MuSiC-Deconvolution: Data generation | bulk | ESet
1.0

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Workflow Type: Galaxy

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

SEEK ID: https://dev.workflowhub.eu/workflows/1230?version=1

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	File
_anonymous_output_1	#main/_anonymous_output_1	n/a	File
_anonymous_output_2	#main/_anonymous_output_2	n/a	File
_anonymous_output_3	#main/_anonymous_output_3	n/a	File
_anonymous_output_4	#main/_anonymous_output_4	n/a	File
_anonymous_output_5	#main/_anonymous_output_5	n/a	File
_anonymous_output_6	#main/_anonymous_output_6	n/a	File
_anonymous_output_7	#main/_anonymous_output_7	n/a	File
_anonymous_output_8	#main/_anonymous_output_8	n/a	File
annotateMyIDs on input dataset(s): Annotated IDs	#main/annotateMyIDs on input dataset(s): Annotated IDs	n/a	File

Version History

1.0 (earliest) Created 25th Jun 2024 at 11:13 by Helena Rasche

Added/updated 4 files

Open master 4ea4a01

Creators and Submitter

Creators

Not specified

Submitter

Helena Rasche

Discussion Channel

GTN Matrix

Tools

annotatemyids

MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC

License

Creative Commons Attribution 4.0 International

Activity

Views: 406 Downloads: 106

Created: 25th Jun 2024 at 11:13

Last updated: 25th Jun 2024 at 11:13

MuSiC-Deconvolution: Data generation | bulk | ESet 1.0