AnnData to Cell Data Set (CDS) conversion
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Download RO-CrateAnnData to CDS format conversion (manually using Galaxy buttons). This workflow does not include renaming the column containing gene symbols.
Associated Tutorial
This workflows is part of the tutorial AnnData to Cell Data Set (CDS) 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
Funder(s): ELIXIR-UK: FAIR Data Stewardship training
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| AnnData | AnnData | Input file in AnnData format |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 2 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 3 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 4 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1 |
| 5 | Monocle3 create | toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Inspect AnnData: obs | Inspect AnnData: obs | n/a |
|
| Inspect AnnData: var | Inspect AnnData: var | n/a |
|
| Inspect AnnData: X | Inspect AnnData: X | n/a |
|
| CDS Monocle file | CDS Monocle file | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:11 by Helena Rasche
Added/updated 4 files
Open
master39af45e
3.0 (earliest) Created 25th Jun 2024 at 11:15 by Helena Rasche
Added/updated 4 files
Frozen
3.03cfd20f
Creators and Submitter
Views: 624 Downloads: 178
Created: 25th Jun 2024 at 11:15
Last updated: 25th Jun 2024 at 11:15
AttributionsNone
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