AnnData to Cell Data Set (CDS) conversion 1.0
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Run on GalaxyAnnData 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 Converting between common single cell data formats, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Julia Jakiela
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 |
|
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
master
Creators and Submitter
Views: 45 Downloads: 5 Runs: 0
Created: 2nd Jun 2025 at 10:57
AttributionsNone
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