EBI SCXA to AnnData (Scanpy) or Seurat Object 2.0
Visit source
Download RO-Crate
Run on GalaxyCreates input file for Filter, Plot, Explore tutorial
Associated Tutorial
This workflows is part of the tutorial Importing files from public atlases, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Julia Jakiela
Tutorial Author(s): Julia Jakiela, Wendi Bacon
Tutorial Contributor(s): Björn Grüning, Julia Jakiela, Wendi Bacon, Helena Rasche, Pablo Moreno, Pavankumar Videm, Mehmet Tekman, Saskia Hiltemann
Grants(s): DASH UK
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| SC-Atlas experiment accession | SC-Atlas experiment accession | EBI Single Cell Atlas accession for the experiment that you want to retrieve. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | EBI SCXA Data Retrieval | toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 |
| 2 | Rename batch numbers | Changes the batch label from "1" to "N01" etc toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 |
| 3 | Mito genes check | Shows how mitochondrial genes are annotated. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1 |
| 4 | Rename cell metadata headers | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1 |
| 5 | Create AnnData | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.9.3+galaxy0 |
| 6 | Seurat Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0 |
| 7 | AnnData Operations | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Mito genes check | Mito genes check | n/a |
|
| AnnData object | AnnData object | n/a |
|
| Seurat object | Seurat object | n/a |
|
| Mito-counted AnnData for downstream analysis | Mito-counted AnnData for downstream analysis | n/a |
|
Version History
master
Creators and Submitter
Views: 1158 Downloads: 168 Runs: 0
Created: 2nd Jun 2025 at 10:57
Tags 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!
