Clustering 3k PBMC with Scanpy

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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

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1259?version=3

Inputs

ID Name Description Type
Barcodes Barcodes n/a
  • File
Genes Genes n/a
  • File
Matrix Matrix n/a
  • File

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
  • File
pl_scatter_n_genes_by_counts_vs_pct_mito pl_scatter_n_genes_by_counts_vs_pct_mito n/a
  • File
pl_violin pl_violin n/a
  • File
pl_highly_variable pl_highly_variable n/a
  • File
pl_pca_overview pl_pca_overview n/a
  • File
pl_pca_overview_genes pl_pca_overview_genes n/a
  • File
pl_pca_loadings pl_pca_loadings n/a
  • File
pl_pca_variance_ratio pl_pca_variance_ratio n/a
  • File
pl_umap_initial pl_umap_initial n/a
  • File
pl_umap_louvain pl_umap_louvain n/a
  • File
pl_rank_gene_groups_t_test_wilcoxon_test pl_rank_gene_groups_t_test_wilcoxon_test n/a
  • File
pl_rank_genes_heatmap pl_rank_genes_heatmap n/a
  • File
pl_stacked_violin_marker_genes pl_stacked_violin_marker_genes n/a
  • File
pl_umap_marker_genes pl_umap_marker_genes n/a
  • File
uns_rank_genes_groups_names_wilcoxon_test uns_rank_genes_groups_names_wilcoxon_test n/a
  • File
anndata_out anndata_out n/a
  • File
pl_violin_louvain pl_violin_louvain n/a
  • File
pl_rank_gene_groups_t_test pl_rank_gene_groups_t_test n/a
  • File
uns_rank_genes_groups_names_t_test uns_rank_genes_groups_names_t_test n/a
  • File
cells_per_cluster cells_per_cluster n/a
  • File
pl_rank_gene_groups_0_vs_1 pl_rank_gene_groups_0_vs_1 n/a
  • File
pl_rank_gene_groups_violin_0_vs_1 pl_rank_gene_groups_violin_0_vs_1 n/a
  • File
pl_umap_celltypes pl_umap_celltypes n/a
  • File
pl_dotplot_marker_genes pl_dotplot_marker_genes n/a
  • File

Version History

2.0 (latest) Created 7th Oct 2024 at 14:09 by Helena Rasche

Added/updated 4 files


Open master ea3ca25

1.0 Created 16th Jul 2024 at 14:11 by Helena Rasche

Added/updated 4 files


Frozen 1.0 48a5bd4

3.0 (earliest) Created 25th Jun 2024 at 11:16 by Helena Rasche

Added/updated 4 files


Frozen 3.0 4a82b5b
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tool
SCANPY
License
Creative Commons Attribution 4.0 International
Activity

Views: 676   Downloads: 228

Created: 25th Jun 2024 at 11:16

Last updated: 7th Oct 2024 at 14:09

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Total size: 447 KB
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