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Sidebar Option

Function

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[Study Name]

When you log in, one study displays in the left sidebar by default. Any study that you select in the My Studies drop-down list in the upper right of the page replaces this default selection.

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Home

Click this to return to the home page for the selected study.

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Search [Study Name]

Click this option to open the Search [Study Name] page from which you can launch queries into your selected study. For more information, see .

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Study Data

Click Saved Queries > My Queries to open the list of previous queries you saved. Click any item in the list to open the saved query, which displays on the Criteria, Columns and Sorting tabs. From those tabs, you can modify criteria and/or launch the query again. For more information, see on page 62.
Click Saved Lists > Global Lists or > My Lists to open gene lists that have been saved for a study. From any page in caIntegrator that shows such a group, you can save a such a list of genes to be used for searches or analyses. See on page 69.
Click Saved Copy Number Analysis to open an Edit GISTIC Analysis page. You can review genes retrived from the analysis or, with appropriate permissions, you can edit the metadata for the analysis. See on page 74.

Analysis Tools

Click any of the listed options to open a page where you can launch an analysis of the data in the selected study.

  • Generate a K-M Plot. See on page 82.
  • Generate a Gene Expression Plots. See on page 88.
  • Launch GenePattern Analysis. on page 101.

Study Management

Click either of the listed options to manage the selected study through editing or deleting it or by creating a new study.

  • Click Manage Studies. See on page 45.
  • Click Create a New Study. See on page 16.

Application Management

Click Manage Platforms to identify, add or remove platforms that caIntegrator supports. For more information, see on page 47.

caIntegrator Menu

  • Click Support to view contact information for Application Support.
  • Click Tutorials to view a tutorial to help you get started using caIntegrator.
  • Click User Guide to open the caIntegrator v.1.3 User's Guide in PDF format.

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The study log which you can open by clicking the Study Log > View link on the study summary page lists the steps used to create a study. For more information, see on page 18.

Using Context Sensitive Online Help

To access online help, click the help icon at the top of each page. The topic that opens is context-sensitive topic, which means that the page displays information (from this user's guide) that corresponds to the page from which help was opened.

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