AnnData to Cell Data Set (CDS) conversion 1.0
Visit source
Download RO-Crate
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: 1286 Downloads: 181 Runs: 0
Created: 2nd Jun 2025 at 10:57
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
