GeneSpring - R Integration Package

The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment.

Last update: 24-Jun-2004

A new version of the R integration package was released 24-Jun-2004. The new features of the release include:

1. Upgrade R to version 1.9.1
   
   The version of R that is included in this release is version 1.9.1, released 21-Jun-2004. This contains numerous changes and bug fixes. For a complete list of the new features in R 1.9.1 consult the R web site.
2. Several new example R scripts have been included:
   
   There are four new scripts that have been added.
   
   • Differential Expression using LPE
   • Differential Expression using SAM
   • Differential Expression using SAM w plots
   • Gap Filter
   For more information about these scripts, see the individual sections in the GeneSpring-R Integration Package PDF document.
3. All of the scripts were updated to work with R version 1.9.
   
   Some changes in version 1.9 resulted in the R scripts that were part of the previous version of the GeneSpring-R integration package to stop working. The scripts have all been updated to work with R version 1.9.
4. Script CV Filter has been improved
   
   The CV Filter scripts now allows the user to select the type of data that needs to be used in the CV calculation.
5. GeneSpring R library part of BioConductor
   
   With the release of BioConductor 1.4, the GeneSpring R library is part of BioConductor and can be directly installed from the BioConductor site via the Install tool in R. The complete install includes the GeneSpring library already, but for those users that want to use their own R programs, can download the GeneSpring library directly. No changes since the previous release have been made to the GeneSpring R library.

The installation package will install R and a number of examples to help you create your own library of R scripts. For those who already have a copy of R, we have provided an installer that only contains the GeneSpring-specific part of the R integration package. This version may require you to edit two files to indicate the path to the R program. For more information on the installation procedure see the GeneSpring-R Integration Package PDF document.

If you are using a Windows system and don't have R and/or BioConductor installed, download the following package:

WINDOWS including R program (1.9.1) and BioConductor + GeneSpring library

Drop the ZIP file you get onto any open window of GeneSpring and this will install everything.

For those who either already have R and/or BioConductor, or want to install R onto a Macintosh or other UNIX system, please see the instructions below:

To install the R-integration package follow these steps below:

1. Download and install R version 1.9 from:
   http://cran.us.r-project.org/
   
   
2. Download and install the BioConductor R (version 1.4) libraries from:
   
   http://www.bioconductor.org/
   
   Installation of the BioConductor libraries is done within the R program. See the installation instructions on the website. The minimum required libraries for implementing the R integration package are the BioBase and GeneSpring libraries.
3. Download and install the GeneSpring-R Integration package ZIP file from our web site.
   
   WINDOWS without the R program or any library
   UNIX without the R program or any library
   
   Drag the ZIP file onto any open window of GeneSpring or use Menu "File->Open GeneSpring Zip"
4. Change the path for the scripts and/or R program (See section 3.3 of the GeneSpring-R Integration Package PDF)
5. Change the permission on the execution scripts (UNIX only, See section 3.3.2)
6. PRESTO! You are done…It's that simple to get started with R in GeneSpring!