Final - Modeling Breast Cancer Subtypes + TABPFN 1.0
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Run on GalaxyThis WF applies Flexynesis on BRCA data from Metabric for a classification task
Associated Tutorial
This workflows is part of the tutorial Modeling Breast Cancer Subtypes with Flexynesis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
- Uses Galaxy Workflow Comments
- Uses subworkflows
Thanks to...
Workflow Author(s): Amirhossein Naghsh Nilchi
Tutorial Author(s): Amirhossein Naghsh Nilchi, Björn Grüning
Steps
| ID | Name | Description |
|---|---|---|
| 8 | Flexynesis niter1 | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/0.2.20+galaxy3 |
| 9 | Flexynesis niter5 | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/0.2.20+galaxy3 |
| 10 | Prepare data for TABPFN | n/a |
| 11 | Prepare data for TABPFN | n/a |
| 12 | Extract prediction table - niter1 | __EXTRACT_DATASET__ |
| 13 | Extract test embeddings - niter1 | __EXTRACT_DATASET__ |
| 14 | Extract prediction table - niter5 | __EXTRACT_DATASET__ |
| 15 | Extract test embeddings - niter5 | __EXTRACT_DATASET__ |
| 16 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 17 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 18 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 19 | Pick parameter value | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 20 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 |
| 21 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy2 |
| 22 | PR cruve plot - flexynesis | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_plot/flexynesis_plot/0.2.20+galaxy3 |
| 23 | TABPFN on gex data 2 | toolshed.g2.bx.psu.edu/repos/bgruening/tabpfn/tabpfn/2.0.9+galaxy0 |
| 24 | TABPFN on cna data 2 | toolshed.g2.bx.psu.edu/repos/bgruening/tabpfn/tabpfn/2.0.9+galaxy0 |
| 25 | Flexynesis plot | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_plot/flexynesis_plot/0.2.20+galaxy3 |
| 26 | UMAP plot on test embeddings | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_plot/flexynesis_plot/0.2.20+galaxy3 |
Version History
master
Creators and Submitter
Views: 596 Downloads: 100 Runs: 0
Created: 18th Aug 2025 at 14:15
AttributionsNone
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