Batch Correction - Seurat

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nInput_SeuratObject"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Inspect before Split"];
  0 -->|output| 1;
  1d9854b2-d825-42cb-94ed-8238660e86a9["Output\nInspect_before_Split"];
  1 --> 1d9854b2-d825-42cb-94ed-8238660e86a9;
  style 1d9854b2-d825-42cb-94ed-8238660e86a9 stroke:#2c3143,stroke-width:4px;
  2["Seurat Data Management"];
  0 -->|output| 2;
  3["Seurat Integrate"];
  0 -->|output| 3;
  4["Inspect after Split"];
  3 -->|rds_out| 4;
  1d4fccd8-ca44-4aa5-88ce-35e7a4f165fe["Output\nInspect_after_Split"];
  4 --> 1d4fccd8-ca44-4aa5-88ce-35e7a4f165fe;
  style 1d4fccd8-ca44-4aa5-88ce-35e7a4f165fe stroke:#2c3143,stroke-width:4px;
  5["Seurat Preprocessing"];
  3 -->|rds_out| 5;
  6["Seurat Preprocessing"];
  5 -->|rds_out| 6;
  7["Seurat Preprocessing"];
  6 -->|rds_out| 7;
  8["Seurat Run Dimensional Reduction"];
  7 -->|rds_out| 8;
  9["Seurat Find Clusters"];
  8 -->|rds_out| 9;
  10["Seurat Find Clusters"];
  9 -->|rds_out| 10;
  11["Seurat Run Dimensional Reduction"];
  10 -->|rds_out| 11;
  12["Seurat Visualize"];
  11 -->|rds_out| 12;
  13["UMAP Plot by Method before Batch Correction"];
  11 -->|rds_out| 13;
  e60c96e7-e1d8-4b21-bf3f-ddfadd51bd27["Output\nUMAP_before_Split"];
  13 --> e60c96e7-e1d8-4b21-bf3f-ddfadd51bd27;
  style e60c96e7-e1d8-4b21-bf3f-ddfadd51bd27 stroke:#2c3143,stroke-width:4px;
  14["Seurat Integrate"];
  11 -->|rds_out| 14;
  15["Seurat Integrate"];
  14 -->|rds_out| 15;
  16["Seurat Find Clusters"];
  15 -->|rds_out| 16;
  17["Seurat Find Clusters"];
  16 -->|rds_out| 17;
  18["Seurat Run Dimensional Reduction"];
  17 -->|rds_out| 18;
  19["Seurat Visualize"];
  18 -->|rds_out| 19;
  20["UMAP Plot by Method after Batch Correction"];
  18 -->|rds_out| 20;
  06ed5938-16e0-460d-9ff0-25aafb1fdb34["Output\nUMAP_after_Split"];
  20 --> 06ed5938-16e0-460d-9ff0-25aafb1fdb34;
  style 06ed5938-16e0-460d-9ff0-25aafb1fdb34 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_Seurat.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