MuSiC Workflow
2.0

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Workflow Type: Galaxy

Bulk RNA Deconvolution with MuSiC

Associated Tutorial

This workflows is part of the tutorial MuSiC Workflow, available in the GTN

Thanks to...

Tutorial Author(s): Mehmet Tekman, Wendi Bacon

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1234?version=1

Inputs

ID Name Description Type
Bulk RNA Annotation Bulk RNA Annotation n/a
  • string
Bulk RNA Assay Tabular Bulk RNA Assay Tabular n/a
  • File
Cell Markers C1 Cell Markers C1 n/a
  • File
Cell Markers C2 Cell Markers C2 n/a
  • File
Cell Types List Cell Types List n/a
  • string
scRNA Assay Tabular scRNA Assay Tabular n/a
  • File
scRNA Metadata scRNA Metadata n/a
  • string
scRNA Phenotype Tabular scRNA Phenotype Tabular n/a
  • File

Steps

ID Name Description
8 Construct scRNA ESet Object toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0
9 Construct Bulk RNA ESet Object toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy0
10 Extract Cell Types toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3
11 Extract General Info toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3
12 Extract General Info (Bulk) toolshed.g2.bx.psu.edu/repos/bgruening/music_inspect_eset/music_inspect_eset/0.1.1+galaxy3
13 Music: Estimate Cell Proportions toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3
14 Music: Compute Dendrogram toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy3

Outputs

ID Name Description Type
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
_anonymous_output_9 _anonymous_output_9 n/a
  • File
_anonymous_output_10 _anonymous_output_10 n/a
  • File
Inspect Expression Set Object on input dataset(s): Inspection Result Inspect Expression Set Object on input dataset(s): Inspection Result n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
MuSiC on input dataset(s): PDF Plots MuSiC on input dataset(s): PDF Plots n/a
  • File

Version History

2.0 (earliest) Created 25th Jun 2024 at 11:13 by Helena Rasche

Added/updated 4 files


Open master cfe5912
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tool
MuSiC suite: PoPMuSiC, HoTMuSiC, and SNPMuSiC
License
Creative Commons Attribution 4.0 International
Activity

Views: 139   Downloads: 49

Created: 25th Jun 2024 at 11:13

Last updated: 25th Jun 2024 at 11:13

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Total size: 111 KB
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