Monocle3 workflow
single-cell-scrna-case_monocle3-trajectories/galaxy-workflow-monocle3-workflow
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flowchart TD 0["ℹ️ Input Dataset\nExpression matrix input"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nCell annotations input"]; style 1 stroke:#2c3143,stroke-width:4px; 2["ℹ️ Input Dataset\nGene annotations input"]; style 2 stroke:#2c3143,stroke-width:4px; 3["Monocle3 create"]; 1 -->|output| 3; 0 -->|output| 3; 2 -->|output| 3; 30db218d-f9e5-426d-ac9b-7823743ab5fb["Output\nMonocle3 create on input dataset(s): cds3"]; 3 --> 30db218d-f9e5-426d-ac9b-7823743ab5fb; style 30db218d-f9e5-426d-ac9b-7823743ab5fb stroke:#2c3143,stroke-width:4px; 4["Monocle3 preprocess"]; 3 -->|output_rds| 4; 38996ee0-0c00-4a01-ad18-f2e505eaf780["Output\nMonocle3 preprocess on input dataset(s): cds3"]; 4 --> 38996ee0-0c00-4a01-ad18-f2e505eaf780; style 38996ee0-0c00-4a01-ad18-f2e505eaf780 stroke:#2c3143,stroke-width:4px; 5["Monocle3 reduceDim"]; 4 -->|output_rds| 5; 21edf68f-72df-457d-aad7-c5fc5afa2b6b["Output\nMonocle3 reduceDim on input dataset(s): cds3"]; 5 --> 21edf68f-72df-457d-aad7-c5fc5afa2b6b; style 21edf68f-72df-457d-aad7-c5fc5afa2b6b stroke:#2c3143,stroke-width:4px; 6["Monocle3 partition"]; 5 -->|output_rds| 6; fdb0e520-27c4-43a0-8f27-a25832a0816d["Output\nMonocle3 partition on input dataset(s): cds3"]; 6 --> fdb0e520-27c4-43a0-8f27-a25832a0816d; style fdb0e520-27c4-43a0-8f27-a25832a0816d stroke:#2c3143,stroke-width:4px; 7["Plot cell type"]; 5 -->|output_rds| 7; 5e309658-e20f-4da1-8841-818f16fa8f01["Output\nCell type plot"]; 7 --> 5e309658-e20f-4da1-8841-818f16fa8f01; style 5e309658-e20f-4da1-8841-818f16fa8f01 stroke:#2c3143,stroke-width:4px; 8["Plot genotype"]; 5 -->|output_rds| 8; aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4["Output\nGenotype plot"]; 8 --> aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4; style aca3b2c0-2d3b-4a4e-8732-cf6ddc7844a4 stroke:#2c3143,stroke-width:4px; 9["Plot batch"]; 5 -->|output_rds| 9; c8eec2e4-1a64-47bb-812b-4002968c57c8["Output\nBatch plot"]; 9 --> c8eec2e4-1a64-47bb-812b-4002968c57c8; style c8eec2e4-1a64-47bb-812b-4002968c57c8 stroke:#2c3143,stroke-width:4px; 10["Plot sex"]; 5 -->|output_rds| 10; c75954dd-34d5-4a20-bcf3-e5cd92d74885["Output\nSex plot"]; 10 --> c75954dd-34d5-4a20-bcf3-e5cd92d74885; style c75954dd-34d5-4a20-bcf3-e5cd92d74885 stroke:#2c3143,stroke-width:4px; 11["Monocle3 top markers"]; 6 -->|output_rds| 11; 12["Plot genes"]; 6 -->|output_rds| 12; f91c22a3-8c6d-432a-92c5-cb010115fa86["Output\nGene expression plot"]; 12 --> f91c22a3-8c6d-432a-92c5-cb010115fa86; style f91c22a3-8c6d-432a-92c5-cb010115fa86 stroke:#2c3143,stroke-width:4px; 13["Plot partition"]; 6 -->|output_rds| 13; f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d["Output\nPartition plot"]; 13 --> f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d; style f4c5f89b-edd7-489c-b4a2-a7a3e7d6a89d stroke:#2c3143,stroke-width:4px; 14["Plot cluster"]; 6 -->|output_rds| 14; a2c1a628-d79d-4e37-ad33-de92033021a8["Output\nCluster plot"]; 14 --> a2c1a628-d79d-4e37-ad33-de92033021a8; style a2c1a628-d79d-4e37-ad33-de92033021a8 stroke:#2c3143,stroke-width:4px; 15["Monocle3 learnGraph"]; 6 -->|output_rds| 15; ed2003aa-4680-409f-8d79-e79b878a786c["Output\nMonocle3 learnGraph on input dataset(s): cds3"]; 15 --> ed2003aa-4680-409f-8d79-e79b878a786c; style ed2003aa-4680-409f-8d79-e79b878a786c stroke:#2c3143,stroke-width:4px; 16["Plot learned trajectory"]; 15 -->|output_rds| 16; 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d["Output\nCell types & learned trajectory path plot"]; 16 --> 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d; style 6fa555f1-b4f2-4e5d-bce1-ed462d8e056d stroke:#2c3143,stroke-width:4px; 17["Monocle3 orderCells"]; 15 -->|output_rds| 17; 96d10412-3d7f-4970-b541-6f4367fa3f37["Output\nMonocle3 orderCells on input dataset(s): cds3"]; 17 --> 96d10412-3d7f-4970-b541-6f4367fa3f37; style 96d10412-3d7f-4970-b541-6f4367fa3f37 stroke:#2c3143,stroke-width:4px; 18["Monocle3 diffExp"]; 17 -->|output_rds| 18; db1dc457-2d6e-47cc-b7ce-d0a4d23e9498["Output\nDifferential expression of genes - table"]; 18 --> db1dc457-2d6e-47cc-b7ce-d0a4d23e9498; style db1dc457-2d6e-47cc-b7ce-d0a4d23e9498 stroke:#2c3143,stroke-width:4px; 19["Plot pseudotime"]; 17 -->|output_rds| 19; d1b3efd2-0a81-4dad-8652-589c2678fbaa["Output\nPseudotime plot"]; 19 --> d1b3efd2-0a81-4dad-8652-589c2678fbaa; style d1b3efd2-0a81-4dad-8652-589c2678fbaa stroke:#2c3143,stroke-width:4px;
Inputs
Input | Label |
---|---|
Input dataset | Expression matrix input |
Input dataset | Cell annotations input |
Input dataset | Gene annotations input |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2 | Monocle3 create | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_preprocess/monocle3_preprocess/0.1.4+galaxy0 | Monocle3 preprocess | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim/0.1.4+galaxy0 | Monocle3 reduceDim | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_partition/monocle3_partition/0.1.4+galaxy0 | Monocle3 partition | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot cell type |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot genotype |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot batch |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot sex |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers/0.1.5+galaxy0 | Monocle3 top markers | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot genes |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot partition |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot cluster |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0 | Monocle3 learnGraph | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot learned trajectory |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0 | Monocle3 orderCells | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1 | Monocle3 diffExp | |
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 | Monocle3 plotCells | Plot pseudotime |
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_monocle3-trajectories/workflows/Galaxy-Workflow-Monocle3_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