Music Stage 4 - Compute metrics 1.0
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This workflows is part of the tutorial Evaluating Reference Data for Bulk RNA Deconvolution, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
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
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 |
|
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 |
|
| Squared Error | #main/Squared Error | n/a |
|
Version History
master
Creators and Submitter
Views: 48 Downloads: 6 Runs: 0
Created: 2nd Jun 2025 at 10:58
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