Gene set enrichment analysis (GSEA)

Typing name : TASK.gws_omix.GSEAEnrichmentGMT

Brick : gws_omix

Pre-ranked GSEA using a signed ranking statistic (stat column) and a single GMT gene set file.

Base class

Input

DE/Full results (Table or CSV file)

2d excel like table

Table

File

Gene sets (GMT file)

File

Output

GSEA results (table + plots + grid)

A set of resources

Resource set

GSEA enrichment plots (PNG)

A set of resources

Resource set

Configuration

genes_colname

Optional

Column containing gene identifiers. Default: 'gene'.

Type : string

Default value : gene

stat_colname

Optional

Column containing the signed ranking statistic. Default: 'stat'.

Type : string

Default value : stat

min_size

Optional

Minimum gene set size after overlap.

Type : int

Default value : 15

max_size

Optional

Maximum gene set size.

Type : int

Default value : 500

nperm

Optional

Number of permutations.

Type : int

Default value : 1000

processes

Optional

Parallel processes used by gseapy.

Type : int

Default value : 4

n_enrichplots

Optional

Number of enrichment plots (PNG) to generate.

Type : int

Default value : 10

grid_genes_per_page

Optional

Genes per page in the interactive grid.

Type : int

Default value : 25

grid_sets_per_page

Optional

Gene sets per page in the interactive grid.

Type : int

Default value : 20

Input

Output

Configuration

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