Music Stage 2 - Inferring cellular proportions
1.0

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Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Evaluating Reference Data for Bulk RNA Deconvolution, available in the GTN

Features

Thanks to...

Workflow Author(s): Morgan Howells

Tutorial Author(s): Morgan Howells

Tutorial Contributor(s): Carlos Chee Mendonc̀§a, Saskia Hiltemann, Morgan Howells

Grants(s): ELIXIR-UK: FAIR Data Stewardship training

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1390?version=1

Inputs

ID Name Description Type
Actuals - A #main/Actuals - A Tabular format Row & Column Headers Rows of cell types Column header "A_actual" or similar
  • array containing
    • File
Actuals - B #main/Actuals - B Tabular format Row & Column Headers Rows of cell types Column header "A_actual" or similar
  • array containing
    • File
Cell Types Label from scRNA dataset #main/Cell Types Label from scRNA dataset Example: cellType
  • string
Cell types to use from scRNA dataset #main/Cell types to use from scRNA dataset Comma list of cell types to use from scRNA dataset. Example: acinar,alpha,beta,delta,ductal,gamma
  • string
ESet Reference scRNA-seq #main/ESet Reference scRNA-seq n/a
  • array containing
    • File
Pseudobulk - A #main/Pseudobulk - A Genes are rows, with one column of values from the pseudobulk Header with 'name' of sample required
  • array containing
    • File
Pseudobulk - B #main/Pseudobulk - B Genes are rows, with one column of values from the pseudobulk Header with 'name' of sample required
  • array containing
    • File
Samples Identifer from scRNA dataset #main/Samples Identifer from scRNA dataset Example: sampleID, Individual
  • string

Steps

ID Name Description
8 Combine Matrices toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/9.3+galaxy1
9 Get phenotype names Extracts the names of the samples/runs and outputs them as columnar values toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
10 Construct Expression Set Object toolshed.g2.bx.psu.edu/repos/bgruening/music_construct_eset/music_construct_eset/0.1.1+galaxy4
11 MuSiC Deconvolution toolshed.g2.bx.psu.edu/repos/bgruening/music_deconvolution/music_deconvolution/0.1.1+galaxy4
12 Transpose inferred cell proportions toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1
13 B_inferred toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2
14 A_inferred toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2
15 B_proportions_actual-infer toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1
16 A_proportions_actual-infer toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool/1.1.1
17 B - Music Results Cut1
18 B - NNLS Results Cut1
19 A - Music Results Cut1
20 A - NNLS Results Cut1

Outputs

ID Name Description Type
A - Music Results #main/A - Music Results n/a
  • File
A - NNLS Results #main/A - NNLS Results n/a
  • File
B - Music Results #main/B - Music Results n/a
  • File
B - NNLS Results #main/B - NNLS Results n/a
  • File
MuSiC Deconvolution on input dataset(s): Proportion Matrices #main/MuSiC Deconvolution on input dataset(s): Proportion Matrices n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File

Version History

1.0 (earliest) Created 3rd Feb 2025 at 13:06 by Helena Rasche

Added/updated 4 files


Open master d895221
help Creators and Submitter
Creators
Not specified
Submitter
Tool
MuSiC Deconvolution
License
No license - no permission to use unless the owner grants a licence
Activity

Views: 23   Downloads: 9

Created: 3rd Feb 2025 at 13:06

help Attributions

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Total size: 178 KB
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