Combining datasets after pre-processing 1.0
Visit source
Download RO-Crate
Run on GalaxyUpdated March 2024
Associated Tutorial
This workflows is part of the tutorial Combining single cell datasets after pre-processing, available in the GTN
Thanks to...
Workflow Author(s): Julia Jakiela, Wendi Bacon
Tutorial Author(s): Wendi Bacon
Tutorial Contributor(s): Helena Rasche, Jonathan Manning, Julia Jakiela, Pavankumar Videm, Saskia Hiltemann, Björn Grüning, Marisa Loach, Wendi Bacon, Bérénice Batut, Mehmet Tekman, Pablo Moreno
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| N701 | N701 | Dataset to be combined |
|
| N702 | N702 | Dataset to be combined |
|
| N703 | N703 | Dataset to be combined |
|
| N704 | N704 | Dataset to be combined |
|
| N705 | N705 | Dataset to be combined |
|
| N706 | N706 | Dataset to be combined |
|
| N707 | N707 | Dataset to be combined |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Concatenating Datasets | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 8 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 9 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 10 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0 |
| 11 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0 |
| 12 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy0 |
| 13 | Cut | Cut1 |
| 14 | Cut | Cut1 |
| 15 | Paste | Paste1 |
| 16 | Adding in cell metadata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 17 | Batching Cell Metadata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.3+galaxy0 |
| 18 | Calculating mitochondrial | toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.9.3+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Combined Object | Combined Object | n/a |
|
| Sex metadata | Sex metadata | n/a |
|
| Genotype metadata | Genotype metadata | n/a |
|
| Cell metadata | Cell metadata | n/a |
|
| AnnData with Cell Metadata | AnnData with Cell Metadata | n/a |
|
| Batched Object | Batched Object | n/a |
|
| Annotated AnnData | Annotated AnnData | n/a |
|
Version History
master
Creators and Submitter
Views: 40 Downloads: 4 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
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!
