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 (3.20)
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("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 | R Script | |
Reference Manual | ||
LICENSE | Text |
Details
biocViews | GraphAndNetwork, Microarray, Software |
Version | 2.57.0 |
In Bioconductor since | BioC 2.4 (R-2.9) (15.5 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_2.57.0.tar.gz |
Windows Binary | SPIA_2.57.0.zip |
macOS Binary (x86_64) | SPIA_2.57.0.tgz |
macOS Binary (arm64) | SPIA_2.57.0.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 |