AnnData to SingleCellExperiment (SCE) conversion
Visit source
Download RO-CrateAnnData to SCE format conversion (manually using Galaxy buttons)
Associated Tutorial
This workflows is part of the tutorial AnnData to SingleCellExperiment (SCE) conversion, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Julia Jakiela, Morgan Howells, Wendi Bacon
Tutorial Contributor(s): Helena Rasche, Pavankumar Videm, Mehmet Tekman
Workflow Author(s): Julia Jakiela, Morgan Howells
Funder(s): ELIXIR-UK: FAIR Data Stewardship training
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
1.0 (latest) Created 16th Jul 2024 at 14:11 by Helena Rasche
Added/updated 4 files
Open
masterb67a802
3.0 (earliest) Created 25th Jun 2024 at 11:15 by Helena Rasche
Added/updated 4 files
Frozen
3.09b8d60b
Creators and Submitter
Views: 522 Downloads: 163
Created: 25th Jun 2024 at 11:15
Last updated: 25th Jun 2024 at 11:15
AttributionsNone
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