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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("gene2pathway")

Documentation

PDF R Script gene2pathway
PDF   Reference Manual

Details

biocViews Microarray, Bioinformatics, Classification, GraphsAndNetworks, Pathways
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
Suggests
System Requirements
License GPL (>= 2)
URL
Depends On Me
Imports Me
Suggests Me
Version 2.2.0
Since Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source gene2pathway_2.2.0.tar.gz
Windows Binary gene2pathway_2.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary gene2pathway_2.2.0.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center