Working with Suites  Print-icon

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

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

Display suite definitions

To display the suite definition:

  1. Click Suites>Manage.
  2. Click the name of the suite that you are interested in.

Send suites to other users

Zip files provide a convenient way to send suites to other GenePattern users.

  • To export a suite to a zip file, click Suites>Manage, click the icon next to a suite to display the suite menu, and select Export Including dependents or Export excluding dependents.
  • To install a suite from a zip file: click Suites>Install from zip.

For more information, see Exporting and Installing Suites Using Zip Files.

Install suites from the repository

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.

Create suites

To create a suite, click Suites>New. For more information, see Creating Suites.

Edit 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.

Delete 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:

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

suite definition

From this page, you can:

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.

suite definition

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 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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Updated on August 30, 2012 16:50