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SPIA

This is the development version of SPIA; for the stable release version, see SPIA.

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


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.55.0
In Bioconductor since BioC 2.4 (R-2.9) (15 years)
License file LICENSE
Depends R (>= 2.14.0), graphics, KEGGgraph
Imports graphics
System Requirements
URL http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1
See More
Suggests graph, Rgraphviz, hgu133plus2.db
Linking To
Enhances
Depends On Me
Imports Me EnrichmentBrowser
Suggests Me graphite, KEGGgraph
Links To Me
Build Report Build Report

Package Archives

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

Source Package SPIA_2.55.0.tar.gz
Windows Binary SPIA_2.55.0.zip
macOS Binary (x86_64) SPIA_2.55.0.tgz
macOS Binary (arm64) SPIA_2.55.0.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