delnx.tl.gsea¶
- delnx.tl.gsea(genes, background=None, gene_sets=None, collection='all', url=None, filepath=None, geneset_key='geneset', genesymbol_key='genesymbol', method='enrichr', return_object=False, min_genes=5, max_genes=500)[source]¶
Run enrichment analysis for a single gene list using Enrichr.
- Parameters:
background (
Sequence[str] |None(default:None)) – Background gene list to use for enrichment analysis. If None, uses all genes in the gene sets.gene_sets (
dict[str,list[str]] |None(default:None)) – Pre-loaded gene sets as a dictionary where keys are gene set names and values are lists of gene symbols. If None, will load gene sets based on the provided collection, URL, or filepath.collection (
str(default:'all')) – Name of the collection to load gene sets from. Default is “all”.url (
str|None(default:None)) – URL to load the GMT file from. If None, uses the default collection.filepath (
str|None(default:None)) – Local file path to load the GMT file from. If None, uses the default collection.geneset_key (
str(default:'geneset')) – Column name for the gene set name in the output dictionary. Default is “geneset”.genesymbol_key (
str(default:'genesymbol')) – Column name for the gene symbol in the output dictionary. Default is “genesymbol”.method (
str(default:'enrichr')) – Method to use for enrichment analysis. Currently only “enrichr” is supported.return_object (
bool(default:False)) – If True, returns the gseapy Enrichr object. If False, returns a pandas DataFrame with results.min_genes (
int(default:5)) – Minimum number of genes in a gene set to include in the analysis. Default is 5.max_genes (
int(default:500)) – Maximum number of genes in a gene set to include in the analysis. Default is 500.
- Return type:
DataFrame|Any