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 MuSiC-Deconvolution: Data generation | sc | matrix + ESet, available in the GTN

Features

Thanks to...

Tutorial Author(s): Wendi Bacon, Mehmet Tekman

Tutorial Contributor(s): Marisa Loach

Workflow Author(s): Wendi Bacon, Mehmet Tekman

gtn star logo followed by the word workflows

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 25th Jun 2024 at 11:16 by Helena Rasche

Added/updated 4 files


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Views: 403   Downloads: 104

Created: 25th Jun 2024 at 11:16

Last updated: 25th Jun 2024 at 11:16

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