Enrichr Ext Tools#

Configuration File: enrichr_ext_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the enrichr_ext_tools.json configuration file.

Available Tools#

Enrichr_enrich (Type: EnrichrExtTool)#

Perform gene set enrichment analysis using Enrichr. Submit a list of genes and get enriched terms…

Enrichr_enrich tool specification

Tool Information:

  • Name: Enrichr_enrich

  • Type: EnrichrExtTool

  • Description: Perform gene set enrichment analysis using Enrichr. Submit a list of genes and get enriched terms from a specific library. Returns ranked terms with p-values, z-scores, combined scores, and overlapping genes. No authentication required. Set species to query the fly, worm, yeast, or fish Enrichr instances; libraries and gene symbols differ per organism.

Parameters:

  • operation (string) (optional) Operation type (fixed: enrich)

  • gene_list (array) (required) List of gene symbols (e.g., [‘TP53’, ‘BRCA1’, ‘EGFR’]). Minimum 1 gene.

  • library (string) (optional) Enrichr library name (default: GO_Biological_Process_2023). Common: GO_Biological_Process_2023, KEGG_2021_Human, Reactome_2022, WikiPathways_2024_Human, MSigDB_Hallmark_2020

  • top_n (integer) (optional) Number of top enriched terms to return (default: 10)

  • species ([‘string’, ‘null’]) (optional) Organism instance to query: ‘human’ (default), ‘mouse’, ‘fly’ (FlyEnrichr), ‘worm’ (WormEnrichr), ‘yeast’ (YeastEnrichr), or ‘fish’ (FishEnrichr). Gene set libraries differ per organism, and gene symbols must match that organism’s nomenclature.

Example Usage:

query = {
    "name": "Enrichr_enrich",
    "arguments": {
        "gene_list": ["item1", "item2"]
    }
}
result = tu.run(query)

Enrichr_gene_to_genesets (Type: EnrichrExtTool)#

Reverse gene-to-geneset membership lookup. Given ONE gene symbol, return every Enrichr term/gene-…

Enrichr_gene_to_genesets tool specification

Tool Information:

  • Name: Enrichr_gene_to_genesets

  • Type: EnrichrExtTool

  • Description: Reverse gene-to-geneset membership lookup. Given ONE gene symbol, return every Enrichr term/gene-set (by name) that contains it, broken down across all ~243 Enrichr libraries (KEGG/Reactome/WikiPathways pathways, GO terms, transcription-factor target sets, disease/drug signatures, GeneSigDB publication tables, etc.). This is the inverse of forward enrichment (which takes a gene list): use it to ask ‘what known programs/signatures is gene X a member of?’ without running an enrichment. Returns a dict of library_name -> list of term/gene-set names containing the gene. Set include_metadata=true to also return per-library category/description metadata. No authentication required. Set species to query the fly, worm, yeast, or fish Enrichr instances; libraries and gene symbols differ per organism.

Parameters:

  • operation (string) (optional) Operation type (fixed: gene_to_genesets)

  • gene (string) (required) A single official HGNC gene symbol (e.g., ‘STAT3’, ‘BRCA1’). Case-sensitive; use the canonical symbol.

  • include_metadata (boolean) (optional) If true, also return library category/description metadata (Enrichr setup=true). Default: false.

  • max_terms_per_library (integer) (optional) Optional cap on the number of term names returned per library (0 = no cap, return all). Default: 0.

  • species ([‘string’, ‘null’]) (optional) Organism instance to query: ‘human’ (default), ‘mouse’, ‘fly’ (FlyEnrichr), ‘worm’ (WormEnrichr), ‘yeast’ (YeastEnrichr), or ‘fish’ (FishEnrichr). Gene set libraries differ per organism, and gene symbols must match that organism’s nomenclature.

Example Usage:

query = {
    "name": "Enrichr_gene_to_genesets",
    "arguments": {
        "gene": "example_value"
    }
}
result = tu.run(query)

Enrichr_get_top_enriched (Type: EnrichrExtTool)#

Get top enriched terms across multiple libraries simultaneously. Submit a gene list and get the m…

Enrichr_get_top_enriched tool specification

Tool Information:

  • Name: Enrichr_get_top_enriched

  • Type: EnrichrExtTool

  • Description: Get top enriched terms across multiple libraries simultaneously. Submit a gene list and get the most significant pathways, processes, and functions from GO, KEGG, Reactome, and WikiPathways in one call. Ideal for quick functional annotation overview. Set species to query the fly, worm, yeast, or fish Enrichr instances; libraries and gene symbols differ per organism.

Parameters:

  • operation (string) (optional) Operation type (fixed: get_top_enriched)

  • gene_list (array) (required) List of gene symbols (e.g., [‘TP53’, ‘BRCA1’, ‘EGFR’])

  • libraries (array) (optional) Libraries to query (default: GO_Biological_Process_2023, KEGG_2021_Human, Reactome_2022, WikiPathways_2024_Human)

  • top_n (integer) (optional) Number of top terms per library (default: 5)

  • species ([‘string’, ‘null’]) (optional) Organism instance to query: ‘human’ (default), ‘mouse’, ‘fly’ (FlyEnrichr), ‘worm’ (WormEnrichr), ‘yeast’ (YeastEnrichr), or ‘fish’ (FishEnrichr). Gene set libraries differ per organism, and gene symbols must match that organism’s nomenclature.

Example Usage:

query = {
    "name": "Enrichr_get_top_enriched",
    "arguments": {
        "gene_list": ["item1", "item2"]
    }
}
result = tu.run(query)

Enrichr_list_libraries (Type: EnrichrExtTool)#

List all available Enrichr gene set libraries with statistics. Enrichr has 225+ libraries coverin…

Enrichr_list_libraries tool specification

Tool Information:

  • Name: Enrichr_list_libraries

  • Type: EnrichrExtTool

  • Description: List all available Enrichr gene set libraries with statistics. Enrichr has 225+ libraries covering pathways (KEGG, Reactome, WikiPathways), gene ontology (GO), transcription factors, diseases, drugs, and more. Optionally filter by keyword in library name. Set species to query the fly, worm, yeast, or fish Enrichr instances; libraries and gene symbols differ per organism.

Parameters:

  • operation (string) (optional) Operation type (fixed: list_libraries)

  • category (string) (optional) Optional keyword to filter libraries (e.g., ‘GO’, ‘KEGG’, ‘Reactome’, ‘disease’, ‘drug’)

  • species ([‘string’, ‘null’]) (optional) Organism instance to query: ‘human’ (default), ‘mouse’, ‘fly’ (FlyEnrichr), ‘worm’ (WormEnrichr), ‘yeast’ (YeastEnrichr), or ‘fish’ (FishEnrichr). Gene set libraries differ per organism, and gene symbols must match that organism’s nomenclature.

Example Usage:

query = {
    "name": "Enrichr_list_libraries",
    "arguments": {
    }
}
result = tu.run(query)