MuSiC-Deconvolution: Data generation | bulk | ESet 1.0
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Run on GalaxyThis workflow creates bulk ESet objects from uploaded raw matrix & metadata files
Associated Tutorial
This workflows is part of the tutorial Bulk matrix to ESet | Creating the bulk RNA-seq 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
Steps
| ID | Name | Description |
|---|---|---|
| 0 | Expression matrix | While the EBI data has the gene symbols in it, these are duplicated, so we still need to thin down the duplications. toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
| 1 | Metadata | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 |
| 2 | annotateMyIDs | Convert EnsemblID to Gene Symbol. Note that some EnsemblID's have multiple Gene Symbols. toolshed.g2.bx.psu.edu/repos/iuc/annotatemyids/annotatemyids/3.14.0+galaxy1 |
| 3 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.2 |
| 4 | Copy of Convert from Ensembl to GeneSymbol, summing duplicate genes | 171557 |
| 5 | Construct Expression Set Object | toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4 |
| 6 | Manipulate Expression Set Object | toolshed.g2.bx.psu.edu/repos/bgruening/music_manipulate_eset/music_manipulate_eset/0.1.1+galaxy4 |
| 7 | 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 |
|---|---|---|---|
| Manipulate Expression Set Object on input dataset(s): ExpressionSet Object | #main/Manipulate Expression Set Object on input dataset(s): ExpressionSet Object | n/a |
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| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
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| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
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| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
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| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
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| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
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| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
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| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
| annotateMyIDs on input dataset(s): Annotated IDs | #main/annotateMyIDs on input dataset(s): Annotated IDs | n/a |
|
Version History
master
Creators and Submitter
Views: 48 Downloads: 4 Runs: 0
Created: 2nd Jun 2025 at 10:57
AttributionsNone
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