Clustering 3k PBMCs with Seurat - Workflow
single-cell-scrna-seurat-pbmc3k/seurat-pbmc-workflow
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flowchart TD 0["ℹ️ Input Dataset\nmatrix.mtx"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\ngenes.tsv"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nbarcodes.tsv"]; style 2 stroke:#2c3143,stroke-width:4px; 3["ℹ️ Input Dataset\nCanonical Markers"]; style 3 stroke:#2c3143,stroke-width:4px; 4["Input 3k PBMC"]; 2 -->|output| 4; 1 -->|output| 4; 0 -->|output| 4; ffbc2339-390e-46ad-b3be-56e9d12646ed["Output\nInput 3k PBMC"]; 4 --> ffbc2339-390e-46ad-b3be-56e9d12646ed; style ffbc2339-390e-46ad-b3be-56e9d12646ed stroke:#2c3143,stroke-width:4px; 5["Seurat Data Management"]; 4 -->|rds_out| 5; 6["Mitochondrial Annotations"]; 4 -->|rds_out| 6; 7["Seurat Visualize"]; 6 -->|rds_out| 7; 8["Seurat Visualize"]; 6 -->|rds_out| 8; 9["Seurat Visualize"]; 6 -->|rds_out| 9; 10["Filtered Dataset"]; 6 -->|rds_out| 10; 11["Seurat Visualize"]; 10 -->|rds_out| 11; 12["Seurat Visualize"]; 10 -->|rds_out| 12; 13["Seurat Visualize"]; 10 -->|rds_out| 13; 14["Seurat Preprocessing"]; 10 -->|rds_out| 14; 15["Seurat Preprocessing"]; 14 -->|rds_out| 15; 16["Preprocessed Data"]; 15 -->|rds_out| 16; d85dec85-68a5-4fe7-8c96-d71c33653a9b["Output\nPreprocessed Data"]; 16 --> d85dec85-68a5-4fe7-8c96-d71c33653a9b; style d85dec85-68a5-4fe7-8c96-d71c33653a9b stroke:#2c3143,stroke-width:4px; 17["Seurat Visualize"]; 16 -->|rds_out| 17; 18["PCA Results"]; 16 -->|rds_out| 18; 19["Seurat Visualize"]; 18 -->|rds_out| 19; 20["Seurat Visualize"]; 18 -->|rds_out| 20; 21["Seurat Visualize"]; 18 -->|rds_out| 21; 22["Seurat Visualize"]; 18 -->|rds_out| 22; 23["Seurat Visualize"]; 18 -->|rds_out| 23; 24["Seurat Visualize"]; 18 -->|rds_out| 24; 25["Seurat Visualize"]; 18 -->|rds_out| 25; 26["Seurat Find Clusters"]; 18 -->|rds_out| 26; 27["Seurat Find Clusters"]; 26 -->|rds_out| 27; 28["UMAP Results"]; 27 -->|rds_out| 28; 29["Seurat Visualize"]; 28 -->|rds_out| 29; 30["Seurat Visualize"]; 28 -->|rds_out| 30; 31["Seurat Visualize"]; 28 -->|rds_out| 31; 32["DE Markers"]; 28 -->|rds_out| 32; 33["Seurat Visualize"]; 28 -->|rds_out| 33; 34["Seurat Visualize"]; 28 -->|rds_out| 34; 35["Seurat Visualize"]; 28 -->|rds_out| 35; 36["Seurat Visualize"]; 28 -->|rds_out| 36; 37["Annotated Clusters"]; 28 -->|rds_out| 37; 0e0eb878-6318-4e30-8d9f-ef8a9e816227["Output\nAnnotated Clusters"]; 37 --> 0e0eb878-6318-4e30-8d9f-ef8a9e816227; style 0e0eb878-6318-4e30-8d9f-ef8a9e816227 stroke:#2c3143,stroke-width:4px; 38["DE Markers Tabular"]; 32 -->|markers_tabular| 38; 39["Seurat Visualize"]; 37 -->|rds_out| 39; 40["Seurat Visualize"]; 3 -->|output| 40; 37 -->|rds_out| 40; 41["Input DE Markers"]; 38 -->|tabular| 41; 9fa0dffb-06f3-493c-931f-dfd8896f2295["Output\nInput DE Markers"]; 41 --> 9fa0dffb-06f3-493c-931f-dfd8896f2295; style 9fa0dffb-06f3-493c-931f-dfd8896f2295 stroke:#2c3143,stroke-width:4px; 42["Seurat Visualize"]; 41 -->|out_file1| 42; 37 -->|rds_out| 42;
Inputs
Input | Label |
---|---|
matrix.mtx | matrix.mtx |
genes.tsv | genes.tsv |
barcodes.tsv | barcodes.tsv |
Canonical Markers | Canonical Markers |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1 | Seurat Create | Input 3k PBMC |
toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0 | Seurat Preprocessing | Preprocessed Data |
toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 | Seurat Data Management | Annotated Clusters |
Cut1 | Cut | Input DE Markers |
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
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 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
- 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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
6 | ddc0ab898 | 2025-01-08 10:15:57 | Correcting file name 3 |
5 | ce9b2844f | 2025-01-08 10:15:12 | Deleting old file |
4 | 1e4cb24f2 | 2024-10-31 14:03:00 | Fixing errors in Seurat_PBMC_Workflow.ga |
3 | 553c45c57 | 2024-10-31 13:55:39 | Adding missing " to workflow |
2 | 6bcca5b8d | 2024-10-31 13:27:31 | Adding workflows with workflow tests |
1 | aa1ea4031 | 2024-10-29 10:14:15 | Shorter name for workflow 1 |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-seurat-pbmc3k/workflows/Seurat_PBMC_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