Pseudobulk with decoupler and edgeR tutorial workflow
2.0

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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

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

SEEK ID: https://workflowhub.eu/workflows/1556?version=1

ID	Name	Description	Type
ncm_pdcs_subset.h5ad	ncm_pdcs_subset.h5ad	n/a	File

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

ID	Name	Description	Type
General AnnData Information	General AnnData Information	n/a	File
anndata_out	anndata_out	n/a	File
genes_metadata	genes_metadata	n/a	File
samples_metadata	samples_metadata	n/a	File
count_matrix	count_matrix	n/a	File
plot_output	plot_output	n/a	File
filter_by_expr_plot	filter_by_expr_plot	n/a	File
Samples Metadata	Samples Metadata	n/a	File
Contrast File	Contrast File	n/a	File
outTables	outTables	n/a	File
output	output	n/a	File
DEG Table	DEG Table	n/a	File
Volcano Plot DEG	Volcano Plot DEG	n/a	File