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Source Code


Object-Oriented Microarray and Proteomics Analysis

OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling , and other high throughput molecular biology data. OOMPA uses S4 classes to construct object-oriented tools with a consistent user interface. All higher level analysis tools in OOMPA work with the expressionSet classes defined in BioConductor. The lower level processing tools offer an alternative to parts of BioConductor, but can also be used to enhance the existing BioConductor packages.

Package Overview

Dependency Graph

This figure shows the dependency relationships between the OOMPA packages. Black arrows indicate dependendencies reflected by Depends or Imports entries in the package DESCRIPTION file. Red arrows indicate a weaker relationship, reflected by a Suggests entry in the packager DESCRFIPTION file.


The simplest way to install OOMPA packages is to start your local version of R and use the following commands:

The oompaLite command installs a small set of "base" OOMPA packages. To get a slightly larger set of (default) packages, you can execute the command:
If you want to get absolutely everything (which may include some experimental packages with very little in the way of documentation), use the command:
Alternatively, if you want more control over which packages get installed, execute the following command and select from the resulting list:


When we moved the source code repository to R-Forge, we set up new discussion forums and other facilities for OOMPA users to obtain help. These include:

Source Code

The source packages for OOMPA are available from R-Forge. To simplify package maintenance, the packages are separated into multiple projects. The projects are color-coded in the figure above and in the table below.

Project NamePackage URL
OOMPA http://r-forge.r-project.org/projects/oompa
Class Prediction http://r-forge.r-project.org/projects/classpred
SuperCurve http://r-forge.r-project.org/projects/supercurve
NameNeedle http://r-forge.r-project.org/projects/nameneedle
SIBER http://r-forge.r-project.org/projects/siber
integIRTy http://r-forge.r-project.org/projects/integirty
UMPIRE http://r-forge.r-project.org/projects/umpire
Thresher http://r-forge.r-project.org/projects/thresher
ArrayCube Under Development
FirstSign Under Development
CRAAC Under Development
AccuPloidy Under Development
drexplorer Available from GitHub


Licenses for individual packages vary, so you should see their DESCRIPTION files for details. Most current packages are released under Version 2.0 of the Apache License. The current version of the SuperCurve packages, and older versions of many other packages, are released under Version 2.0 of the Perl Artistic License.

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