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.

MuSiC-Deconvolution: Data generation | bulk | ESet
Wendi Bacon, Mehmet Tekman

Last updated Nov 27, 2022

Launch in Tutorial Mode
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

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flowchart TD
  0["Expression matrix"];
  1["Metadata"];
  2["annotateMyIDs"];
  0 -->|output_tabular| 2;
  8415bac0-6beb-467d-a0fa-fb6465987ff7["Output\nannotateMyIDs on input dataset(s): Annotated IDs"];
  2 --> 8415bac0-6beb-467d-a0fa-fb6465987ff7;
  style 8415bac0-6beb-467d-a0fa-fb6465987ff7 stroke:#2c3143,stroke-width:4px;
  3["Regex Find And Replace"];
  1 -->|output| 3;
  4["🛠️ Subworkflow\nCopy of Convert from Ensembl to GeneSymbol, summing duplicate genes"];
  style 4 fill:#edd,stroke:#900,stroke-width:4px;
  2 -->|out_tab| 4;
  0 -->|output_tabular| 4;
  5["Construct Expression Set Object"];
  4 -->|Gene Symbol Count Matrix| 5;
  3 -->|out_file1| 5;
  6["Manipulate Expression Set Object"];
  5 -->|out_rds| 6;
  88196d0b-7254-4794-b08a-5409f19c8323["Output\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object"];
  6 --> 88196d0b-7254-4794-b08a-5409f19c8323;
  style 88196d0b-7254-4794-b08a-5409f19c8323 stroke:#2c3143,stroke-width:4px;
  7["Manipulate Expression Set Object"];
  5 -->|out_rds| 7;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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: