Batch Correction - Scanpy

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nInput_AnnData"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Inspect AnnData"];
  0 -->|output| 1;
  d7e307be-d4f6-4936-bff2-3c2e4efb91af["Output\nInspect_Input_Anndata"];
  1 --> d7e307be-d4f6-4936-bff2-3c2e4efb91af;
  style d7e307be-d4f6-4936-bff2-3c2e4efb91af stroke:#2c3143,stroke-width:4px;
  2["Inspect AnnData"];
  0 -->|output| 2;
  3["Scanpy normalize"];
  0 -->|output| 3;
  4["Count"];
  2 -->|obs| 4;
  5["Scanpy Inspect and manipulate"];
  3 -->|anndata_out| 5;
  6["Scanpy filter"];
  5 -->|anndata_out| 6;
  7["Find HVGs by Batch"];
  5 -->|anndata_out| 7;
  8["Scanpy Inspect and manipulate"];
  6 -->|anndata_out| 8;
  9["Scanpy Inspect and manipulate"];
  7 -->|anndata_out| 9;
  10["Scanpy cluster, embed"];
  8 -->|anndata_out| 10;
  11["Scanpy cluster, embed"];
  9 -->|anndata_out| 11;
  12["Scanpy Inspect and manipulate"];
  10 -->|anndata_out| 12;
  13["Harmony Integration"];
  11 -->|anndata_out| 13;
  14["Scanpy cluster, embed"];
  12 -->|anndata_out| 14;
  15["Scanpy Inspect and manipulate"];
  13 -->|anndata_out| 15;
  16["Unintegrated AnnData"];
  14 -->|anndata_out| 16;
  17["Scanpy cluster, embed"];
  15 -->|anndata_out| 17;
  18["UMAP Plots before Batch Correction"];
  16 -->|anndata_out| 18;
  bc97da67-3d78-4944-bd86-fde12db9bc6f["Output\nUMAP_before_Integrate"];
  18 --> bc97da67-3d78-4944-bd86-fde12db9bc6f;
  style bc97da67-3d78-4944-bd86-fde12db9bc6f stroke:#2c3143,stroke-width:4px;
  19["Integrated AnnData"];
  17 -->|anndata_out| 19;
  20["UMAP Plot after Batch Correction"];
  19 -->|anndata_out| 20;
  84edd00a-d986-4ffc-92be-4e1ccd4e0daf["Output\nUMAP_after_Integrate"];
  20 --> 84edd00a-d986-4ffc-92be-4e1ccd4e0daf;
  style 84edd00a-d986-4ffc-92be-4e1ccd4e0daf 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/scrna_batch_correction/workflows/workflow_Scanpy.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