MuSiC-Deconvolution: Data generation | sc | matrix + ESet 1.0
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Run on GalaxyThis workflow creates an ESet object from scRNA metadata file and EBI SCXA retrieveal
Associated Tutorial
This workflows is part of the tutorial Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution, available in the GTN
Features
- Uses subworkflows
Thanks to...
Workflow Author(s): Wendi Bacon, Mehmet Tekman
Tutorial Author(s): Wendi Bacon, Mehmet Tekman
Tutorial Contributor(s): Marisa Loach, Mehmet Tekman, Saskia Hiltemann, Wendi Bacon, Helena Rasche, Pablo Moreno, Julia Jakiela, Pavankumar Videm
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Single cell metadata | Single cell metadata | This should be output from the MuSiC Deconvolution | Data generation | sc | metadata workflow |
|
Steps
| ID | Name | Description |
|---|---|---|
| 0 | EBI SCXA Data Retrieval | toolshed.g2.bx.psu.edu/repos/ebi-gxa/retrieve_scxa/retrieve_scxa/v0.0.2+galaxy2 |
| 2 | Scanpy Read10x | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_read_10x/scanpy_read_10x/1.8.1+galaxy0 |
| 3 | Inspect AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1 |
| 4 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.1.0+galaxy2 |
| 5 | annotateMyIDs | toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1 |
| 6 | 1st step removed - Convert from Ensembl to GeneSymbol, summing duplicate genes | 171553 |
| 7 | Construct Expression Set Object | toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4 |
| 8 | Manipulate Expression Set Object | toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4 |
| 9 | Manipulate Expression Set Object | toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | _anonymous_output_1 | n/a |
|
| _anonymous_output_2 | _anonymous_output_2 | n/a |
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| _anonymous_output_3 | _anonymous_output_3 | n/a |
|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| Scanpy Read10x on input dataset(s): anndata | Scanpy Read10x on input dataset(s): anndata | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
|
| _anonymous_output_6 | _anonymous_output_6 | n/a |
|
| annotateMyIDs on input dataset(s): Annotated IDs | annotateMyIDs on input dataset(s): Annotated IDs | n/a |
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| _anonymous_output_7 | _anonymous_output_7 | n/a |
|
| _anonymous_output_8 | _anonymous_output_8 | n/a |
|
| Construct Expression Set Object on input dataset(s): RData ESet Object | Construct Expression Set Object on input dataset(s): RData ESet Object | n/a |
|
| Construct Expression Set Object on input dataset(s): General Info | Construct Expression Set Object on input dataset(s): General Info | n/a |
|
| Manipulate Expression Set Object on input dataset(s): ExpressionSet Object | Manipulate Expression Set Object on input dataset(s): ExpressionSet Object | n/a |
|
| _anonymous_output_9 | _anonymous_output_9 | n/a |
|
Version History
master
Creators and Submitter
Views: 1220 Downloads: 169 Runs: 0
Created: 2nd Jun 2025 at 10:58
AttributionsNone
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