Monocle3 workflow

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

Author(s)

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

Features
Tutorial
Inferring single cell trajectories with Monocle3
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00200
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
output_rds
ℹ️ Input Dataset
Expression matrix input
ℹ️ Input Dataset
Cell annotations input
ℹ️ Input Dataset
Gene annotations input
Monocle3 create
Monocle3 preprocess
Monocle3 reduceDim
Monocle3 partition
Plot cell type
Plot genotype
Plot batch
Plot sex
Monocle3 top markers
Plot genes
Plot partition
Plot cluster
Monocle3 learnGraph
Plot learned trajectory
Monocle3 orderCells
Monocle3 diffExp
Plot pseudotime
Output
Monocle3 create on input dataset(s): cds3
Output
Monocle3 preprocess on input dataset(s): cds3
Output
Monocle3 reduceDim on input dataset(s): cds3
Output
Monocle3 partition on input dataset(s): cds3
Output
Cell type plot
Output
Genotype plot
Output
Batch plot
Output
Sex plot
Output
Gene expression plot
Output
Partition plot
Output
Cluster plot
Output
Monocle3 learnGraph on input dataset(s): cds3
Output
Cell types & learned trajectory path plot
Output
Monocle3 orderCells on input dataset(s): cds3
Output
Differential expression of genes - table
Output
Pseudotime plot

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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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