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

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Workflow Type: Galaxy

This workflow creates an ESet object from scRNA metadata file and EBI SCXA retrieveal

Associated Tutorial

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/1261?version=1

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

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

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