Menu

The MENU 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:

• Workbooks - Workbooks store the Analyses you create – and their related data. Basically, the worksheets you create to conduct analysis based on the source data selected (i.e. Genes, Variables and Cohorts – further explained later) For additional details, see Read the Docs - Workbooks. From the “Workbook” link you will be able to 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)
  • Sample Workbooks - (Coming Soon)

• Projects - You can upload from your own research projects or request a GCP project be setup by following the directions under Support and Other Useful Links - Your Own Project. For additional details see Read the Docs - Saved Projects

  • Saved - This has two “Tabs” Saved Projects you have created and Public Projects (see below)
  • Upload Project Data - Data uploading requires that you have a Google Cloud project set up for your account. Once a request is received (see How to Request), a project is created in GCP for you and you will receive a completion confirmation email).
  • Public Projects - (Future Home for accessible public projects). There are no public projects available at the moment. This also has two “Tabs” Public Projects and Saved Projects you have created (see above).

• Analyses - From here you can Create, Edit Details, Duplicate, Delete, or Share Sample Analyses. The analysis can be piloted by creating a customized workbook with the specific data (Genes, Variables, Cohorts) you select to analyze and visualized/plot in one of the following manners:

  • Bar Chart
  • Histogram
  • Scatter Plot
  • Violin Plot
  • Violin Plot with Axis Swap
  • Cubby Hole Plot

• Genes - From this Menu selection you can Manage Gene Favorites, Create Gene Favorite(s) or Select Genes for a New Workbook. For additional details, see Read the Docs - Gene Favorites. Each of these categories provide a quick link to additional application-specific functions / features such as:

  • Manage Gene Favorites - Here you can:
    • Edit or Delete a Saved Gene Favorite(s),
    • Start a New Workbook,
    • Create a New Gene Favorites or
    • Edit Gene Favorites (see Create Gene Favorite(s) description below).
  • Create Gene Favorite - Here you can:
    • Create a Gene Favorite for Analysis, To Create a New Gene Favorite - You provide a name and select the Gene. You can upload a stored Gene List or 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.
    • Save or Cancel a new creation.
  • Select Genes for a New Workbook - This sub-menu has two feature:
    • Apply to New Analysis - Select a Favorite(s) Gene from the list shown of stored Favorites to Analyze
    • Add (+) Apply to New Analysis - Basically navigates back to the Create Gene 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.

  • Manage Variables Favorite - Shows your saved Variables as Favorites:
    • Edit,
    • Delete,
    • Start New Workbook - (Create a New Workbook using the selected Favorite Variables)
  • Add (+) Create New Favorite - 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
    • Data Types
    • Projects (Previously Uploaded and Saved)

• 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.

  • 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.

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