MuSiC: Deconvolution

single-cell-bulk-music/main-workflow

Author(s)
Morgan Howells
Version
3
Last updated
Feb 10, 2025
License
MIT
Tags
transcriptomics
single-cell

Features
Tutorial
Bulk RNA Deconvolution with MuSiC
Other workflows associated with this material
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00186
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nscRNA Assay Tabular"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nscRNA Phenotype Tabular"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nBulk RNA Assay Tabular"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nBulk RNA Phenotype Tabular"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Parameter\nCell Types List"];
  style 4 fill:#ded,stroke:#393,stroke-width:4px;
  5["Construct Expression Set Object"];
  0 -->|output| 5;
  1 -->|output| 5;
  6["Construct Expression Set Object"];
  2 -->|output| 6;
  3 -->|output| 6;
  7["Extract Cell Types"];
  5 -->|out_rds| 7;
  8["Extract General Info scrna"];
  5 -->|out_rds| 8;
  9["Extract General Info Bulk"];
  6 -->|out_rds| 9;
  10["Music: Estimate Cell Proportions"];
  6 -->|out_rds| 10;
  4 -->|output| 10;
  5 -->|out_rds| 10;

Inputs

Input Label
Input dataset scRNA Assay Tabular
Input dataset scRNA Phenotype Tabular
Input dataset Bulk RNA Assay Tabular
Input dataset Bulk RNA Phenotype Tabular
Input parameter Cell Types List

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy4 Inspect Expression Set Object Extract Cell Types
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy4 Inspect Expression Set Object Extract General Info (Bulk)
toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4 MuSiC Deconvolution Music: Estimate Cell Proportions

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy4 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 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
4 41b51b9ee 2025-02-10 14:16:31 rename main workflow
3 34c646737 2024-12-12 11:46:51 add new workflows
2 e2453dfb5 2023-05-15 14:00:47 use full tool ID
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/bulk-music/workflows/main_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