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.

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)

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.

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.

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.

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)

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.

Parameters:

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

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

Example Usage:

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