scRNA Plant Analysis

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Parameter\nLeiden Resolution"];
  style 0 fill:#ded,stroke:#393,stroke-width:4px;
  1["ℹ️ Input Dataset\nSHR CSV.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nWT CSV.gz"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Parameter\nMin Genes"];
  style 3 fill:#ded,stroke:#393,stroke-width:4px;
  4["ℹ️ Input Parameter\nMin Cells"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["ℹ️ Input Parameter\nMax Features"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Parameter\nMax Lib Size"];
  style 6 fill:#ded,stroke:#393,stroke-width:4px;
  7["Import Anndata and loom"];
  1 -->|output| 7;
  8["Import Anndata and loom"];
  2 -->|output| 8;
  9["Manipulate AnnData"];
  7 -->|anndata| 9;
  8 -->|anndata| 9;
  10["Rename Batches"];
  9 -->|anndata| 10;
  680180f6-edfc-4f66-b265-7a63aaa22b39["Output\nscRNA Concatenated Datasets"];
  10 --> 680180f6-edfc-4f66-b265-7a63aaa22b39;
  style 680180f6-edfc-4f66-b265-7a63aaa22b39 stroke:#2c3143,stroke-width:4px;
  11["QC metrics"];
  10 -->|anndata| 11;
  12["Filter genes"];
  11 -->|anndata_out| 12;
  3 -->|output| 12;
  13["Plot Violin"];
  11 -->|anndata_out| 13;
  14["Filter Cells"];
  12 -->|anndata_out| 14;
  4 -->|output| 14;
  15["Filter Max Features"];
  14 -->|anndata_out| 15;
  5 -->|output| 15;
  16["Filter Max Library Size"];
  15 -->|anndata| 16;
  6 -->|output| 16;
  17["Save RAW"];
  16 -->|anndata| 17;
  18["Norm to 1e4"];
  17 -->|anndata| 18;
  19["Log1p"];
  18 -->|anndata_out| 19;
  20["Regress total counts"];
  19 -->|anndata_out| 20;
  21["Scale"];
  20 -->|anndata_out| 21;
  22["PCA"];
  21 -->|anndata_out| 22;
  23["Neighborhod"];
  22 -->|anndata_out| 23;
  24["UMAP"];
  23 -->|anndata_out| 24;
  25["Leiden"];
  24 -->|anndata_out| 25;
  0 -->|output| 25;
  48cf0465-84ba-461a-bdb9-61625626de42["Output\nscRNA with clusters Dataset"];
  25 --> 48cf0465-84ba-461a-bdb9-61625626de42;
  style 48cf0465-84ba-461a-bdb9-61625626de42 stroke:#2c3143,stroke-width:4px;
  26["Plot PCA batch"];
  24 -->|anndata_out| 26;
  27["Plot UMAP batch"];
  24 -->|anndata_out| 27;
  28["Plot UMAP leiden, batch"];
  25 -->|anndata_out| 28;
  29["Rename Clusters"];
  25 -->|anndata_out| 29;
  30["Complex DotPlot"];
  25 -->|anndata_out| 30;
  31["Complex DotPlot with new labels"];
  29 -->|anndata| 31;
  32["Plot UMAP with new labels"];
  29 -->|anndata| 32;

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

• 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-plant/workflows/main_workflow.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