Pseudobulk with decoupler and edgeR tutorial workflow
single-cell-pseudobulk-analysis/pseudo-bulk-edger
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Inputs
Input | Label |
---|---|
Input dataset | ncm_pdcs_subset.h5ad |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1 | Inspect AnnData | Inspect AnnData Object |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3 | Scanpy filter | Filter Cell-Type |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8 | Decoupler pseudo-bulk | Pseudobulk with decoupler |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 | Replace Text | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 | Text reformatting | Generating Contrast File |
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 | edgeR | |
__EXTRACT_DATASET__ | Extract dataset | |
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 | Remove columns | |
toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6 | Volcano 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 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 | 2568b8bc7 | 2025-05-06 12:52:18 | Update pseudo-bulk_edgeR.ga |
5 | 1013fd838 | 2025-05-06 12:49:22 | Pseudobtutorial final gta fixes (#6) |
4 | a4799836a | 2025-05-06 12:39:32 | Update pseudo-bulk_edgeR.ga file |
3 | cc7888368 | 2024-12-11 14:41:36 | Update pseudo-bulk_edgeR.ga |
2 | 95f00fe4e | 2024-12-11 14:33:57 | Update pseudo-bulk_edgeR.ga |
1 | 45bf38997 | 2024-12-06 18:55:00 | Add pseudobulk-analysis tutorial and associated files |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/pseudobulk-analysis/workflows/pseudo-bulk_edgeR.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