Single-cell QC with scater
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Download RO-CrateSingle-cell quality control with scater
Associated Tutorial
This workflows is part of the tutorial Single-cell quality control with scater, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Graham Etherington, Nicola Soranzo, Pavankumar Videm
Tutorial Author(s): Graham Etherington, Nicola Soranzo
Tutorial Contributor(s): Pavankumar Videm, Saskia Hiltemann, Helena Rasche, Mehmet Tekman, Nicola Soranzo, Graham Etherington, Björn Grüning, Gildas Le Corguillé, Stéphanie Robin, Anthony Bretaudeau, Simon Bray
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| annotation.txt | annotation.txt | n/a |
|
| counts.txt | counts.txt | n/a |
|
| mt_controls.txt | mt_controls.txt | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Scater: Calculate QC metrics | toolshed.g2.bx.psu.edu/repos/iuc/scater_create_qcmetric_ready_sce/scater_create_qcmetric_ready_sce/1.12.2 |
| 4 | Library QC | toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2 |
| 5 | Filter SCE | toolshed.g2.bx.psu.edu/repos/iuc/scater_filter/scater_filter/1.12.2 |
| 6 | Filtered Library QC | toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_dist_scatter/scater_plot_dist_scatter/1.12.2 |
| 7 | PCA Plot | toolshed.g2.bx.psu.edu/repos/iuc/scater_plot_pca/scater_plot_pca/1.12.2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| lib_qc_plot | lib_qc_plot | n/a |
|
| output_loom | output_loom | n/a |
|
| filtered_lib_qc_plot | filtered_lib_qc_plot | n/a |
|
| pca_plot | pca_plot | n/a |
|
Version History
2.0 (latest) Created 20th Jan 2025 at 13:06 by Helena Rasche
Added/updated 4 files
Open
masterb4b22cf
1.0 (earliest) Created 25th Jun 2024 at 11:14 by Helena Rasche
Added/updated 4 files
Frozen
1.012fa947
Creators and Submitter
Views: 538 Downloads: 116
Created: 25th Jun 2024 at 11:14
Last updated: 20th Jan 2025 at 13:06
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
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