SPIA

Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

Bioconductor version: 2.8

This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.

Author: Adi Laurentiu Tarca <atarca at med.wayne.edu>, Purvesh Kathri <purvesh at cs.wayne.edu> and Sorin Draghici <sorin at wayne.edu>

Maintainer: Adi Laurentiu Tarca <atarca at med.wayne.edu>

To install this package, start R and enter:

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

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

    citation("SPIA")

Documentation

PDF R Script SPIA
PDF   Reference Manual

Details

biocViews Microarray, GraphsAndNetworks
Depends R (>= 2.8.0), graphics
Imports graphics
Suggests graph, Rgraphviz, KEGGgraph, hgu133plus2.db
System Requirements
License GPL (>= 2)
URL http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
Depends On Me
Imports Me
Suggests Me KEGGgraph
Version 2.2.0
Since Bioconductor 2.4 (R-2.9)

Package Downloads

Package Source SPIA_2.2.0.tar.gz
Windows Binary SPIA_2.2.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary SPIA_2.2.0.tgz
Package Downloads Report Download Stats

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