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SPIA

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

Bioconductor version: Release (3.17)

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 (version "4.3") and enter: 

if (!require("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")
SPIA PDF R Script
Reference Manual PDF
LICENSE Text

Details

biocViews GraphAndNetwork, Microarray, Software
Version 2.52.0
In Bioconductor since BioC 2.4 (R-2.9) (14.5 years)
License file LICENSE
Depends R (>= 2.14.0), graphics, KEGGgraph
Imports graphics
Linking To
Suggests graph, Rgraphviz, hgu133plus2.db
System Requirements
Enhances
URL http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
See More
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_2.52.0.tar.gz
Windows Binary SPIA_2.52.0.zip
macOS Binary (x86_64) SPIA_2.52.0.tgz
macOS Binary (arm64) SPIA_2.52.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SPIA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SPIA
Bioc Package Browser https://code.bioconductor.org/browse/SPIA/
Package Short Url https://bioconductor.org/packages/SPIA/
Package Downloads Report Download Stats