Seurat Filter, Plot and Exlore tutorial
single-cell-scrna-case_FilterPlotandExplore_SeuratTools/workflow-seurat-filter-plot-explore
Launch in Tutorial Mode
question
galaxy-download Download
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
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