To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SPIA")
In most cases, you don't need to download the package archive at all.
SPIA
|
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SPIA.
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Bioconductor version: 3.0
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SPIA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SPIA")
| R Script | SPIA | |
| Reference Manual |
Details
| biocViews | GraphAndNetwork, Microarray, Software |
| Version | 2.18.0 |
| In Bioconductor since | BioC 2.4 (R-2.9) (7 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.14.0), graphics, KEGGgraph |
| Imports | graphics |
| LinkingTo | |
| Suggests | graph, Rgraphviz, hgu133plus2.db |
| SystemRequirements | |
| Enhances | |
| URL | http://bioinformatics.oxfordjournals.org/cgi/reprint/btn577v1 |
| Depends On Me | |
| Imports Me | EnrichmentBrowser, ToPASeq |
| Suggests Me | graphite, KEGGgraph |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | SPIA_2.18.0.tar.gz |
| Windows Binary | SPIA_2.18.0.zip |
| Mac OS X 10.6 (Snow Leopard) | SPIA_2.18.0.tgz |
| Mac OS X 10.9 (Mavericks) | SPIA_2.18.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SPIA/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/SPIA/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
