Clustering 3k PBMCs with Seurat - Workflow

single-cell-scrna-seurat-pbmc3k/seurat-pbmc-workflow

Author(s)
Marisa Loach
Version
1
Last updated
Jan 23, 2025
License
CC-BY-4.0
Tags
name:singlecell
name:seurat

Features
Tutorial
Clustering 3K PBMCs with Seurat
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00305
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
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ℹ️ Input Dataset
matrix.mtx
ℹ️ Input Dataset
genes.tsv
ℹ️ Input Dataset
barcodes.tsv
ℹ️ Input Dataset
Canonical Markers
Input 3k PBMC
Seurat Data Management
Mitochondrial Annotations
Seurat Visualize
Seurat Visualize
Seurat Visualize
Filtered Dataset
Seurat Visualize
Seurat Visualize
Seurat Visualize
Seurat Preprocessing
Seurat Preprocessing
Preprocessed Data
Seurat Visualize
PCA Results
Seurat Visualize
Seurat Visualize
Seurat Visualize
Seurat Visualize
Seurat Visualize
Seurat Visualize
Seurat Visualize
Seurat Find Clusters
Seurat Find Clusters
UMAP Results
Seurat Visualize
Seurat Visualize
Seurat Visualize
DE Markers
Seurat Visualize
Seurat Visualize
Seurat Visualize
Seurat Visualize
Annotated Clusters
DE Markers Tabular
Seurat Visualize
Seurat Visualize
Input DE Markers
Seurat Visualize
Output
Input 3k PBMC
Output
Preprocessed Data
Output
Annotated Clusters
Output
Input DE Markers

Inputs

Input Label
matrix.mtx matrix.mtx
genes.tsv genes.tsv
barcodes.tsv barcodes.tsv
Canonical Markers Canonical Markers

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1 Seurat Create Input 3k PBMC
toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0 Seurat Preprocessing Preprocessed Data
toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 Seurat Data Management Annotated Clusters
Cut1 Cut Input DE Markers

Tools

Tool Links
Cut1
csv_to_tabular
toolshed.g2.bx.psu.edu/repos/iuc/seurat_clustering/seurat_clustering/5.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seurat_create/seurat_create/5.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seurat_data/seurat_data/5.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seurat_plot/seurat_plot/5.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seurat_preprocessing/seurat_preprocessing/5.0+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seurat_reduce_dimension/seurat_reduce_dimension/5.0+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
6 ddc0ab898 2025-01-08 10:15:57 Correcting file name 3
5 ce9b2844f 2025-01-08 10:15:12 Deleting old file
4 1e4cb24f2 2024-10-31 14:03:00 Fixing errors in Seurat_PBMC_Workflow.ga
3 553c45c57 2024-10-31 13:55:39 Adding missing " to workflow
2 6bcca5b8d 2024-10-31 13:27:31 Adding workflows with workflow tests
1 aa1ea4031 2024-10-29 10:14:15 Shorter name for workflow 1

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-seurat-pbmc3k/workflows/Seurat_PBMC_Workflow.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