Subclustering Version 1
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Workflow Type: Galaxy
Open
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 |
|
| Final object - including louvain annotation | Final object - including louvain annotation | n/a |
|
| Number of louvain cluster to investigate | Number of louvain cluster to investigate | Put here the cluster number you would like to investigate |
|
| Observation of interest-1 | Observation of interest-1 | Observation category should be in the metadata of the sample, such as genotype |
|
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 |
|
| output_h5ad | output_h5ad | n/a |
|
| UMAP Plot by Obs-1 | UMAP Plot by Obs-1 | n/a |
|
| PCA Plot by Obs-1 | PCA Plot by Obs-1 | n/a |
|
| tSNE Plot by Obs-1 | tSNE Plot by Obs-1 | n/a |
|
| PCA Plot | PCA Plot | n/a |
|
| tSNE Plot | tSNE Plot | n/a |
|
| UMAP Plot | UMAP Plot | n/a |
|
| Obs-1 Marker Gene List | Obs-1 Marker Gene List | n/a |
|
| Cluster Marker Gene List | Cluster Marker Gene List | n/a |
|
Version History
Version 1 (earliest) Created 13th May 2025 at 11:21 by Diana Chiang Jurado
Initial commit
Open
master9944955
Creators and Submitter
Activity
Views: 1666 Downloads: 217 Runs: 1
Created: 13th May 2025 at 11:21
Annotated Properties
Topic annotations
AttributionsNone
Related items
https://orcid.org/0000-0002-5857-1477
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