Seurat Filter, Plot and Exlore tutorial 1.0
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This workflows is part of the tutorial Filter, plot, and explore single cell RNA-seq data with Seurat, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Camila Goclowski, Julia Jakiela
Tutorial Author(s): Camila Goclowski
Tutorial Contributor(s): Pablo Moreno, Pavankumar Videm, Helena Rasche, Camila Goclowski, Wendi Bacon, Julia Jakiela, Björn Grüning, Saskia Hiltemann
Steps
| ID | Name | Description |
|---|---|---|
| 0 | EBI SCXA Data Retrieval | toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 |
| 1 | Seurat Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0 |
| 2 | Plot | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0 |
| 3 | Seurat FilterCells | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0 |
| 4 | Seurat NormaliseData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0 |
| 5 | Seurat FindVariableGenes | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0 |
| 6 | Seurat ScaleData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+galaxy0 |
| 7 | Seurat RunPCA | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0 |
| 8 | Seurat FindNeighbours | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0 |
| 9 | Seurat FindClusters | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0 |
| 10 | Seurat UMAP | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0 |
| 11 | Plot | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| matrix_mtx | matrix_mtx | n/a |
|
| genes_tsv | genes_tsv | n/a |
|
| design_tsv | design_tsv | n/a |
|
| barcode_tsv | barcode_tsv | n/a |
|
| rds_seurat_clusters | rds_seurat_clusters | n/a |
|
| rds_seurat_umap | rds_seurat_umap | n/a |
|
Version History
master
Creators and Submitter
Views: 1153 Downloads: 158 Runs: 0
Created: 2nd Jun 2025 at 10:59
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