AnnData to SingleCellExperiment (SCE) conversion 1.0
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Run on GalaxyAnnData to SCE format conversion (manually using Galaxy buttons)
Associated Tutorial
This workflows is part of the tutorial Converting between common single cell data formats, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Julia Jakiela, Morgan Howells
Tutorial Author(s): Julia Jakiela, Morgan Howells, Wendi Bacon
Tutorial Contributor(s): Helena Rasche, Pavankumar Videm, Mehmet Tekman, Pablo Moreno, Julia Jakiela, Saskia Hiltemann, Björn Grüning, Wendi Bacon
Grants(s): DASH UK
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AnnData | AnnData | Input file in AnnData format |
|
| Cell ID column | Cell ID column | Values must match those provided in the expression matrix. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 3 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 4 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1 |
| 5 | DropletUtils | toolshed.g2.bx.psu.edu/repos/iuc/dropletutils/dropletutils/1.10.0+galaxy2 |
| 6 | DropletUtils Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/dropletutils_read_10x/dropletutils_read_10x/1.0.4+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Inspect AnnData: obs | Inspect AnnData: obs | n/a |
|
| Inspect AnnData: X | Inspect AnnData: X | n/a |
|
| Converted SCE object | Converted SCE object | n/a |
|
Version History
master
Creators and Submitter
Views: 47 Downloads: 6 Runs: 0
Created: 2nd Jun 2025 at 10:57
AttributionsNone
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Organizations: Galaxy
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