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Menu Bar
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Clicking on the Menu icon or word in the upper-right corner of your browser window (next to your name), will insert the
blue menu bar in your current view.  You can make this menu bar disappear by clicking the on the blue **X** or the 
word Menu again.

The **MENU** bar is a graphical control element which contains application navigational drop downs (sub-links). 
The Menu bar's purpose is to supply quick and common links for application-specific functions / features such as: 


 * **DASHBOARD** - This link takes you to *Your Dashboard* main page.

 * **WORKBOOKS** - Workbooks store the Analyses you create -- and their related data.  You can create worksheets as you explore and analyze selected underlying data (i.e. Genes and miRNAs, Variables and Cohorts – further explained later).  From the "Workbook" link you can quick link to the following:
     - *Recent* - Displays your created workbooks and allow quick navigation to them;
     - *Saved* - Displays all your saved workbooks and allows you to edit, duplicate or delete the workbook;
     - *Create a New Workbook* - Quick Link to Workbook Creation, where you can select the data source
     
 * **PROGRAMS** - These are shortcuts to the programs you have created if you uploaded your own data.
    - *Saved Programs* - Here you Can: 

       * Edit or delete a Saved Program
       * Start a New Workbook
       * Create a New Program
    - *Upload Program Data* - Here you can:
     
        * Create a new program for analysis. To create a new program you provide a name for program, name for your project, and attach files that meet our Data Type requirements. Please see `Program Data Upload <program_data_upload.html>`_ for more information on data type accepted by the ISB-CGC. 
        * Save or cancel a new creation
    -   *Public Programs* - Here you can:
        
          *  View the programs and project that are currently in the ISB-CGC system. 

 * **ANALYSES** - From here you can Create, Edit Details, Duplicate, Delete, or Share Analyses. You can use a specific analysis type to create a new workbook customized with the specific data (Genes and miRNAs, Variables, Cohorts) you have selected.  The plot types that you can select from include:
    - *Bar Chart*
    - *Histogram*
    - *Scatter Plot*
    - *Violin Plot*
    - *Cubby Hole Plot*
    - *SeqPeek*
    - *Browse All Analyses*

 * **GENES & miRNA** - From this Menu selection you can **Manage Gene and miRNA Favorites**, **Create Gene and miRNA Favorite(s)** or **Select Genes and miRNAs for a New Workbook**. 

      For additional details, see `Read the Docs - Gene & miRNA Favorites <Gene-and-miRNA-Favorites.html>`_. Each of these categories provide a quick link to additional application-specific functions / features such as:

    - *Manage Gene & miRNA Favorites* - Here you can:
    
      * Edit or Delete a Saved Gene and miRNA Favorite(s) 
      * Start a New Workbook
      * Create a New Gene and miRNA Favorites 
    - *Create Gene & miRNA Favorite* - Here you can:

      * Create a Gene & miRNA Favorite for Analysis. To Create a New Gene and miRNA Favorite - You provide a name and select the Gene and/or miRNA. You can upload a stored Gene and miRNA List or type in Gene name  or miRNA (**Note:** This will auto fill as you type in Gene name or miRNA name). To aid in Gene selection, you can access the HGNC portal (Hugo Gene Nomenclature Committee) via the "**View Gene Identifiers**" link under this Menu selection. Also, to aid in miRNA selection, you can access the miRBASE via the "**View miRNA Identifier**" link next to the View Gene Identifiers link. 
      * Save or Cancel a new creation. 
    - *Select Genes & miRNA for a New Workbook* - This sub-menu has two features:
      
      * Apply to New Analysis - Select a Favorite(s) Gene and miRNA from the list shown of stored Favorites to Analyze 
      * Add (+) Apply to New Analysis - Basically navigates back to the **Create Gene and miRNA Favorite** (See description above)  

 * **VARIABLES** -  This sub-menu allows you to **Manage Variables Favorite** or **Create New Favorite** (see descriptions below) For additional details, see `Read the Docs - Variable Favorites. <Variable-Favorites.html>`_  
    - *Manage Favorite Variable(s) Lists* - Shows your saved Variables as Favorites:

      * Edit 
      * Delete 
      * Start New Workbook - (Create a New Workbook using the selected Favorite Variables)

    - *Create Favorite Variable(s) List* - Here you "Name" your new favorite and select variables from four (4) available data sources to incorporate in your analysis- 

      * Common Variables
      * Favorite(s) Saved
      * Programs (Previously Uploaded and Saved) 
      
    - *Select Variables for a New Workbook* - This sub-menu has two features:
      
      * Apply to New Worksheet - Select a Favorite(s) variables from the list shown of stored Favorites to Analyze 
      * Add (+) Apply New Variable List - Basically navigates back to the **Create Variables Favorite** (See description above)  
  
 * **COHORTS** - Here you can **Manage Saved Cohorts**, select **Public Cohorts** and **Select Cohorts for a New Workbook** or **Create your First Cohort** if it's empty. For additional details, see `Read the Docs - Cohort Favorites <Saved-Cohorts.html>`_.

    - *Manage Saved Cohorts* - There are two tabs here 

      * Saved Cohorts - Displays previously created cohorts which can be selected. If not cohorts exist, you can create your first Cohort here by selecting the "Create Your First Cohort" link displayed and selecting Donors and Data Types. Within Saved Cohorts you can:
         - Create a "New Workbook" from a saved Cohort
         - Delete a Saved Cohort
         - Set Operations (i.e., Union, Intersection or complement) from a Base or Subtracted Cohort.
  
      * Public Cohorts - Displays any public cohorts which can be selected.
         - Create a "New Workbook" from a saved Public Cohort
         - Set Operations (i.e., Union, Intersection or complement) from a Base or Subtracted Cohort.

    - *Public Cohorts* - This is a quick link performing the same functions described in the respective tabs of Saved Cohorts above.
    - *Select Cohorts for a New Workbook* - This is a quick link performing the same functions described in the respective tabs of Saved Cohorts and Public Cohorts above.