MuSiC-Deconvolution: Data generation | sc | matrix + ESet

single-cell-bulk-music-2-preparescref/sc-matrix

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

Features
Tutorial
hands_on Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00187
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["EBI SCXA Data Retrieval"];
  1["ℹ️ Input Dataset\nSingle cell metadata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Scanpy Read10x"];
  0 -->|barcode_tsv| 2;
  0 -->|genes_tsv| 2;
  0 -->|matrix_mtx| 2;
  6bd01730-f0b5-4824-8cfc-d563cc9c7f7d["Output\nScanpy Read10x on input dataset(s): anndata"];
  2 --> 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d;
  style 6bd01730-f0b5-4824-8cfc-d563cc9c7f7d stroke:#2c3143,stroke-width:4px;
  3["Inspect AnnData"];
  2 -->|output_h5| 3;
  4["Transpose"];
  3 -->|X| 4;
  5["annotateMyIDs"];
  4 -->|out_file| 5;
  c39c7d69-550e-4b54-a412-317b599c5e55["Output\nannotateMyIDs on input dataset(s): Annotated IDs"];
  5 --> c39c7d69-550e-4b54-a412-317b599c5e55;
  style c39c7d69-550e-4b54-a412-317b599c5e55 stroke:#2c3143,stroke-width:4px;
  6["🛠️ Subworkflow\n1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes"];
  style 6 fill:#edd,stroke:#900,stroke-width:4px;
  5 -->|out_tab| 6;
  4 -->|out_file| 6;
  7["Construct Expression Set Object"];
  6 -->|Gene Symbol Count Matrix| 7;
  1 -->|output| 7;
  e8c91df0-4e6c-4eb2-9807-c2679b494958["Output\nConstruct Expression Set Object on input dataset(s): RData ESet Object"];
  7 --> e8c91df0-4e6c-4eb2-9807-c2679b494958;
  style e8c91df0-4e6c-4eb2-9807-c2679b494958 stroke:#2c3143,stroke-width:4px;
  2912d09b-b178-4035-b7c8-7038392e2bf2["Output\nConstruct Expression Set Object on input dataset(s): General Info"];
  7 --> 2912d09b-b178-4035-b7c8-7038392e2bf2;
  style 2912d09b-b178-4035-b7c8-7038392e2bf2 stroke:#2c3143,stroke-width:4px;
  8["Manipulate Expression Set Object"];
  7 -->|out_rds| 8;
  08de92d8-32fe-4b47-9038-298cdd13fac5["Output\nManipulate Expression Set Object on input dataset(s): ExpressionSet Object"];
  8 --> 08de92d8-32fe-4b47-9038-298cdd13fac5;
  style 08de92d8-32fe-4b47-9038-298cdd13fac5 stroke:#2c3143,stroke-width:4px;
  9["Manipulate Expression Set Object"];
  7 -->|out_rds| 9;

Inputs

Input Label
Input dataset Single cell metadata

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 EBI SCXA Data Retrieval
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0 Scanpy Read10x
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 Inspect AnnData
toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2 Transpose
toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1 annotateMyIDs
171553 1st step removed - 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/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 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/datamash_transpose/datamash_transpose/1.1.0+galaxy2 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
  • 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 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-2-preparescref/workflows/sc_matrix.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