Workflows

These workflows are associated with Removing the effects of the cell cycle

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.

Cell Cycle Regression Workflow

Last updated Nov 21, 2022

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

Download Galaxy Workflow.ga Galaxy France Galaxy Australia Galaxy Main Galaxy Europe Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Dataset\nAnnData After QC, normalisation, scaling"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nS Phase Genes"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nG2M Phase Genes"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nPasted Entry"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Inspect AnnData"];
  0 -->|output| 4;
  5["All Cell Cycle Genes Concatenate S and G2M Genes"];
  1 -->|output| 5;
  2 -->|output| 5;
  6["Inspect and manipulate"];
  0 -->|output| 6;
  2 -->|output| 6;
  1 -->|output| 6;
  7["Table Compute"];
  4 -->|var| 7;
  8["Add column"];
  5 -->|out_file1| 8;
  9["Scanpy RegressOut"];
  6 -->|anndata_out| 9;
  026b02d3-97ee-4847-9347-40773ab76356["Output\nScanpy RegressOut on input dataset(s): Regressed out  AnnData"];
  9 --> 026b02d3-97ee-4847-9347-40773ab76356;
  style 026b02d3-97ee-4847-9347-40773ab76356 stroke:#2c3143,stroke-width:4px;
  10["Add column"];
  7 -->|table| 10;
  11["Join"];
  10 -->|out_file1| 11;
  8 -->|out_file1| 11;
  12["Sort"];
  11 -->|output| 12;
  13["Table Compute"];
  12 -->|out_file1| 13;
  14["Concatenate datasets"];
  3 -->|output| 14;
  13 -->|table| 14;
  15["Manipulate AnnData"];
  6 -->|anndata_out| 15;
  14 -->|out_file1| 15;
  16["Manipulate AnnData"];
  9 -->|output_h5ad| 16;
  14 -->|out_file1| 16;
  17["Manipulate AnnData"];
  15 -->|anndata| 17;
  18["Manipulate AnnData"];
  16 -->|anndata| 18;
  19["Cluster, infer trajectories and embed"];
  17 -->|anndata| 19;
  20["Cluster, infer trajectories and embed"];
  18 -->|anndata| 20;
  09d97ef7-ed92-4d90-a597-2032581c2d4a["Output\nCluster, infer trajectories and embed (tl.louvain) on input dataset(s): Annotated data matrix"];
  20 --> 09d97ef7-ed92-4d90-a597-2032581c2d4a;
  style 09d97ef7-ed92-4d90-a597-2032581c2d4a stroke:#2c3143,stroke-width:4px;
  21["Plot"];
  19 -->|anndata_out| 21;
  22["Plot"];
  20 -->|anndata_out| 22;

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: