Subclustering
Version 1

Workflow Type: Galaxy
Stable

This workflow was built for the 2024 Bioinformatics Bootcamp at The Open University. It is meant to occur after the (universal) Filter, plot and explore tutorial to allow analysis of a single cluster.

Inputs

ID Name Description Type
Filtered but unprocessed AnnData Object Filtered but unprocessed AnnData Object n/a
  • File
Final object - including louvain annotation Final object - including louvain annotation n/a
  • File
Number of louvain cluster to investigate Number of louvain cluster to investigate Put here the cluster number you would like to investigate
  • string
Observation of interest-1 Observation of interest-1 Observation category should be in the metadata of the sample, such as genotype
  • string

Steps

ID Name Description
4 Add louvain metadata to unprocessed object toolshed.g2.bx.psu.edu/repos/ebi-gxa/anndata_ops/anndata_ops/1.8.1+galaxy93
5 Manipulate AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_manipulate/anndata_manipulate/0.7.5+galaxy1
6 Scanpy FilterGenes toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_filter_genes/scanpy_filter_genes/1.8.1+galaxy9
7 Scanpy NormaliseData toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_normalise_data/scanpy_normalise_data/1.8.1+galaxy9
8 Scanpy FindVariableGenes toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_variable_genes/scanpy_find_variable_genes/1.8.1+galaxy9
9 Scanpy ScaleData toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_scale_data/scanpy_scale_data/1.8.1+galaxy9
10 Scanpy RunPCA toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_pca/scanpy_run_pca/1.8.1+galaxy9
11 Plot toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1
12 Scanpy ComputeGraph toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_compute_graph/scanpy_compute_graph/1.8.1+galaxy9
13 Scanpy RunTSNE toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_run_tsne/scanpy_run_tsne/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 FindMarkers toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9
17 FindMarkers by Cluster toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_find_markers/scanpy_find_markers/1.8.1+galaxy9
18 Inspect AnnData toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.3+galaxy0
19 UMAP Plot by Obs-1 toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
20 PCA Plot by Obs-1 toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
21 tSNE Plot by Obs-1 toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
22 PCA Plot toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
23 tSNE Plot toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
24 UMAP Plot toolshed.g2.bx.psu.edu/repos/ebi-gxa/scanpy_plot_embed/scanpy_plot_embed/1.8.1+galaxy9
25 Obs-1 Marker List join1
26 Cluster Marker Gene List join1

Outputs

ID Name Description Type
out_png out_png n/a
  • File
output_h5ad output_h5ad n/a
  • File
UMAP Plot by Obs-1 UMAP Plot by Obs-1 n/a
  • File
PCA Plot by Obs-1 PCA Plot by Obs-1 n/a
  • File
tSNE Plot by Obs-1 tSNE Plot by Obs-1 n/a
  • File
PCA Plot PCA Plot n/a
  • File
tSNE Plot tSNE Plot n/a
  • File
UMAP Plot UMAP Plot n/a
  • File
Obs-1 Marker Gene List Obs-1 Marker Gene List n/a
  • File
Cluster Marker Gene List Cluster Marker Gene List n/a
  • File

Version History

Version 1 (earliest) Created 13th May 2025 at 11:21 by Diana Chiang Jurado

Initial commit


Open master 9944955
help Creators and Submitter
Creator
  • Wendi Bacon
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The Open University

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Views: 39   Downloads: 7   Runs: 0

Created: 13th May 2025 at 11:21

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