Scanpy Parameter Iterator workflow full (imported from URL)
Visit source
Download RO-CrateAssociated Tutorial
This workflows is part of the tutorial Scanpy Parameter Iterator workflow full (imported from URL), available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): Julia Jakiela
Tutorial Contributor(s): Wendi Bacon
Workflow Author(s): Julia Jakiela
Funder(s): EOSC-Life
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Scanpy ComputeGraph on data X and data Y: Graph object AnnData | #main/Scanpy ComputeGraph on data X and data Y: Graph object AnnData | n/a |
|
| Scanpy RunPCA: AnnData object | #main/Scanpy RunPCA: AnnData object | n/a |
|
| Scanpy RunUMAP on data X: UMAP object AnnData | #main/Scanpy RunUMAP on data X: UMAP object AnnData | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | ParameterIterator n-neighbors | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9 |
| 3 | ParameterIterator perplexity | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9 |
| 5 | ParameterIterator resolution | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_parameter_iterator/scanpy_parameter_iterator/0.0.1+galaxy9 |
| 6 | Scanpy ComputeGraph | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9 |
| 7 | Scanpy RunTSNE | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9 |
| 8 | Scanpy FindCluster | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9 |
| 9 | Scanpy RunTSNE | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/1.8.1+galaxy9 |
| 10 | Scanpy RunUMAP | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/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 | Scanpy RunUMAP | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_umap/scanpy_run_umap/1.8.1+galaxy9 |
| 15 | Scanpy FindCluster | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9 |
| 16 | Scanpy FindCluster | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_cluster/scanpy_find_cluster/1.8.1+galaxy9 |
| 17 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
| 18 | Scanpy PlotEmbed | toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Scanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours) | #main/Scanpy ComputeGraph on collection X: Graph object AnnData (n-neighbours) | n/a |
|
| Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours) | #main/Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours) | n/a |
|
| Scanpy FindCluster on collection X: Clusters AnnData (perplexity) | #main/Scanpy FindCluster on collection X: Clusters AnnData (perplexity) | n/a |
|
| Scanpy FindCluster on collection X: Clusters AnnData (resolution) | #main/Scanpy FindCluster on collection X: Clusters AnnData (resolution) | n/a |
|
| Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours) | #main/Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours) | n/a |
|
| Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity) | #main/Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity) | n/a |
|
| Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours) | #main/Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours) | n/a |
|
| Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity) | #main/Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity) | n/a |
|
| n-neighbors_plots | #main/n-neighbors_plots | n/a |
|
| perplexity_plots | #main/perplexity_plots | n/a |
|
| resolution_pca_plots | #main/resolution_pca_plots | n/a |
|
| resolution_tsne_plots | #main/resolution_tsne_plots | n/a |
|
| resolution_umap_plots | #main/resolution_umap_plots | n/a |
|
Version History
1.0 (latest) Created 16th Jul 2024 at 14:10 by Helena Rasche
Added/updated 4 files
Open
master9d5e8c3
2.0 (earliest) Created 25th Jun 2024 at 11:14 by Helena Rasche
Added/updated 4 files
Frozen
2.0f11d1e9
Creators and Submitter
Views: 591 Downloads: 181
Created: 25th Jun 2024 at 11:14
Last updated: 25th Jun 2024 at 11:14
AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Space: General
Public web page: https://galaxy.training
