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

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

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:training
name:transcriptomics

Features
Tutorial
Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00187
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
barcode_tsv
genes_tsv
matrix_mtx
output_h5
X
out_file
out_tab
out_file
Gene Symbol Count Matrix
output
out_rds
out_rds
EBI SCXA Data Retrieval
ℹ️ Input Dataset
Single cell metadata
Scanpy Read10x
Inspect AnnData
Transpose
annotateMyIDs
🛠️ Subworkflow
1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes
Construct Expression Set Object
Manipulate Expression Set Object
Manipulate Expression Set Object
Output
Scanpy Read10x on input dataset(s): anndata
Output
annotateMyIDs on input dataset(s): Annotated IDs
Output
Construct Expression Set Object on input dataset(s): RData ESet Object
Output
Construct Expression Set Object on input dataset(s): General Info
Output
Manipulate Expression Set Object on input dataset(s): ExpressionSet Object

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
  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-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