Workflow Type: Galaxy
Pseudobulk Analysis Workflow for Tutorial
Associated Tutorial
This workflows is part of the tutorial Pseudobulk Analysis with Decoupler and EdgeR, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): Diana Chiang Jurado, Pavankumar Videm
Tutorial Author(s): Diana Chiang Jurado
Tutorial Contributor(s): Pavankumar Videm, Björn Grüning, Saskia Hiltemann, Diana Chiang Jurado
Inputs
ID | Name | Description | Type |
---|---|---|---|
ncm_pdcs_subset.h5ad | ncm_pdcs_subset.h5ad | n/a |
|
Steps
ID | Name | Description |
---|---|---|
1 | Inspect AnnData Object | Retrieve general information of the AnnData object toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.10.9+galaxy1 |
2 | Filter Cell-Type | Filter pDC and/or Non_Classical_Monocyte clusters for DEG analysis. toolshed.g2.bx.psu.edu/repos/iuc/scanpy_filter/scanpy_filter/1.10.2+galaxy3 |
3 | Pseudobulk with decoupler | Generate pseudobulk counts, samples metadata, genes metadata files plus two plots to inspect the pseudobulk results. toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8 |
4 | Replace Text | replace [ --+*^]+ with _ for easier file handling toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
5 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1 |
6 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
7 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1 |
8 | Generating Contrast File | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
9 | edgeR | toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5 |
10 | Extract dataset | __EXTRACT_DATASET__ |
11 | Remove columns | toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0 |
12 | Volcano Plot | toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
General AnnData Information | General AnnData Information | n/a |
|
anndata_out | anndata_out | n/a |
|
genes_metadata | genes_metadata | n/a |
|
samples_metadata | samples_metadata | n/a |
|
count_matrix | count_matrix | n/a |
|
plot_output | plot_output | n/a |
|
filter_by_expr_plot | filter_by_expr_plot | n/a |
|
Samples Metadata | Samples Metadata | n/a |
|
Contrast File | Contrast File | n/a |
|
outTables | outTables | n/a |
|
output | output | n/a |
|
DEG Table | DEG Table | n/a |
|
Volcano Plot DEG | Volcano Plot DEG | n/a |
|
Version History

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Views: 39 Downloads: 3 Runs: 0
Created: 2nd Jun 2025 at 10:58


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