gene2pathway

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

Bioconductor version: 2.5

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:///biocLite.R")
biocLite("gene2pathway")    

Documentation

PDF

R Script

gene2pathway

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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Version	1.4.0

Package Downloads

Package Source	gene2pathway_1.4.0.tar.gz
Windows Binary	gene2pathway_1.4.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	gene2pathway_1.4.0.tgz
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