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GSRI package: Gene Set Regulation Index

Table of Contents

Summary

The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).

Authors: Julian Gehring, Kilian Bartholomé, Clemens Kreutz, Jens Timmer
Maintainer: Julian Gehring <julian.gehring (at) fdm.uni-freiburg.de>

Methodology

For a detailed description of the approach, a comparison to other methods, and an application to experimental data, please see the paper:

Kilian Bartholomé, Clemens Kreutz, Jens Timmer:
Estimating of gene induction enables a relevance-based ranking of genes sets
J. Comp. Biol. 16, 2009, 959-967

Availability, source code, and licensing

The GSRI package is written for R and part of the bioconductor project since the 2.6 release in April 2010. This provides the latest stable release version and the current developer version, including builts for major platforms supported by R.

The complete source code of the package is publically accessible at github and licenced under the General Public License version 3 (GPL-3). You are free to use the software for any purposes and you are also welcome to contribute to it in any way.

Usage

Installation

In order to install the latest stable version of the GSRI package from the bioconductor repository, simply run in your R session:

   source("http://bioconductor.org/biocLite.R")
   biocLite("GSRI")

Alternatively, you can also obtain the built packages from bioconductor and install them manually:

   install.packages("path/to/GSRI_x.y.z")

Please note that the first method is generally the best choice.

Loading the package

After the package has been installed, you can load it:

   library(GSRI)

Documentation

A comprehensive example session on how to analyze gene sets with the GSRI package can be found in the vignette of the package. This can also be assessed as a pdf file from the bioconductor website or within R:

   vignette("gsri")

Detailed descriptions of the objects, functions, and their parameters are provided in the help pages. For details about individual parts, e.g. the gsri method, you can read the help file within R:

   ?gsri

Contact and contribution

If you have any questions, comments, or contributions:

Date: 2011-08-05 22:40:08 CEST

Author: Julian Gehring