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 |
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pl_scatter_n_genes_by_counts_vs_pct_mito | pl_scatter_n_genes_by_counts_vs_pct_mito | n/a |
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pl_violin | pl_violin | n/a |
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pl_highly_variable | pl_highly_variable | n/a |
|
pl_pca_overview | pl_pca_overview | n/a |
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pl_pca_overview_genes | pl_pca_overview_genes | n/a |
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pl_pca_loadings | pl_pca_loadings | n/a |
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pl_pca_variance_ratio | pl_pca_variance_ratio | n/a |
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pl_umap_initial | pl_umap_initial | n/a |
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pl_umap_louvain | pl_umap_louvain | n/a |
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pl_rank_gene_groups_t_test_wilcoxon_test | pl_rank_gene_groups_t_test_wilcoxon_test | n/a |
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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 |
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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 |
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pl_rank_gene_groups_t_test | pl_rank_gene_groups_t_test | n/a |
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uns_rank_genes_groups_names_t_test | uns_rank_genes_groups_names_t_test | n/a |
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cells_per_cluster | cells_per_cluster | n/a |
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pl_rank_gene_groups_0_vs_1 | pl_rank_gene_groups_0_vs_1 | n/a |
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pl_rank_gene_groups_violin_0_vs_1 | pl_rank_gene_groups_violin_0_vs_1 | n/a |
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pl_umap_celltypes | pl_umap_celltypes | n/a |
|
pl_dotplot_marker_genes | pl_dotplot_marker_genes | n/a |
|
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Created: 2nd Jun 2025 at 10:56

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