NIH | National Cancer Institute | NCI Wiki  

Error rendering macro 'rw-search'

null

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

The caIntegrator Welcome workspace enables quick access to all caIntegrator functions and information before and after you login, before you open any studies.
Welcome page that displays before and after loginImage Modified

...

Without logging in, you can browse any public studies. To do so, select from the drop-down list of public studies in the upper right-hand corner of your browser, identified in the accompanying figure.

...

Sidebar Option

Function

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="137621c92f449062-cb62e844-4d254641-bdecb4f3-bf33a10d47244408cd82fa95"><ac:plain-text-body><![CDATA[

[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.

]]></ac:plain-text-body></ac:structured-macro>

Home

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

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="ec561afe1e95cae4-2616fbf3-4e054342-b248ab63-14ec067091c68a0e1c562636"><ac:plain-text-body><![CDATA[

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 .

]]></ac:plain-text-body></ac:structured-macro>

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.

Help

Click the Help icon at the top of each page to open a context-sensitive topic. The help page displays information (from this user's guide) that corresponds to the page from which help was opened.

...

  • If you have not logged into caIntegrator, you can view any public studies in your browser.
  • After logging in, you can view existing studies for which you have been granted permission. In the upper right corner of the page, in the My Studies drop down list, shown in the following figure, select the study you want to review or work in.
    Image Removed AnchorRTF36393035393a204361707469RTF36393035393a204361707469Drop-down list for selecting existing studies Drop-down list for selecting existing studiesImage Added

After selecting the study name in the My Studies drop-down list, a study summary including a status field should appear. If the status is not deployed, or if the study summary does not appear, then the study is not deployed and available for analysis.

...

A link on a study home page, as shown by the arrow in the following screen shot, opens a data dictionary summary. The link to open the Data Dictionary is identified by an arrowImage Modified

The Data Dictionary table clarifies all annotations used in the study. It displays their field descriptors, descriptions, caDSR identifiers (if used), caDSR IDs and definitions, data type, and permissible settings, shown in the following figure. The Restrictions column indicates whether or not masks have been applied to numeric data in the study. For more information, see on page 23.. Image Removed

...

The table for viewing details in the data dictionaryImage Added

For more information about study details, see on page 17.

...