Pseudobulk with decoupler and edgeR tutorial workflow

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy France
• Galaxy Australia
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nncm_pdcs_subset.h5ad"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Inspect AnnData Object"];
  0 -->|output| 1;
  e76ac983-3089-4a4f-be16-49de8d491ba4["Output\nGeneral AnnData Information"];
  1 --> e76ac983-3089-4a4f-be16-49de8d491ba4;
  style e76ac983-3089-4a4f-be16-49de8d491ba4 stroke:#2c3143,stroke-width:4px;
  2["Filter Cell-Type"];
  0 -->|output| 2;
  41908539-a944-457b-b02f-cf3464971b8e["Output\nanndata_out"];
  2 --> 41908539-a944-457b-b02f-cf3464971b8e;
  style 41908539-a944-457b-b02f-cf3464971b8e stroke:#2c3143,stroke-width:4px;
  3["Pseudobulk with decoupler"];
  0 -->|output| 3;
  90c68071-01bf-471a-958a-9f391556debd["Output\ngenes_metadata"];
  3 --> 90c68071-01bf-471a-958a-9f391556debd;
  style 90c68071-01bf-471a-958a-9f391556debd stroke:#2c3143,stroke-width:4px;
  0de9d115-6e5a-446b-abc1-15c11dcaefb1["Output\nsamples_metadata"];
  3 --> 0de9d115-6e5a-446b-abc1-15c11dcaefb1;
  style 0de9d115-6e5a-446b-abc1-15c11dcaefb1 stroke:#2c3143,stroke-width:4px;
  7ff680d1-cd92-43fe-a9cf-9eb53a76996a["Output\ncount_matrix"];
  3 --> 7ff680d1-cd92-43fe-a9cf-9eb53a76996a;
  style 7ff680d1-cd92-43fe-a9cf-9eb53a76996a stroke:#2c3143,stroke-width:4px;
  c23b46c6-de2f-4c4d-886d-2f83ad61017a["Output\nplot_output"];
  3 --> c23b46c6-de2f-4c4d-886d-2f83ad61017a;
  style c23b46c6-de2f-4c4d-886d-2f83ad61017a stroke:#2c3143,stroke-width:4px;
  6f8d0a60-352e-49bd-82e2-68f4c64d529f["Output\nfilter_by_expr_plot"];
  3 --> 6f8d0a60-352e-49bd-82e2-68f4c64d529f;
  style 6f8d0a60-352e-49bd-82e2-68f4c64d529f stroke:#2c3143,stroke-width:4px;
  4["Replace Text"];
  3 -->|samples_metadata| 4;
  5["Replace Text"];
  3 -->|count_matrix| 5;
  6["Remove columns"];
  3 -->|genes_metadata| 6;
  7["Replace Text"];
  4 -->|outfile| 7;
  06fde552-a874-4272-81e7-b9ca26987826["Output\nSamples Metadata"];
  7 --> 06fde552-a874-4272-81e7-b9ca26987826;
  style 06fde552-a874-4272-81e7-b9ca26987826 stroke:#2c3143,stroke-width:4px;
  8["Generating Contrast File"];
  7 -->|outfile| 8;
  abbea492-6106-4370-a968-e5e1a3142033["Output\nContrast File"];
  8 --> abbea492-6106-4370-a968-e5e1a3142033;
  style abbea492-6106-4370-a968-e5e1a3142033 stroke:#2c3143,stroke-width:4px;
  9["edgeR"];
  6 -->|output_tabular| 9;
  8 -->|outfile| 9;
  5 -->|outfile| 9;
  7 -->|outfile| 9;
  14e63c6b-511c-468d-954e-cb115be9ac95["Output\noutTables"];
  9 --> 14e63c6b-511c-468d-954e-cb115be9ac95;
  style 14e63c6b-511c-468d-954e-cb115be9ac95 stroke:#2c3143,stroke-width:4px;
  10["Extract dataset"];
  9 -->|outTables| 10;
  2f1d41da-719c-4226-9de0-856c6a086091["Output\noutput"];
  10 --> 2f1d41da-719c-4226-9de0-856c6a086091;
  style 2f1d41da-719c-4226-9de0-856c6a086091 stroke:#2c3143,stroke-width:4px;
  11["Remove columns"];
  10 -->|output| 11;
  352ef726-9dff-4fb8-81af-006dd9c7126d["Output\nDEG Table"];
  11 --> 352ef726-9dff-4fb8-81af-006dd9c7126d;
  style 352ef726-9dff-4fb8-81af-006dd9c7126d stroke:#2c3143,stroke-width:4px;
  12["Volcano Plot"];
  11 -->|output_tabular| 12;
  5e9faae5-8b4f-4a6c-8098-69937c9e5b80["Output\nVolcano Plot DEG"];
  12 --> 5e9faae5-8b4f-4a6c-8098-69937c9e5b80;
  style 5e9faae5-8b4f-4a6c-8098-69937c9e5b80 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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.

Importing into Galaxy

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. Click the Import workflow button

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

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/pseudobulk-analysis/workflows/pseudo-bulk_edgeR.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows