Batch Correction - Scanpy 1.0
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Run on Galaxy Workflow for GTN tutorial on single-cell batch correction, using the Scanpy pipeline with Harmony.
Associated Tutorial
This workflows is part of the tutorial Batch Correction and Integration with Seurat or Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
Thanks to...
Workflow Author(s): Marisa Loach
Tutorial Author(s): Marisa Loach
Tutorial Contributor(s): Wendi Bacon, Diana Chiang Jurado
Funder(s): BioFAIR
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input_AnnData | Input_AnnData | An AnnData of human PBMCs profiled with seven different single cell technologies. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.11.4+galaxy3 |
| 2 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.11.4+galaxy3 |
| 3 | Scanpy normalize | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.11.5+galaxy0 |
| 4 | Count | Count1 |
| 5 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.11.5+galaxy0 |
| 6 | Scanpy filter | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.11.5+galaxy0 |
| 7 | Find HVGs by Batch | Method is used as the batch key for finding Highly Variable Genes. toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.11.5+galaxy0 |
| 8 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.11.5+galaxy0 |
| 9 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.11.5+galaxy0 |
| 10 | Scanpy cluster, embed | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.11.5+galaxy0 |
| 11 | Scanpy cluster, embed | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.11.5+galaxy0 |
| 12 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.11.5+galaxy0 |
| 13 | Harmony Integration | Harmony is used to correct for differences between batches, which in this case are the different experimental Methods. toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.11.5+galaxy0 |
| 14 | Scanpy cluster, embed | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.11.5+galaxy0 |
| 15 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.11.5+galaxy0 |
| 16 | Unintegrated AnnData | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.11.5+galaxy0 |
| 17 | Scanpy cluster, embed | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.11.5+galaxy0 |
| 18 | UMAP Plots before Batch Correction | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.11.5+galaxy0 |
| 19 | Integrated AnnData | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.11.5+galaxy0 |
| 20 | UMAP Plot after Batch Correction | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.11.5+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Inspect_Input_Anndata | Inspect_Input_Anndata | n/a |
|
| UMAP_before_Integrate | UMAP_before_Integrate | n/a |
|
| UMAP_after_Integrate | UMAP_after_Integrate | n/a |
|
Version History
master
Creators and Submitter
Views: 4 Downloads: 0 Runs: 0
Created: 13th Jul 2026 at 15:05
AttributionsNone
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Teams: Galaxy Training Network
Organizations: Galaxy
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