.org/packages/PathNet/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |