CS3_Filter, Plot and Explore Single-cell RNA-seq Data

Run Workflow in Galaxy

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

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  1["Inspect AnnData"];
  0 -->|output| 1;
  2["Scanpy FilterCells"];
  0 -->|output| 2;
  08175d7f-f4f4-413c-ad86-f59587ff692e["Output\nGenes-filtered Object"];
  2 --> 08175d7f-f4f4-413c-ad86-f59587ff692e;
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  3["Plot"];
  0 -->|output| 3;
  bfc499ee-630a-498b-9be6-696d9bb78837["Output\nScatter - genes x UMIs"];
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  0 -->|output| 4;
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  5["Plot"];
  0 -->|output| 5;
  348818e6-9def-41fd-a390-6f8525c57cd8["Output\nViolin - genotype - log"];
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  0 -->|output| 6;
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  0 -->|output| 7;
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  0 -->|output| 8;
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  0 -->|output| 9;
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  0 -->|output| 10;
  a639cdc0-da40-4df9-8348-23117528b24a["Output\nViolin - sex - log"];
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  11["Plot"];
  2 -->|output_h5ad| 11;
  69bf3e42-63e2-4b5b-9d63-5aac9d6b5691["Output\nViolin - Filterbygenes"];
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  12["Scanpy FilterCells"];
  2 -->|output_h5ad| 12;
  f378cb4e-0a77-49d9-b92a-752dbea4b09a["Output\nCounts-filtered Object"];
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  13["Inspect AnnData"];
  2 -->|output_h5ad| 13;
  f9e862db-eb22-4124-8fe0-0fdcfcfb8393["Output\nGeneral - Filterbygenes"];
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  14["Inspect AnnData"];
  12 -->|output_h5ad| 14;
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  15["Scanpy FilterCells"];
  12 -->|output_h5ad| 15;
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  16["Plot"];
  12 -->|output_h5ad| 16;
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  17["Inspect AnnData"];
  15 -->|output_h5ad| 17;
  cd94a4c6-5665-4bdf-88ea-4f4d41efa893["Output\nGeneral - Filterbymito"];
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  18["Scanpy FilterGenes"];
  15 -->|output_h5ad| 18;
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  19["Plot"];
  15 -->|output_h5ad| 19;
  7e48a14f-08fd-45ab-b613-606bf64dcf9d["Output\nViolin - Filterbymito"];
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  20["Inspect AnnData"];
  18 -->|output_h5ad| 20;
  d59efa9b-d049-4f0e-8bd8-8ae982a45d0a["Output\nGeneral - Filtered object"];
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  21["Scanpy NormaliseData"];
  18 -->|output_h5ad| 21;
  22["Scanpy FindVariableGenes"];
  21 -->|output_h5ad| 22;
  23["Scanpy ScaleData"];
  22 -->|output_h5ad| 23;
  24["Scanpy RunPCA"];
  23 -->|output_h5ad| 24;
  25["Plot"];
  24 -->|output_h5ad| 25;
  993dea99-990f-460a-beb9-46e5c97ee898["Output\nPCA Variance"];
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  26["Scanpy ComputeGraph"];
  24 -->|output_h5ad| 26;
  27["Scanpy RunTSNE"];
  26 -->|output_h5ad| 27;
  28["Scanpy RunUMAP"];
  27 -->|output_h5ad| 28;
  29["Scanpy FindCluster"];
  28 -->|output_h5ad| 29;
  30["Scanpy FindMarkers"];
  29 -->|output_h5ad| 30;
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  035bbbce-fb57-48c8-83d5-2b0cd0376541["Output\nFinal object"];
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  31["Scanpy FindMarkers"];
  29 -->|output_h5ad| 31;
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  32["Scanpy PlotEmbed"];
  30 -->|output_h5ad| 32;
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  30 -->|output_h5ad| 33;
  34["Manipulate AnnData"];
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  30 -->|output_h5ad| 35;
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  30 -->|output_h5ad| 36;
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  30 -->|output_h5ad| 37;
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  30 -->|output_tsv| 38;
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  31 -->|output_tsv| 39;
  36 -->|var| 39;
  40["AnnData Operations"];
  37 -->|output_h5ad| 40;
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  43["Scanpy PlotEmbed"];
  40 -->|output_h5ad| 43;

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-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.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