gene2pathway

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

Bioconductor version: Release (2.11)

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	Classification, GraphsAndNetworks, Microarray, NetworkEnrichment, Pathways, Software
Version	2.12.0
In Bioconductor since	BioC 2.4 (R-2.9)
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
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Package Downloads

Package Source	gene2pathway_2.12.0.tar.gz
Windows Binary	gene2pathway_2.12.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard)	gene2pathway_2.12.0.tgz
Package Downloads Report	Download Stats

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