Workflow Type: Galaxy
Open
This workflow creates bulk ESet objects from uploaded raw matrix & metadata files
Associated Tutorial
This workflows is part of the tutorial MuSiC-Deconvolution: Data generation | bulk | ESet, available in the GTN
Features
- Uses subworkflows
Thanks to...
Tutorial Author(s): Wendi Bacon, Mehmet Tekman
Tutorial Contributor(s): Marisa Loach
Workflow Author(s): Wendi Bacon, Mehmet Tekman
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 |
|
_anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
_anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
_anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
_anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
_anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
_anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
_anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
_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
1.0 (earliest) Created 25th Jun 2024 at 11:13 by Helena Rasche
Added/updated 4 files
Open
master
4ea4a01
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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Activity
Views: 142 Downloads: 50
Created: 25th Jun 2024 at 11:13
Last updated: 25th Jun 2024 at 11:13
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
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