Working with Suites  

GenePattern includes close to 200 analysis and visualization modules, and the list is constantly growing. With so many modules, it's helpful to have shortcuts for finding your favorites. Suites can help you organize modules in much the same way playlists help you organize music. Each suite is a themed collection of user-selected modules. You can create as many suites as you like.  The GenePattern team has created several suites, which are included on the GenePattern public server. For example, the ClusteringSuite contains the HierachicalClustering, KMeansClustering, and SOMClustering modules. If you are unfamiliar with GenePattern suites, see Concepts.

• Basic Operations
• Displaying Suite Definitions
• Creating Suites
• Editing Suites

Basic Operations

The following table summarizes the different ways you can work with GenePattern suites.

Displaying Suite Definitions

To display the definition of a suite:

1. Click Suites>Manage.
2. Click the name of the suite that you want to display. GenePattern displays the suite definition:

• Name: The name of the suite.
• Description: A brief description of the suite.
• Author: The author's name and affiliation (company or academic institution). This is a comment-only field.
• Privacy: Select Private (default) or Public. A private suite may be accessed only by the person who created or installed the suite (or by an administrator); a public suite can be accessed by all users of this GenePattern server.
• Support files: Any files included with the suite. Public suites generally include documentation.
• Modules & Pipelines: The remainder of the definition form lists all of the modules and pipelines that are on your GenePattern server by category. The ClusteringSuite in this figure contains modules from only one category, the Clustering category.

From this page, you can:

• Click the menu icon next to the suite name to display the suite menu.
• Click open all and close all to show and hide the modules and pipelines in all categories.
• Click the arrow icon next to a category to show/hide the modules and pipelines in that category.

Creating Suites

To create a suite:

1. Click Suites>New. GenePattern displays an empty suite definition form.
2. Define the suite by entering values for each field. For descriptions of these fields, see Displaying Suite Definitions.
3. To add modules and pipelines to the suite:
   • Select the check box next to a module/pipeline to add that module/pipeline to the suite.
   • Select the check box next to a category name to add all modules and pipelines in that category to the suite.
4. Click Save. GenePattern creates the suite.

Editing Suites

To view or edit a suite:

1. Click Suites>Manage. GenePattern displays the Manage Suites page, which lists the suites on your GenePattern server.
2. To view the suite definition, click the suite name.
3. To edit the suite definition:
   1. Click the menu icon next to the suite name and select Edit. This option is available only if you created the suite.
   2. Edit the suite definition.
   3. Click Save to update the suite definition.

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