Screen Tools#

Configuration File: screen_tools.json Tool Type: Local Tools Count: 1

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

Available Tools#

SCREEN_get_regulatory_elements (Type: SCREENRESTTool)#

Resolve an official human gene symbol to its GRCh38 coordinates with Ensembl, then return genuine…

SCREEN_get_regulatory_elements tool specification

Tool Information:

  • Name: SCREEN_get_regulatory_elements

  • Type: SCREENRESTTool

  • Description: Resolve an official human gene symbol to its GRCh38 coordinates with Ensembl, then return genuine ENCODE SCREEN cCREs overlapping the gene interval plus a configurable flank (default 10 kb). Filters real cCRE classes: enhancer=pELS/dELS, promoter=PLS, insulator=CTCF-only. Results use exact client-side offset pagination. This reports genomic-window overlap only and explicitly does not claim the cCRE functionally regulates the gene.

Parameters:

  • gene_name (string) (optional) Gene symbol to search for regulatory elements (e.g., BRCA1, TP53). Alias: ‘query’.

  • query (string) (optional) Gene symbol to search for regulatory elements (alias for gene_name).

  • element_type (string) (optional) cCRE class filter: enhancer (pELS+dELS), promoter (PLS), insulator (CTCF-only), all, or a raw SCREEN class (PLS, pELS, dELS, CTCF-only, DNase-H3K4me3).

  • limit (integer) (optional) Page size for filtered cCREs.

  • offset (integer) (optional) Zero-based filtered cCRE offset. Continue with metadata.next_offset while metadata.has_more is true.

  • flank_bp (integer) (optional) Base pairs added on both sides of the Ensembl gene interval (default 10000).

  • assembly (string) (optional) Genome assembly. This gene-symbol resolver currently supports human GRCh38 only.

Example Usage:

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