Clustering 3k PBMC with Scanpy

single-cell-scrna-scanpy-pbmc3k/clustering-3k-pbmc-with-scanpy

Author(s)
Bérénice Batut, Hans-Rudolf Hotz, Mehmet Tekman, Pavankumar Videm
Version
2
Last updated
Oct 4, 2024
License
CC-BY-4.0
Tags
name:scRNA-seq
name:single-cell

Features
Tutorial
Clustering 3K PBMCs with Scanpy
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00212
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
anndata
anndata
anndata
anndata
anndata
anndata_out
anndata
anndata
anndata_out
anndata_out
anndata_out
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anndata
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anndata
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anndata_out
obs
anndata_out
anndata_out
anndata
anndata
ℹ️ Input Dataset
Barcodes
ℹ️ Input Dataset
Genes
ℹ️ Input Dataset
Matrix
Import Anndata
Inspect AnnData
Scanpy filter
Inspect AnnData
Inspect AnnData
Inspect AnnData
Manipulate AnnData
Scanpy Inspect and manipulate
Inspect AnnData
Scanpy plot
Scanpy filter
Scanpy plot
Scanpy plot
Scanpy filter
Manipulate AnnData
Scanpy normalize
Scanpy Inspect and manipulate
Manipulate AnnData
Scanpy filter
Manipulate AnnData
Scanpy plot
Scanpy remove confounders
Scanpy Inspect and manipulate
Scanpy cluster, embed
Scanpy plot
Scanpy plot
Scanpy plot
Scanpy Inspect and manipulate
Scanpy plot
Scanpy cluster, embed
Scanpy plot
Scanpy cluster, embed
Scanpy plot
Scanpy Inspect and manipulate
Scanpy Inspect and manipulate
Inspect clusters
Scanpy plot
Scanpy plot
Scanpy plot
Scanpy plot
Scanpy Inspect and manipulate
Inspect AnnData
Manipulate AnnData
Scanpy plot
Scanpy plot
Inspect AnnData
Datamash
Scanpy plot
Scanpy plot
Scanpy plot
Scanpy plot
Output
pl_scatter_total_counts_vs_n_genes_by_counts
Output
pl_scatter_n_genes_by_counts_vs_pct_mito
Output
pl_violin
Output
pl_highly_variable
Output
pl_pca_overview
Output
pl_pca_overview_genes
Output
pl_pca_loadings
Output
pl_pca_variance_ratio
Output
pl_umap_initial
Output
pl_umap_louvain
Output
pl_rank_gene_groups_t_test_wilcoxon_test
Output
pl_rank_genes_heatmap
Output
pl_stacked_violin_marker_genes
Output
pl_umap_marker_genes
Output
uns_rank_genes_groups_names_wilcoxon_test
Output
anndata_out
Output
pl_violin_louvain
Output
pl_rank_gene_groups_t_test
Output
uns_rank_genes_groups_names_t_test
Output
cells_per_cluster
Output
pl_rank_gene_groups_0_vs_1
Output
pl_rank_gene_groups_violin_0_vs_1
Output
pl_umap_celltypes
Output
pl_dotplot_marker_genes

Inputs

Input Label
Input dataset Barcodes
Input dataset Genes
Input dataset Matrix

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 Inspect AnnData
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 Manipulate AnnData
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 Inspect AnnData
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 Datamash
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 Scanpy plot

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.10.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.10.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_cluster_reduce_dimension/scanpy_cluster_reduce_dimension/1.10.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_inspect/scanpy_inspect/1.10.2+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_normalize/scanpy_normalize/1.10.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.10.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_remove_confounders/scanpy_remove_confounders/1.10.2+galaxy0 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands On: Importing a workflow
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
4 30dbb347e 2024-10-04 15:27:24 Update tutorials and add histories as answer_histories
3 88dc62713 2023-11-21 16:41:05 add CC 4.0 license
2 f5d15e869 2023-11-21 16:28:21 add links to a control history and workflow
1 a0fbcfe2e 2023-11-21 16:08:06 add workflow and tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-scanpy-pbmc3k/workflows/Clustering-3k-PBMC-with-Scanpy.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows