Comparative and Downstream Analysis of Samples Using the Genboree Workbench

  • We have a number of different downstream / comparative analysis tools available in the exRNA Atlas.
  • By selecting your samples of interest and then selecting your tool of interest, you can move into the Genboree Workbench where you can then perform your analysis.
  • We will go through the process step-by-step below.

Step 1: Selecting Your Samples of Interest

  • The first step to running your analysis is selecting your samples of interest.
    • We recommend using the faceted charts (all tools may not be available for other types of grids).
    • Click the appropriate facets and then click the magnifying glass icon to show corresponding samples in a grid.

  • After you have generated your grid, you will need to select the specific samples you want to analyze.
    • You can select specific samples by using the checkboxes to the left of each sample.
    • To select all samples, click the checkbox in the upper left corner of the grid.
    • The different metadata columns (Condition, Anatomical Location, etc.) should help you figure out which specific samples you want to analyze.
    • You can also click on the right side of a given column to sort that column, place filters on that column, or disable any column in the grid.

Step 2: Selecting Your Tool

  • After you've selected your samples, you'll need to pick out a tool to run on those samples.
    • You can click the "Go to Genboree Workbench" button to see available tools.

  • You will be prompted to log into the Genboree Workbench once you choose a tool.
  • This means that you must have a Genboree account in order to use the tools.
    • If you have an account already, just fill in your login information and then click the "Login" button.
    • If you don't have an account, you can click the "Register here!" link to create one.
    • Once you've logged in once, you won't need to log in again for that Atlas session.

  • After you've logged in, you'll be able to select the Group and Database which you want to use to store your output files for that tool run.
    • Each Genboree account starts with a Group (named after your username), but you will need to create a Database to use the tools.
    • If the Group you select doesn't already have a Database, we will offer to create a Database for you (named "Exrna-atlas Output").

  • To learn more about Genboree Groups and Databases, see this FAQ page.

Step 3: Running Your Tool

  • Once you click "Activate Tool", you will be taken to the Genboree Workbench.
  • Your Input Data panel and Output Targets panel will be filled in automatically by the Atlas.
  • You can then select your tool of interest from the Workbench menu bar, fill out the appropriate settings, and then launch a tool job.

Also available in: HTML TXT