Eqtl Tools

Configuration File: eqtl_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

eQTL_get_associations (Type: BaseRESTTool)

Get eQTL associations (variant-gene expression correlations) from a specific dataset in the EBI e…

eQTL_get_associations tool specification

Tool Information:

  • Name: eQTL_get_associations

  • Type: BaseRESTTool

  • Description: Get eQTL associations (variant-gene expression correlations) from a specific dataset in the EBI eQTL Catalogue. Returns statistical associations between genetic variants and molecular traits (gene/exon/transcript expression or splicing). Each result includes beta effect size, p-value, allele frequency, and variant coordinates. Use eQTL_list_datasets first to find available dataset IDs. Can filter by gene_id (Ensembl gene ID) or variant (chr_pos_ref_alt format).

Parameters:

  • dataset_id (string) (required) Dataset identifier from eQTL_list_datasets (e.g., ‘QTD000001’, ‘QTD000584’)

  • size (integer) (optional) Number of associations to return (default 20)

  • gene_id ([‘string’, ‘null’]) (optional) Filter by Ensembl gene ID (e.g., ‘ENSG00000141510’ for TP53). Returns all eQTLs affecting this gene.

  • variant ([‘string’, ‘null’]) (optional) Filter by variant in chr_pos_ref_alt format (e.g., ‘chr1_791100_G_GGGA’). Returns all genes affected by this variant.

  • molecular_trait_id ([‘string’, ‘null’]) (optional) Filter by molecular trait ID (usually same as gene_id for ‘ge’ datasets)

Example Usage:

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

eQTL_list_datasets (Type: BaseRESTTool)

List available eQTL (expression Quantitative Trait Loci) datasets from the EBI eQTL Catalogue. Ea…

eQTL_list_datasets tool specification

Tool Information:

  • Name: eQTL_list_datasets

  • Type: BaseRESTTool

  • Description: List available eQTL (expression Quantitative Trait Loci) datasets from the EBI eQTL Catalogue. Each dataset represents a study-tissue-quantification combination with measured genetic associations to gene expression. Returns dataset IDs, study labels, tissue types, sample sizes, and quantification methods (ge=gene expression, exon, tx=transcript, txrev=transcript ratio, leafcutter=splicing). Use dataset IDs with eQTL_get_associations for specific variant-gene associations.

Parameters:

  • size (integer) (optional) Number of datasets to return (default 20)

  • quant_method ([‘string’, ‘null’]) (optional) Filter by quantification method: ‘ge’ (gene expression), ‘exon’, ‘tx’ (transcript), ‘txrev’ (transcript ratio), ‘leafcutter’ (splicing)

  • tissue_id ([‘string’, ‘null’]) (optional) Filter by tissue ontology ID (e.g., ‘CL_0000235’ for macrophage, ‘UBERON_0002107’ for liver)

Example Usage:

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