SPIA

This is the released version of SPIA; for the devel version, see SPIA.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

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

Bioconductor version: Release (3.23)

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")):

Adi Laurentiu Tarca, Purvesh Kathri and Sorin Draghici. SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations. doi:10.18129/B9.bioc.SPIA, R package version 2.64.0, https://bioconductor.org/packages/SPIA.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GraphAndNetwork, Microarray, Software
Version	2.64.0
In Bioconductor since	BioC 2.4 (R-2.9) (17.5 years)
License	file LICENSE
Depends	R (>= 2.14.0), graphics, KEGGgraph
Imports	graphics
System Requirements
URL	http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1

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, r-universe

Package Archives

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

Source Package	SPIA_2.64.0.tar.gz
Windows Binary (x86_64)	SPIA_2.64.0.zip
macOS Binary (big-sur-x86_64)	SPIA_2.64.0.tgz
macOS Binary (sonoma-arm64)	SPIA_2.64.0.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