Batch Correction - Seurat 1.0
Visit source
Download RO-Crate
Run on Galaxy This is the workflow for the Batch Correction and Integration tutorial if you use Seurat.
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_SeuratObject | Input_SeuratObject | A SeuratObject of human PBMCs profiled with seven different single cell technologies. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Inspect before Split | toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 |
| 2 | Seurat Data Management | toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 |
| 3 | Seurat Integrate | toolshed.g2.bx.psu.edu/repos/iuc/seurat_integrate/seurat_integrate/5.0+galaxy0 |
| 4 | Inspect after Split | toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 |
| 5 | Seurat Preprocessing | toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0 |
| 6 | Seurat Preprocessing | toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0 |
| 7 | Seurat Preprocessing | toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0 |
| 8 | Seurat Run Dimensional Reduction | toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0 |
| 9 | Seurat Find Clusters | toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 |
| 10 | Seurat Find Clusters | toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 |
| 11 | Seurat Run Dimensional Reduction | toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0 |
| 12 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 13 | UMAP Plot by Method before Batch Correction | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 14 | Seurat Integrate | toolshed.g2.bx.psu.edu/repos/iuc/seurat_integrate/seurat_integrate/5.0+galaxy0 |
| 15 | Seurat Integrate | toolshed.g2.bx.psu.edu/repos/iuc/seurat_integrate/seurat_integrate/5.0+galaxy0 |
| 16 | Seurat Find Clusters | toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 |
| 17 | Seurat Find Clusters | toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 |
| 18 | Seurat Run Dimensional Reduction | toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0 |
| 19 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 20 | UMAP Plot by Method after Batch Correction | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Inspect_before_Split | Inspect_before_Split | n/a |
|
| Inspect_after_Split | Inspect_after_Split | n/a |
|
| UMAP_before_Split | UMAP_before_Split | n/a |
|
| UMAP_after_Split | UMAP_after_Split | n/a |
|
Version History
master
Creators and Submitter
Views: 4 Downloads: 0 Runs: 0
Created: 13th Jul 2026 at 15:05
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
