TracNav(xQTL)?

xQTL workbench - Browse or search available data

Start by exploring the data by click on Browse data in the main menu. This will take you to a screen with four tabs, which are explained in more detail below.

Overview

• The first tab named Overview will present you with a summary view of all entries in this investigation.
• You can change investigations with the arrowed buttons at the top.
• Clicking on a type of data will take you there. This is a shorthand: you can always browse to all datatypes using the tabs View data, View annotations, and View files.
• Similarly, the Add button is a shorthand to be taken to the tabs of this data category (data, annotations or file) where you can start adding data with the Add new record button.
• The default view will display 4 entries for each type: use Show all to expand.

View data

• This tab allows you to add, view and remove data matrices. These are rectangular pieces of (raw) experimental data accompanied by row- and column names.
• Matrices themselves are annoted with the 'Data' entries, while their row- and column entries are annotated as separate (strong) datatypes found in the View annotations tab.
• There are a number of plugins that will help you deal with matrices:
  • Manager = Uploads data and views the numerical/textual data.
  • Heatmap = View numerical values as a customizable heatmap.
  • Rplot = Create graphical plots using R.
  • Inspector = Check whether annotations are missing.
  • Delete storage = Delete source data linked to this Data entry.

View annotations

• This section allows you to add, view and remove annotations such as Individual, Gene or Marker.
• These annotations are often linked to a data matrix, but they don't have to be.
• You can view display a list of records which is manipulatable using the View menu, search box, or paging buttons.
• When clicking edit record you can change the values of a record.
• Click More annotions to see more exotic data types such as DerivedTrait or EnvironmentalFactor.

View files

• Here you can add files.
• Specify the name and extension of the file in a standard record.
• Now upload its contents.
• A viewer will serve out the contents based on the extension.