To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

SPIA

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

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("SPIA")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SPIA")

 

PDF R Script SPIA
PDF   Reference Manual

Details

biocViews GraphAndNetwork, Microarray, Software
Version 2.16.0
In Bioconductor since BioC 2.4 (R-2.9)
License GPL (>= 2)
Depends R (>= 2.14.0), graphics, KEGGgraph
Imports graphics
Suggests graph, Rgraphviz, hgu133plus2.db
System Requirements
URL http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
Depends On Me
Imports Me
Suggests Me graphite, KEGGgraph

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source SPIA_2.16.0.tar.gz
Windows Binary SPIA_2.16.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SPIA_2.16.0.tgz
Mac OS X 10.9 (Mavericks) SPIA_2.16.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

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

Fred Hutchinson Cancer Research Center