SPIA

DOI: 10.18129/B9.bioc.SPIA    

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

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SPIA")

For older versions of R, please refer to the appropriate Bioconductor release.

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
Text		LICENSE

Details

biocViews	GraphAndNetwork, Microarray, Software
Version	2.40.0
In Bioconductor since	BioC 2.4 (R-2.9) (11.5 years)
License	file LICENSE
Depends	R (>= 2.14.0), graphics, KEGGgraph
Imports	graphics
LinkingTo
Suggests	graph, Rgraphviz, hgu133plus2.db
SystemRequirements
Enhances
URL	http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
Depends On Me
Imports Me	EnrichmentBrowser
Suggests Me	graphite, KEGGgraph
Links To Me
Build Report

Package Archives

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

Source Package	SPIA_2.40.0.tar.gz
Windows Binary	SPIA_2.40.0.zip
macOS 10.13 (High Sierra)	SPIA_2.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SPIA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SPIA
Package Short Url	https://bioconductor.org/packages/SPIA/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive