Final - Modeling Breast Cancer Subtypes (flexynesis only)
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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
Thanks to...
Workflow Author(s): Amirhossein Naghsh Nilchi
Tutorial Author(s): Amirhossein Naghsh Nilchi, Björn Grüning
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| clin_test | clin_test | test clinical data |
|
| clin_train | clin_train | training clinical data |
|
| cna_test | cna_test | test omics 2 data |
|
| cna_train | cna_train | training omics 2 data |
|
| gex_test | gex_test | test omics 1 data |
|
| gex_train | gex_train | training omics 1 data |
|
Steps
| ID | Name | Description |
|---|---|---|
| 6 | Flexynesis niter1 | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/1.1.10+galaxy0 |
| 7 | Flexynesis niter5 | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis/flexynesis/1.1.10+galaxy0 |
| 8 | Extract prediction table - niter1 | __EXTRACT_DATASET__ |
| 9 | Extract test embeddings - niter1 | __EXTRACT_DATASET__ |
| 10 | Extract prediction table - niter5 | __EXTRACT_DATASET__ |
| 11 | Extract test embeddings - niter5 | __EXTRACT_DATASET__ |
| 12 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy3 |
| 13 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.5+galaxy3 |
| 14 | Flexynesis plot | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_plot/flexynesis_plot/1.1.10+galaxy0 |
| 15 | UMAP plot on test embeddings | toolshed.g2.bx.psu.edu/repos/bgruening/flexynesis_plot/flexynesis_plot/1.1.10+galaxy0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| niter1 flexynesis output | niter1 flexynesis output | n/a |
|
| niter5 flexynesis output | niter5 flexynesis output | n/a |
|
| embedding plot umap - niter1 | embedding plot umap - niter1 | n/a |
|
| embedding plot umap - niter5 | embedding plot umap - niter5 | n/a |
|
Version History
master
1.0
Creators and Submitter
Views: 1978 Downloads: 299 Runs: 0
Created: 18th Aug 2025 at 14:15
Last updated: 18th May 2026 at 15:14
AttributionsNone
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Teams: Galaxy Training Network
Organizations: Galaxy
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