Inferring Trajectories with Scanpy Tutorial Workflow 1.0
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This workflows is part of the tutorial Inferring single cell trajectories with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Marisa Loach
Tutorial Author(s): Marisa Loach, Wendi Bacon, Julia Jakiela, Mehmet Tekman
Tutorial Contributor(s): Pavankumar Videm, Helena Rasche, Björn Grüning, Marisa Loach, Wendi Bacon, Saskia Hiltemann, Mehmet Tekman
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input Anndata | Input Anndata | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Manipulate AnnData | toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1 |
| 2 | Scanpy RunFDG | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_fdg/scanpy_run_fdg/1.8.1+galaxy9 |
| 3 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
| 4 | Scanpy DiffusionMap | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_diffmap/scanpy_run_diffmap/1.8.1+galaxy9 |
| 5 | Scanpy ComputeGraph | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9 |
| 6 | Scanpy RunFDG | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_fdg/scanpy_run_fdg/1.8.1+galaxy9 |
| 7 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
| 8 | Scanpy PAGA | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_paga/scanpy_run_paga/1.8.1+galaxy9 |
| 9 | Scanpy PlotTrajectory | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_trajectory/scanpy_plot_trajectory/1.8.1+galaxy9 |
| 10 | Scanpy RunFDG | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_fdg/scanpy_run_fdg/1.8.1+galaxy9 |
| 11 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
| 12 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
| 13 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
| 14 | Final Anndata with Trajectory and DPT | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_dpt/scanpy_run_dpt/1.8.1+galaxy9 |
| 15 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
Version History
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Views: 1152 Downloads: 172 Runs: 0
Created: 2nd Jun 2025 at 10:57
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