MuSiC-Deconvolution: Data generation | sc | matrix + ESet
1.0

Workflow Type: Galaxy

This 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

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

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Inputs

ID Name Description Type
Single cell metadata Single cell metadata This should be output from the MuSiC Deconvolution | Data generation | sc | metadata workflow
  • File

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
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
Scanpy Read10x on input dataset(s): anndata Scanpy Read10x on input dataset(s): anndata n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
annotateMyIDs on input dataset(s): Annotated IDs annotateMyIDs on input dataset(s): Annotated IDs n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_8 _anonymous_output_8 n/a
  • File
Construct Expression Set Object on input dataset(s): RData ESet Object Construct Expression Set Object on input dataset(s): RData ESet Object n/a
  • File
Construct Expression Set Object on input dataset(s): General Info Construct Expression Set Object on input dataset(s): General Info n/a
  • File
Manipulate Expression Set Object on input dataset(s): ExpressionSet Object Manipulate Expression Set Object on input dataset(s): ExpressionSet Object n/a
  • File
_anonymous_output_9 _anonymous_output_9 n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:58 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:58

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