MuSiC-Deconvolution: Data generation | sc | matrix + ESet
Version 1

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Workflow Type: Galaxy

Galaxy workflow

SEEK ID: https://dev.workflowhub.eu/workflows/828?version=1

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 (earliest) Created 22nd Apr 2024 at 10:34 by Helena Rasche

Added/updated 3 files


Open master dd6014a
help Creators and Submitter
Creators
  • Wendi Bacon
  • Mehmet Tekman
Submitter
Tools
SCANPY
annotatemyids
MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC
License
Creative Commons Attribution 4.0 International
Activity

Views: 54

Created: 22nd Apr 2024 at 10:34

Last updated: 22nd Apr 2024 at 10:34

help Attributions

None

Total size: 51.9 KB
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