Monocle3 workflow

single-cell-scrna-case_monocle3-trajectories/galaxy-workflow-monocle3-workflow

Author(s)

version Version
1
last_modification Last updated
Nov 18, 2022
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
name:trajectory_analysis
name:transcriptomics
name:scRNA-seq

Features

Tutorial
hands_on Inferring single cell trajectories with Monocle3
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00200
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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

Tool Links
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_create/monocle3_create/0.1.4+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_diffexp/monocle3_diffExp/0.1.4+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_learngraph/monocle3_learnGraph/0.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_ordercells/monocle3_orderCells/0.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_partition/monocle3_partition/0.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_plotcells/monocle3_plotCells/0.1.5+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_preprocess/monocle3_preprocess/0.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_reducedim/monocle3_reduceDim/0.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/monocle3_topmarkers/monocle3_topmarkers/0.1.5+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
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