omicverse.utils.geneset_prepare

omicverse.utils.geneset_prepare#

omicverse.utils.geneset_prepare(geneset_path, organism='Human', auto_download=True)[source]#

Load and prepare gene sets from GMT/TXT files for enrichment analysis.

Parameters:

  • geneset_path (str) – Path to geneset file.

  • organism (str) – Organism name used for gene-symbol case normalization.

  • auto_download (bool, default=True) – If the path does not exist AND its basename matches a known omicverse pathway resource (GO_*_2021, Reactome_2022, WikiPathway_2021_Human, WikiPathways_2019_Mouse), call download_pathway_database() to fetch all standard genesets into ./genesets/ and retry. Disable to fail fast offline.

Returns:

Dictionary where keys are pathway names and values are gene symbol lists.

Return type:

dict

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