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.
The Broad Institute maintains a repository of modules, pipelines, and suites. To install suites from the Broad repository, click Suites>Install from Repository. For more information, see Installing Suites from the Repository.
To create a suite, click Suites>New. For more information, see Creating Suites.
You can edit a suite that you have created or copy a public suite and edit your copy of the public suite. For more information, see Editing Suites.
To delete a suite from your GenePattern server, click Suites>Manage. For more information, see Managing Suites.
Displaying Suite Definitions
To display the definition of a suite:
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.
To create a suite:
Click Suites>New. GenePattern displays an empty suite definition form.