List of All MAEPlugins By Origin and Analysis Method

This document lists all of the MAEPlugins alphabetically, by analysis method, and also links to MAEPlugins available on other Web sites. The MAEPlugins include those donated to the MAExplorer Open source Web site. All plugins distributed from this Web site will have the Java source code, JAR file and documentation. Some of these MAEPlugins were incorporated into MAExplorer after they were written because of their key functionality. However, we are leaving them on the Web site to serve as examples.

If you want to use the jar file plugins directly: (1) install MAExplorer from the list of Jar files on this Web site, (2) get the jar file(s) from the plugins below and save them in the Plugins/ directory where you installed MAExplorer, (3) run MAExplorer and use the (Plugins | Load Plugin) menu command to load the plugin. After it is loaded, just use it as you would any other menu command. The Plugins-jar.tar file is available with all of the MAEPlugin jar files. Simply unpack the directory using Unix tar or a Windows unzip program into a directory you can access when running MAExplorer. To let MAExplorer go directly to these files when you do a (Plugins | Load plugins) menu command, copy the .jar files into the Plugins/ directory where you previously installed MAExplorer. We also periodically update the MAEPlugins-....-src.tar.gz file in the Files download area. Files from the following list of MAEPlugins are archived as follows: source files are from the CVS archive, jar files are from the Web server archive of plugin .jar files, documentation is also from the CVS archive.

If you want to use these plugins as a basis for developing your own plugins, see developing a plugin and other resources available on this Web site. The source code for each plugin is available beow. We encourage, but don't require, plugin writers to donate their new plugin analytic methods to the MAExplorer Open Source Web site for others to use.

1. List of all MAEPlugins sorted alphabetically

1.1 Alpha-level MAEPlugins (not fully developed)

1. RtestPlugin is a R program - MAExplorer editor for creating and testing R scripts for extending MAExplorer. One creates "R LayOuts" (RLOs) using RtestPlugin. These can then be evaluated by R using data exported from MAExplorer and data computed by R imported back into the MAExplorer state. These use the new MJAReval API to manage the RLO resources. It is available as source code and as jar file, with a documentation page. [NOTE: this is very alpha-level code - read the documentation for details. We are interested in working with groups wishing to integrate R code with MAExplorer. Please contact us for more information.]

2. ExampleXYdataFilterPlugin is an example of an X/Y data Filter plugin to filter by X/Y ratios under various data modes (Cy3 vs Cy5 for HP-X, single HP-X vs HP-Y, and HP-X 'set' vs HP-Y 'set' means). It can serve as an example for those wishing to write other data filters using this type of data. Available as source code and as jar file, with a documentation page.

3. FilterTestPlugin is an example Filter plugin to halve the number of genes accepted by the other filters. Available as source code and as jar file, with a documentation page.

4. FtestNconditionsFilterPlugin is an example of an F-test data Filter plugin to filter by the current Ordered Condition List (current OCL) by the F-test (fixed effects). It can serve as an example for those wishing to write other data filters using this type of data. It has been merged into MAExplorer as the (Filter menu | Filter by current Ordered Condition List (OCL) F-Test [p-Value] slider [RB]) command. Available as source code and as jar file, with a documentation page.

5. GenericNormalizationPlugin is an example of an generic normalization plugin. Rather than being used itself, it was designed to serve as an example for those wishing to write other normalization methods. It contains code to access global sample data as well as local (i.e., per-spot data) that can be used for designing your own normalization methods. Available as source code and as jar file, with a documentation page.

6. GeoCachePlugin downloads genomic ID from NCBI's GEO server by Geo Platform Identifier and installs the data into MAExplorer. Available as source code and as jar file, with a documentation page. Written by Alan Li.

7. ScatterPlotAllSamplesPlugin generates a scatter plot of filtered genes for all samples (very primitive at this point). Available as source code and as jar file, with a documentation page.

1.2 Stable MAEPlugins

1. ConditionChooserPlugin generates lets you define new or edit named condition lists of samples and assign additional characteristics to those lists. A condition list may contain a set of replicates. It has been merged into MAExplorer as the (Samples menu | Choose named condition lists of samples) command. Available as source code and as jar file, with a documentation page.

2. ListActiveFiltersPlugin lists the state of the data filter options, modes and threshold values. Available as source code and as jar file, with a documentation page.

3. OrderedCondChooser generates lets you define new or edit named ordered lists of conditions (OCL) and assign additional annotation to those lists. The OCL may be used for various analysis including the F-test on a set of conditions with replicates. It has been merged into MAExplorer as the (Samples menu | Choose ordered condition lists of conditions) command. Available as source code and as jar file, with a documentation page.

4. MontagePlugin shows a montage composite image of subregions around current gene "cut" out of the original images (if the data is available to MAExplorer supports it. The NCI/CIT mAdb exported data does support this feature). Available as source code and as jar file, with a documentation page.

5. TestCheckBoxPlugin is a very simple plugin to toggle a checkbox in the menu. It is meant to be used as a simple example of a checkbox plugin. Available as source code and as jar file, with a documentation page.

6. TestMenuPlugin is a very simple plugin to be invoked when selected from the menu. It is meant to be used as a simple example of a menu plugin. Available as source code and as jar file, with a documentation page.

2.1 Access outside servers to acquire data

1. GeoCachePlugin downloads genomic ID from NCBI's GEO server by Geo Platform Identifier and installs the data into MAExplorer. Available as source code and as jar file, with a documentation page. Written by Alan Li.

2.2 Connections to servers

2.3 Clustering methods

2.4 Data filtering methods

1. ExampleXYdataFilterPlugin is an example of an X/Y data Filter plugin to filter by X/Y ratios under various data modes (Cy3 vs Cy5 for HP-X, single HP-X vs HP-Y, and HP-X 'set' vs HP-Y 'set' means). It can serve as an example for those wishing to write other data filters using this type of data. Available as source code and as jar file, with a documentation page.

2. FtestNconditionsFilterPlugin is an example of an F-test data Filter plugin to filter by the current Ordered Condition List (current OCL) by the F-test (fixed effects). It can serve as an example for those wishing to write other data filters using this type of data. It has been merged into MAExplorer as the (Filter menu | Filter by current Ordered Condition List (OCL) F-Test [p-Value] slider [RB]) command. Available as source code and as jar file, with a documentation page.

3. ListActiveFiltersPlugin lists the state of the data filter options, modes and threshold values. Available as source code and as jar file, with a documentation page.

2.5 Normalization methods

• GenericNormalizationPlugin is an example of an generic normalization plugin. Rather than being used itself, it was designed to serve as an example for those wishing to write other normalization methods. It contains code to access global sample data as well as local (i.e., per-spot data) that can be used for designing your own normalization methods. Available as source code and as jar file, with a documentation page.

  2.6 Plot methods

  1. ScatterPlotAllSamplesPlugin generates a scatter plot of filtered genes for all samples (very primitive at this point). Available as source code and as jar file, with a documentation page.

  2.7 Report methods

  2.8 Sample and condition list manipulation methods

  1. ConditionChooserPlugin generates lets you define new or edit named condition lists of samples and assign additional characteristics to those lists. A condition list may contain a set of replicates. It has been merged into MAExplorer as the (Samples menu | Choose named condition lists of samples) command. Available as source code and as jar file, with a documentation page.

  2. OrderedCondChooser generates lets you define new or edit named ordered lists of conditions (OCL) and assign additional annotation to those lists. The OCL may be used for various analysis including the F-test on a set of conditions with replicates. It has been merged into MAExplorer as the (Samples menu | Choose ordered condition lists of conditions) command. Available as source code and as jar file, with a documentation page.

  2.9 Visualization methods

  1. MontagePlugin shows a montage composite image of subregions around current gene "cut" out of the original images (if the data is available to MAExplorer supports it. The NCI/CIT mAdb exported data does support this feature). Available as source code and as jar file, with a documentation page.

  2.10 Other methods

  1. TestCheckBoxPlugin is a very simple plugin to toggle a checkbox in the menu. It is meant to be used as a simple example of a checkbox plugin. Available as source code and as jar file, with a documentation page.

  2. TestMenuPlugin is a very simple plugin to be invoked when selected from the menu. It is meant to be used as a simple example of a menu plugin. Available as source code and as jar file, with a documentation page.