Cluster 3k PBMCs with Seurat - Workflow - SCTransform Version 1.0
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Run on GalaxyThis is the workflow for the Clustering 3K PBMCs with Seurat tutorial if you use SCTransform for preprocessing.
Associated Tutorial
This workflows is part of the tutorial Clustering 3K PBMCs with Seurat, 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): Pavankumar Videm, Saskia Hiltemann, Björn Grüning, Wendi Bacon, Teresa Müller
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Canonical Markers | Canonical Markers | Paste in a list of canonical markers for PBMCs - this is given in the Clustering 3K PBMCs with Seurat tutorial. |
|
| barcodes.tsv | barcodes.tsv | Table of barcodes for the cells in the matrix. |
|
| genes.tsv | genes.tsv | Table of gene names for the features in the matrix. |
|
| matrix.mtx | matrix.mtx | Single cell expression data in Matrix Market (mtx) format. This is the table that shows the counts of each RNA in each cell. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Input 3k PBMCs | toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1 |
| 5 | Seurat Data Management | toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 |
| 6 | Mitochondrial Annotations | toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1 |
| 7 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 8 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 9 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 10 | Filtered Dataset | toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1 |
| 11 | Preprocessed Data | toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0 |
| 12 | Seurat Data Management | toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 |
| 13 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 14 | PCA Results | toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0 |
| 15 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 16 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 17 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 18 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 19 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 20 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 21 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 22 | Seurat Find Clusters | toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 |
| 23 | Seurat Find Clusters | toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 |
| 24 | UMAP Results | toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+galaxy0 |
| 25 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 26 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 27 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 28 | DE Markers | toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 |
| 29 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 30 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 31 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 32 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 33 | Annotated Clusters | This is the final annotated Seurat Object with each cluster labelled by cell type. toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 |
| 34 | DE Markers (Tabular) | csv_to_tabular |
| 35 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 36 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
| 37 | Input DE Markers | Cut1 |
| 38 | Seurat Visualize | toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input 3k PBMC | Input 3k PBMC | n/a |
|
| Preprocessed Data | Preprocessed Data | n/a |
|
| Annotated Clusters | Annotated Clusters | n/a |
|
| Input DE Markers | Input DE Markers | n/a |
|
Version History
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Creators and Submitter
Views: 1215 Downloads: 168 Runs: 0
Created: 2nd Jun 2025 at 10:58
AttributionsNone
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