Scanpy Parameter Iterator workflow full (imported from URL)
1.0

Workflow Type: Galaxy

Associated Tutorial

This workflows is part of the tutorial Scanpy Parameter Iterator, available in the GTN

Features

Thanks to...

Workflow Author(s): Julia Jakiela

Tutorial Author(s): Julia Jakiela

Tutorial Contributor(s): Wendi Bacon, Helena Rasche, Julia Jakiela, Saskia Hiltemann, Mehmet Tekman, Matthias Bernt, Björn Grüning

Grants(s): EOSC-Life

gtn star logo followed by the word workflows

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
  • File
Scanpy RunPCA: AnnData object #main/Scanpy RunPCA: AnnData object n/a
  • File
Scanpy RunUMAP on data X: UMAP object AnnData #main/Scanpy RunUMAP on data X: UMAP object AnnData n/a
  • File

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
  • File
Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours) #main/Scanpy FindCluster on collection X: Clusters AnnData (n-neighbours) n/a
  • File
Scanpy FindCluster on collection X: Clusters AnnData (perplexity) #main/Scanpy FindCluster on collection X: Clusters AnnData (perplexity) n/a
  • File
Scanpy FindCluster on collection X: Clusters AnnData (resolution) #main/Scanpy FindCluster on collection X: Clusters AnnData (resolution) n/a
  • File
Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours) #main/Scanpy RunTSNE on collection X: tSNE object AnnData (n-neighbours) n/a
  • File
Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity) #main/Scanpy RunTSNE on collection X: tSNE object AnnData (perplexity) n/a
  • File
Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours) #main/Scanpy RunUMAP on collection X: UMAP object AnnData (n-neighbours) n/a
  • File
Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity) #main/Scanpy RunUMAP on collection X: UMAP object AnnData (perplexity) n/a
  • File
n-neighbors_plots #main/n-neighbors_plots n/a
  • File
perplexity_plots #main/perplexity_plots n/a
  • File
resolution_pca_plots #main/resolution_pca_plots n/a
  • File
resolution_tsne_plots #main/resolution_tsne_plots n/a
  • File
resolution_umap_plots #main/resolution_umap_plots n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:56 by GTN Bot

Added/updated 4 files


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Created: 2nd Jun 2025 at 10:56

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