gene2pathway

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

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 , contributions by Tim Beissbarth
Maintainer	Holger Froehlich

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("gene2pathway")

Documentation

gene2pathway	PDF	R Script
Reference Manual

Details

biocViews	Microarray , Bioinformatics , Classification , GraphsAndNetworks , Pathways
Depends	R , kernlab , KEGG.db , biomaRt , KEGGSOAP , RBGL , AnnotationDbi , org.Dm.eg.db
Imports	SSOAP , RCurl
Suggests
System Requirements
License	GPL (>= 2)
URL
Depends On Me
Imports Me
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Development History	Bioconductor Changelog

Package Downloads

Package source	gene2pathway_1.2.0.tar.gz
Windows binary	gene2pathway_1.2.0.zip
MacOS X 10.4 (Tiger) binary	gene2pathway_1.2.0.tgz
MacOS X 10.5 (Leopard) binary	gene2pathway_1.2.0.tgz
Package Downloads Report	Downloads Stats