Overview
Installation
Support
Source Code
License
Packages

OOMPA

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

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.

Installation

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

source("http://silicovore.com/OOMPA/oompaLite.R")
oompaLite()

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:

oompainstall()

If you want to get absolutely everything (which may include some experimental packages with very little in the way of documentation), use the command:

oompainstall(groupName="all")

Alternatively, if you want more control over which packages get installed, execute the following command and select from the resulting list:

install.packages(repos="http://silicovore.com/OOMPA/")

Support

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:

• User Help Forum
• Feature Requests
• Bug Tracker
• Developer Forum

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 Name	Package 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

License

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.