Seurat Filter, Plot and Exlore tutorial

single-cell-scrna-case_FilterPlotandExplore_SeuratTools/workflow-seurat-filter-plot-explore

Author(s)
Camila Goclowski, Julia Jakiela
version Version
1
last_modification Last updated
Dec 5, 2024
license License
CC-BY-4.0
galaxy-tags Tags
single-cell

Features

Tutorial
hands_on Filter, plot, and explore single cell RNA-seq data with Seurat

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00292
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["EBI SCXA Data Retrieval"];
  a5a4504c-013b-4b87-8ef2-643a3e1804bb["Output\nmatrix_mtx"];
  0 --> a5a4504c-013b-4b87-8ef2-643a3e1804bb;
  style a5a4504c-013b-4b87-8ef2-643a3e1804bb stroke:#2c3143,stroke-width:4px;
  b4ce8ebe-421f-4259-b822-3ac79c5f9817["Output\ngenes_tsv"];
  0 --> b4ce8ebe-421f-4259-b822-3ac79c5f9817;
  style b4ce8ebe-421f-4259-b822-3ac79c5f9817 stroke:#2c3143,stroke-width:4px;
  83aed959-6dce-4115-86dd-7b2d2eeceb00["Output\ndesign_tsv"];
  0 --> 83aed959-6dce-4115-86dd-7b2d2eeceb00;
  style 83aed959-6dce-4115-86dd-7b2d2eeceb00 stroke:#2c3143,stroke-width:4px;
  ca12560b-ca83-4447-8096-acbd51760079["Output\nbarcode_tsv"];
  0 --> ca12560b-ca83-4447-8096-acbd51760079;
  style ca12560b-ca83-4447-8096-acbd51760079 stroke:#2c3143,stroke-width:4px;
  1["Seurat Read10x"];
  0 -->|barcode_tsv| 1;
  0 -->|genes_tsv| 1;
  0 -->|matrix_mtx| 1;
  0 -->|design_tsv| 1;
  2["Plot"];
  1 -->|rds_seurat_file| 2;
  3["Seurat FilterCells"];
  1 -->|rds_seurat_file| 3;
  4["Seurat NormaliseData"];
  3 -->|rds_seurat_file| 4;
  5["Seurat FindVariableGenes"];
  4 -->|rds_seurat_file| 5;
  6["Seurat ScaleData"];
  5 -->|output_tab| 6;
  5 -->|rds_seurat_file| 6;
  7["Seurat RunPCA"];
  6 -->|rds_seurat_file| 7;
  5 -->|output_tab| 7;
  8["Seurat FindNeighbours"];
  7 -->|rds_seurat_file| 8;
  9["Seurat FindClusters"];
  8 -->|rds_seurat_file| 9;
  ac5e668c-341b-4887-867c-0ba165d2a874["Output\nrds_seurat_clusters"];
  9 --> ac5e668c-341b-4887-867c-0ba165d2a874;
  style ac5e668c-341b-4887-867c-0ba165d2a874 stroke:#2c3143,stroke-width:4px;
  10["Seurat UMAP"];
  9 -->|rds_seurat_file| 10;
  831e32ad-773b-417c-8b7e-4b7ca0e12488["Output\nrds_seurat_umap"];
  10 --> 831e32ad-773b-417c-8b7e-4b7ca0e12488;
  style 831e32ad-773b-417c-8b7e-4b7ca0e12488 stroke:#2c3143,stroke-width:4px;
  11["Plot"];
  10 -->|rds_seurat_file| 11;

Inputs

Input Label

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 EBI SCXA Data Retrieval
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0 Seurat FindClusters
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0 Seurat UMAP

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_filter_cells/seurat_filter_cells/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_clusters/seurat_find_clusters/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_neighbours/seurat_find_neighbours/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_find_variable_genes/seurat_find_variable_genes/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_normalise_data/seurat_normalise_data/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_plot/seurat_plot/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_read10x/seurat_read10x/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_pca/seurat_run_pca/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_run_umap/seurat_run_umap/4.0.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/seurat_scale_data/seurat_scale_data/4.0.4+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
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • 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”
  • 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
2 4c5dee5c0 2024-12-05 13:13:30 add tag
1 545fd2100 2024-12-05 13:02:34 rename workflow files

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_FilterPlotandExplore_SeuratTools/workflows/workflow-seurat-filter-plot-explore.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