Clustering 3k PBMC with Scanpy
single-cell-scrna-scanpy-pbmc3k/clustering-3k-pbmc-with-scanpy
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30["Plot"]; 28 -->|anndata_out| 30; 31["Remove confounders"]; 29 -->|anndata| 31; 32["Inspect and manipulate"]; 31 -->|anndata_out| 32; 33["Cluster, infer trajectories and embed"]; 32 -->|anndata_out| 33; 96cbb37e-e755-4479-9f14-f0e14f689868["Output\nanndata_out"]; 33 --> 96cbb37e-e755-4479-9f14-f0e14f689868; style 96cbb37e-e755-4479-9f14-f0e14f689868 stroke:#2c3143,stroke-width:4px; 34["Plot"]; 33 -->|anndata_out| 34; 35["Plot"]; 33 -->|anndata_out| 35; 5dc45ef9-c56e-4dbd-9817-367c981a2041["Output\nout_png"]; 35 --> 5dc45ef9-c56e-4dbd-9817-367c981a2041; style 5dc45ef9-c56e-4dbd-9817-367c981a2041 stroke:#2c3143,stroke-width:4px; 36["Inspect and manipulate"]; 33 -->|anndata_out| 36; 37["Plot"]; 33 -->|anndata_out| 37; 38["Plot"]; 33 -->|anndata_out| 38; 39["Cluster, infer trajectories and embed"]; 36 -->|anndata_out| 39; 40["Cluster, infer trajectories and embed"]; 39 -->|anndata_out| 40; 41["Plot"]; 39 -->|anndata_out| 41; 29513947-d16c-48b2-93ff-dd78cd99ecb7["Output\nout_png"]; 41 --> 29513947-d16c-48b2-93ff-dd78cd99ecb7; 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61["Datamash"]; 52 -->|obs| 61;
Inputs
Input | Label |
---|---|
Input dataset | Barcodes |
Input dataset | Genes |
Input dataset | Matrix |
Input dataset | mito header |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.9.6+galaxy1 | Cluster, infer trajectories and embed | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.9.6+galaxy1 | Inspect and manipulate | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 | Manipulate AnnData | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.9.6+galaxy1 | Plot |
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 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:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
3 | 88dc62713 | 2023-11-21 16:41:05 | add CC 4.0 license |
2 | f5d15e869 | 2023-11-21 16:28:21 | add links to a control history and workflow |
1 | a0fbcfe2e | 2023-11-21 16:08:06 | add workflow and tests |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.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