Current Version 1.1.1 (June 7th, 2011)

About J/maanova

J/maanova is an open sourced desktop application developed by The Churchill Group at The Jackson Laboratory with the aim of simplifying the analysis of microarray experiments. J/maanova allows researchers to access a subset of the functionality available in the R/maanova package through a graphical user interface. R/maanova contains a powerful library of algorithms and graphing functions for the analysis of microarray data but it requires users to become familiar with the R scripting language before they are able to take advantage of these functions. By removing the requirement of learning a scripting language J/maanova makes the analytical methods developed for R/maanova available to a wider group of researchers.

J/maanova has other advantages including a level of graphical interaction which is not available in R. For example, J/maanova allows users to highlight a list of probe sets that they have selected in a volcano plot and use that list to filter items in a results table. Users can also save their sessions to project files which can be shared with collaborators or used later to generate an R script containing all of the R commands that were executed.

Warranty Disclaimer and Copyright Notice

The Jackson Laboratory makes no representation about the suitability or accuracy of this software for any purpose, and makes no warranties, either express or implied, including merchantability and fitness for a particular purpose or that the use of this software will not infringe any third party patents, copyrights, trademarks, or other rights. The software are provided "as is".

This software is provided to enhance knowledge and encourage progress in the scientific community. This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The source code for J/maanova can be found at the source code repository on github



  • R 2.13.*
  • Java 5.0 or greater (all Mac OS X computers come preinstalled with Java)
  • RAM: memory requirements will vary depending on the size of the data that you are analyzing and the type of analysis you perform, but 2Gb or greater is recommended
  • Supported operating systems:
    • Mac OS X 10.5.8 or greater
    • Windows XP (Windows Vista and Windows 7 should also work but are untested)

After you have ensured that your computer meets these requirements you can Launch the J/maanova Installer


The software was written by Hao Wu, Lei Wu and Keith Sheppard. Keith Sheppard is the current maintainer of J/maanova.

Help and Contact Information

For help on using J/maanova the help documentation is a good place to start. Additionally some people have had installation troubles on Mac OS X depending on how Java is configured this FAQ entry may help you if you are experiencing installation problems on OS X

For any other problems/questions/suggestions, please use our MAANOVA google group.

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