scRNA Plant Analysis 1.0
Visit source
Download RO-Crate
Run on GalaxyDownstream Single-cell RNA Plant analysis with ScanPy
Associated Tutorial
This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, Beatriz Serrano-Solano, Cristóbal Gallardo, Pavankumar Videm
Tutorial Contributor(s): Mehmet Tekman, Wendi Bacon, Helena Rasche, Beatriz Serrano-Solano, Björn Grüning
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Leiden Resolution | #main/Leiden Resolution | n/a |
|
| Max Features | #main/Max Features | n/a |
|
| Max Lib Size | #main/Max Lib Size | n/a |
|
| Min Cells | #main/Min Cells | n/a |
|
| Min Genes | #main/Min Genes | n/a |
|
| SHR (CSV.gz) | #main/SHR (CSV.gz) | n/a |
|
| WT (CSV.gz) | #main/WT (CSV.gz) | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 7 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0 |
| 8 | Import Anndata and loom | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy0 |
| 9 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 |
| 10 | Rename Batches | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 |
| 11 | QC metrics | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0 |
| 12 | Filter genes | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 |
| 13 | Plot Violin | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
| 14 | Filter Cells | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.7.1+galaxy0 |
| 15 | Filter Max Features | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 |
| 16 | Filter Max Library Size | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 |
| 17 | Save RAW | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 |
| 18 | Norm to 1e4 | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.7.1+galaxy0 |
| 19 | Log1p | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0 |
| 20 | Regress total counts | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.7.1+galaxy0 |
| 21 | Scale | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0 |
| 22 | PCA | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0 |
| 23 | Neighborhod | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.7.1+galaxy0 |
| 24 | UMAP | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0 |
| 25 | Leiden | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.7.1+galaxy0 |
| 26 | Plot PCA (batch) | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
| 27 | Plot UMAP (batch) | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
| 28 | Plot UMAP (leiden, batch) | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
| 29 | Rename Clusters | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy0 |
| 30 | Complex DotPlot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
| 31 | Complex DotPlot with new labels | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
| 32 | Plot UMAP with new labels | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| scRNA Concatenated Datasets | #main/scRNA Concatenated Datasets | n/a |
|
| scRNA with clusters Dataset | #main/scRNA with clusters Dataset | n/a |
|
Version History
master
Creators and Submitter
Views: 1333 Downloads: 192 Runs: 0
Created: 2nd Jun 2025 at 10:59
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!
