To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gene2pathway")

In most cases, you don't need to download the package archive at all.

gene2pathway

   

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see gene2pathway.

Prediction of KEGG pathway membership for individual genes based on InterPro domain signatures

Bioconductor version: 2.8

The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained.

Author: Holger Froehlich <frohlich at bit.uni-bonn.de>

Maintainer: Holger Froehlich <frohlich at bit.uni-bonn.de>

Citation (from within R, enter citation("gene2pathway")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gene2pathway")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("gene2pathway")

 

PDF gene2pathway.pdf
PDF   Reference Manual

Details

biocViews Bioinformatics, Classification, GraphsAndNetworks, Microarray, Pathways, Software
Version 2.2.0
In Bioconductor since BioC 2.4 (R-2.9) (7 years)
License GPL (>= 2)
Depends R (>= 2.10.0), kernlab (>= 0.9), biomaRt(>= 1.12.1), KEGGSOAP(>= 1.12.0), RBGL, AnnotationDbi, org.Dm.eg.db, keggorthology(>= 2.0)
Imports SSOAP, RCurl
LinkingTo
Suggests
SystemRequirements
Enhances doMC
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source gene2pathway_2.2.0.tar.gz
Windows Binary gene2pathway_2.2.0.zip
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/gene2pathway/tree/release-2.8
Package Short Url http://bioconductor.org/packages/gene2pathway/
Package Downloads Report Download Stats

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