Workflows

These workflows are associated with Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

flowchart TD
  0["Remove columns"];
  1["Advanced Cut"];
  2["annotateMyIDs"];
  3["Regex Find And Replace"];
  4["Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes"];
  5["Construct Expression Set Object"];
  6["Manipulate Expression Set Object"];
  7["Manipulate Expression Set Object"];
  0 -->|output_tabular| 2;
  1 -->|output| 3;
  2 -->|out_tab| 4;
  0 -->|output_tabular| 4;
  4 -->|Gene Symbol Count Matrix| 5;
  3 -->|out_file1| 5;
  5 -->|out_rds| 6;
  5 -->|out_rds| 7;

	

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure: