MuSiC-Deconvolution: Data generation | bulk | ESet
1.0

Workflow Type: Galaxy

This 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

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

gtn star logo followed by the word workflows

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 2nd Jun 2025 at 10:57 by GTN Bot

Added/updated 4 files


Open master 85e19e6
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Created: 2nd Jun 2025 at 10:57

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