Clustering 3k PBMC with Scanpy 2.0
Visit source
Download RO-Crate
Run on Galaxy
Workflow Type: Galaxy
Workflow based on clustering 3K PBMCs with Scanpy tutorial
Associated Tutorial
This workflows is part of the tutorial Clustering 3K PBMCs with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman, Pavankumar Videm
Tutorial Author(s): Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman, Pavankumar Videm, Diana Chiang Jurado
Tutorial Contributor(s): Björn Grüning, Teresa Müller, Amirhossein Naghsh Nilchi, Saskia Hiltemann, Pavankumar Videm, Mehmet Tekman, Wendi Bacon, Helena Rasche, Hans-Rudolf Hotz, Nicola Soranzo, Marius van den Beek, Anthony Bretaudeau, Nate Coraor
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Barcodes | Barcodes | n/a |
|
| Genes | Genes | n/a |
|
| Matrix | Matrix | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Import Anndata | toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 |
| 4 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 5 | Scanpy filter | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0 |
| 6 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 7 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 8 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 9 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 10 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 |
| 11 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 12 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 13 | Scanpy filter | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0 |
| 14 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 15 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 16 | Scanpy filter | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0 |
| 17 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 18 | Scanpy normalize | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy0 |
| 19 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 |
| 20 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 21 | Scanpy filter | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0 |
| 22 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 23 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 24 | Scanpy remove confounders | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy0 |
| 25 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 |
| 26 | Scanpy cluster, embed | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0 |
| 27 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 28 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 29 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 30 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 |
| 31 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 32 | Scanpy cluster, embed | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0 |
| 33 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 34 | Scanpy cluster, embed | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0 |
| 35 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 36 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 |
| 37 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 |
| 38 | Inspect clusters | Here I inspected the louviain clusters... toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 39 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 40 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 41 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 42 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 43 | Scanpy Inspect and manipulate | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 |
| 44 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 45 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 |
| 46 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 47 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 48 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 |
| 49 | Datamash | toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 |
| 50 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 51 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 52 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
| 53 | Scanpy plot | toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| pl_scatter_total_counts_vs_n_genes_by_counts | pl_scatter_total_counts_vs_n_genes_by_counts | n/a |
|
| pl_scatter_n_genes_by_counts_vs_pct_mito | pl_scatter_n_genes_by_counts_vs_pct_mito | n/a |
|
| pl_violin | pl_violin | n/a |
|
| pl_highly_variable | pl_highly_variable | n/a |
|
| pl_pca_overview | pl_pca_overview | n/a |
|
| pl_pca_overview_genes | pl_pca_overview_genes | n/a |
|
| pl_pca_loadings | pl_pca_loadings | n/a |
|
| pl_pca_variance_ratio | pl_pca_variance_ratio | n/a |
|
| pl_umap_initial | pl_umap_initial | n/a |
|
| pl_umap_louvain | pl_umap_louvain | n/a |
|
| pl_rank_gene_groups_t_test_wilcoxon_test | pl_rank_gene_groups_t_test_wilcoxon_test | n/a |
|
| pl_rank_genes_heatmap | pl_rank_genes_heatmap | n/a |
|
| pl_stacked_violin_marker_genes | pl_stacked_violin_marker_genes | n/a |
|
| pl_umap_marker_genes | pl_umap_marker_genes | n/a |
|
| uns_rank_genes_groups_names_wilcoxon_test | uns_rank_genes_groups_names_wilcoxon_test | n/a |
|
| anndata_out | anndata_out | n/a |
|
| pl_violin_louvain | pl_violin_louvain | n/a |
|
| pl_rank_gene_groups_t_test | pl_rank_gene_groups_t_test | n/a |
|
| uns_rank_genes_groups_names_t_test | uns_rank_genes_groups_names_t_test | n/a |
|
| cells_per_cluster | cells_per_cluster | n/a |
|
| pl_rank_gene_groups_0_vs_1 | pl_rank_gene_groups_0_vs_1 | n/a |
|
| pl_rank_gene_groups_violin_0_vs_1 | pl_rank_gene_groups_violin_0_vs_1 | n/a |
|
| pl_umap_celltypes | pl_umap_celltypes | n/a |
|
| pl_dotplot_marker_genes | pl_dotplot_marker_genes | n/a |
|
Version History
master
Creators and Submitter
Discussion Channel
Activity
Views: 247 Downloads: 56 Runs: 0
Created: 2nd Jun 2025 at 10:56
AttributionsNone
Related items
Advanced People list for this Workflow with search and filtering
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.
Advanced Spaces list for this Workflow with search and filtering
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/
Advanced Teams list for this Workflow with search and filtering
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!
