CS3_Filter, Plot and Explore Single-cell RNA-seq Data
single-cell-scrna-case_basic-pipeline/cs3-filter--plot-and-explore-single-cell-rna-seq-data
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21["Scanpy NormaliseData"]; 18 -->|output_h5ad| 21; 22["Scanpy FindVariableGenes"]; 21 -->|output_h5ad| 22; 23["Scanpy ScaleData"]; 22 -->|output_h5ad| 23; 24["Scanpy RunPCA"]; 23 -->|output_h5ad| 24; 25["Plot"]; 24 -->|output_h5ad| 25; 993dea99-990f-460a-beb9-46e5c97ee898["Output\nPCA Variance"]; 25 --> 993dea99-990f-460a-beb9-46e5c97ee898; style 993dea99-990f-460a-beb9-46e5c97ee898 stroke:#2c3143,stroke-width:4px; 26["Scanpy ComputeGraph"]; 24 -->|output_h5ad| 26; 27["Scanpy RunTSNE"]; 26 -->|output_h5ad| 27; 28["Scanpy RunUMAP"]; 27 -->|output_h5ad| 28; 29["Scanpy FindCluster"]; 28 -->|output_h5ad| 29; 30["Scanpy FindMarkers"]; 29 -->|output_h5ad| 30; 308b4961-4d50-442b-9bca-bbb1992426ba["Output\nMarkers - cluster"]; 30 --> 308b4961-4d50-442b-9bca-bbb1992426ba; style 308b4961-4d50-442b-9bca-bbb1992426ba stroke:#2c3143,stroke-width:4px; 035bbbce-fb57-48c8-83d5-2b0cd0376541["Output\nFinal object"]; 30 --> 035bbbce-fb57-48c8-83d5-2b0cd0376541; style 035bbbce-fb57-48c8-83d5-2b0cd0376541 stroke:#2c3143,stroke-width:4px; 31["Scanpy FindMarkers"]; 29 -->|output_h5ad| 31; 1705e219-192a-4f52-9b26-64fcbcd303ea["Output\nMarkers - genotype"]; 31 --> 1705e219-192a-4f52-9b26-64fcbcd303ea; style 1705e219-192a-4f52-9b26-64fcbcd303ea stroke:#2c3143,stroke-width:4px; 32["Scanpy PlotEmbed"]; 30 -->|output_h5ad| 32; 33["Scanpy PlotEmbed"]; 30 -->|output_h5ad| 33; 34["Manipulate AnnData"]; 30 -->|output_h5ad| 34; 35["Scanpy PlotEmbed"]; 30 -->|output_h5ad| 35; 36["Inspect AnnData"]; 30 -->|output_h5ad| 36; 37["AnnData Operations"]; 34 -->|anndata| 37; 30 -->|output_h5ad| 37; 38["Join two Datasets"]; 30 -->|output_tsv| 38; 36 -->|var| 38; 39["Join two Datasets"]; 31 -->|output_tsv| 39; 36 -->|var| 39; 40["AnnData Operations"]; 37 -->|output_h5ad| 40; a6d48df0-403f-4efc-a75f-9504a960884e["Output\nFinal cell annotated object"]; 40 --> a6d48df0-403f-4efc-a75f-9504a960884e; style a6d48df0-403f-4efc-a75f-9504a960884e stroke:#2c3143,stroke-width:4px; 41["Cut"]; 38 -->|out_file1| 41; 0ee7f9b6-b065-4e26-93df-6e6e2fe458a9["Output\nMarkers - cluster - named"]; 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Inputs
Input | Label |
---|---|
Input dataset | Mito-counted AnnData |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0 | Scanpy FilterCells | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0 | Scanpy FilterCells | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_cells/scanpy_filter_cells/1.8.1+galaxy0 | Scanpy FilterCells | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy0 | Scanpy FilterGenes | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy0 | Scanpy NormaliseData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy0 | Scanpy FindVariableGenes | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy0 | Scanpy ScaleData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy0 | Scanpy RunPCA | |
toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1 | Plot | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy1 | Scanpy ComputeGraph | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy1 | Scanpy RunTSNE | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy0 | Scanpy RunUMAP | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy0 | Scanpy FindCluster | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0 | Scanpy FindMarkers | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy0 | Scanpy FindMarkers | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 | Scanpy PlotEmbed | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 | Scanpy PlotEmbed | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 | Manipulate AnnData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 | Scanpy PlotEmbed | |
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 | Inspect AnnData | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0 | AnnData Operations | |
join1 | Join two Datasets | |
join1 | Join two Datasets | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy0 | AnnData Operations | |
Cut1 | Cut | |
Cut1 | Cut | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy0 | Scanpy PlotEmbed |
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 |
---|---|---|---|
1 | 327fd2b84 | 2022-11-12 17:14:25 | Making a single cell topics |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_basic-pipeline/workflows/CS3_Filter,_Plot_and_Explore_Single-cell_RNA-seq_Data.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