SPIA
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Bioconductor version: Release (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("SPIA")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | GraphAndNetwork, Microarray, Software |
| Version | 2.56.0 |
| 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 | KEGGgraph, graphite |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPIA_2.56.0.tar.gz |
| Windows Binary (x86_64) | SPIA_2.56.0.zip |
| macOS Binary (x86_64) | SPIA_2.56.0.tgz |
| macOS Binary (arm64) | SPIA_2.56.0.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 |
| Old Source Packages for BioC 3.19 | Source Archive |