wiki:xQTLBiologistBrowse

Version 7 (modified by jvelde, 13 years ago) (diff)

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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.