Music Stage 4 - Compute metrics
1.0

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 Mendonça, Saskia Hiltemann, Morgan Howells, Björn Grüning, Wendi Bacon

Grants(s): DASH UK

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Cell Proportions #main/Cell Proportions Tabular dataset with row and column headers Rows = cell types Columns = ACTUAL followed by INFERRED Numbers = cell proportions
  • File

Steps

ID Name Description
1 Compute mean toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
2 Compute squared error This computes (actual-expected)^2 toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
3 Remove duplicate Remove beginning1
4 Cut RMSE column Takes the (actual-inferred)^2 column alone Cut1
5 Paste Paste1
6 Average error values toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
7 Add mean column toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
8 Square root error Finally we take the square root of the number to get the RSME toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
9 Compute differences toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
10 Cut Cut1
11 Sum rows toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0
12 Transpose toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.8+galaxy1
13 Final Pearson correlation toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1
14 Cut Pearson column Cut1

Outputs

ID Name Description Type
Pearson Correlation #main/Pearson Correlation n/a
  • File
Squared Error #main/Squared Error n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:59 by GTN Bot

Added/updated 4 files


Open master db02976
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Created: 2nd Jun 2025 at 10:58

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