MuSiC-Deconvolution: Data generation | bulk | ESet

single-cell-bulk-music-3-preparebulk/bulk-eset

Author(s)
Wendi Bacon, Mehmet Tekman
Version
1
Last updated
Jan 20, 2023
License
None Specified, defaults to CC-BY-4.0
Tags
name:singlecell
name:transcriptomics
name:training

Features
Tutorial
Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00189
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["Expression matrix"];
  1["Metadata"];
  2["annotateMyIDs"];
  0 -->|output_tabular| 2;
  8415bac0-6beb-467d-a0fa-fb6465987ff7["Output\nannotateMyIDs on input dataset(s): Annotated IDs"];
  2 --> 8415bac0-6beb-467d-a0fa-fb6465987ff7;
  style 8415bac0-6beb-467d-a0fa-fb6465987ff7 stroke:#2c3143,stroke-width:4px;
  3["Regex Find And Replace"];
  1 -->|output| 3;
  4["🛠️ Subworkflow\nCopy of Convert from Ensembl to GeneSymbol, summing duplicate genes"];
  style 4 fill:#edd,stroke:#900,stroke-width:4px;
  2 -->|out_tab| 4;
  0 -->|output_tabular| 4;
  5["Construct Expression Set Object"];
  4 -->|Gene Symbol Count Matrix| 5;
  3 -->|out_file1| 5;
  6["Manipulate Expression Set Object"];
  5 -->|out_rds| 6;
  88196d0b-7254-4794-b08a-5409f19c8323["Output\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object"];
  6 --> 88196d0b-7254-4794-b08a-5409f19c8323;
  style 88196d0b-7254-4794-b08a-5409f19c8323 stroke:#2c3143,stroke-width:4px;
  7["Manipulate Expression Set Object"];
  5 -->|out_rds| 7;

Inputs

Input Label

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 Remove columns Expression matrix
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 Advanced Cut Metadata
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1 annotateMyIDs
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2 Regex Find And Replace
171557 Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes
toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4 Construct Expression Set Object
toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4 Manipulate Expression Set Object
toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4 Manipulate Expression Set Object

Tools

Tool Links
sort1
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_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+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 9a561b375 2022-11-27 20:30:42 update workflows

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/bulk-music-3-preparebulk/workflows/bulk_ESet.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