Screen Ccre Tools

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

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

Available Tools

SCREEN_get_cCRE_by_accession (Type: ScreenCcreTool)

Look up one or more candidate cis-Regulatory Elements (cCREs) in the ENCODE SCREEN registry by SC…

SCREEN_get_cCRE_by_accession tool specification

Tool Information:

  • Name: SCREEN_get_cCRE_by_accession

  • Type: ScreenCcreTool

  • Description: Look up one or more candidate cis-Regulatory Elements (cCREs) in the ENCODE SCREEN registry by SCREEN accession (e.g. ‘EH38E2666166’). Returns the element classification (PLS=promoter-like, pELS/dELS=proximal/distal enhancer-like, CTCF-only, DNase-H3K4me3), its genomic coordinates, the underlying representative DNase hypersensitive site (rDHS) accession, and whether it is CTCF-bound. Default assembly is GRCh38. Accessions are obtained from SCREEN_search_cCREs_by_region. Reliability note: queries the SCREEN staging GraphQL endpoint (the production host is rate-limited/unavailable for the API), so it may be intermittently unstable.

Parameters:

  • accession ([‘string’, ‘array’]) (required) A single SCREEN cCRE accession string, or a list of accession strings (e.g. ‘EH38E2666166’).

  • assembly (string) (optional) Genome assembly: ‘GRCh38’ (human, default) or ‘mm10’ (mouse).

Example Usage:

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

SCREEN_search_cCREs_by_region (Type: ScreenCcreTool)

Query the ENCODE SCREEN Registry of candidate cis-Regulatory Elements (cCREs) overlapping a genom…

SCREEN_search_cCREs_by_region tool specification

Tool Information:

  • Name: SCREEN_search_cCREs_by_region

  • Type: ScreenCcreTool

  • Description: Query the ENCODE SCREEN Registry of candidate cis-Regulatory Elements (cCREs) overlapping a genomic region. Returns experimentally grounded regulatory annotations: each cCRE’s element type (PLS=promoter-like, pELS/dELS=proximal/distal enhancer-like, CTCF-only, DNase-H3K4me3) and its DNase, H3K4me3 (promoter), H3K27ac (enhancer), and CTCF z-scores aggregated across ENCODE biosamples. This is the curated regulatory-genomics counterpart to sequence-to-track deep-learning predictors (Enformer/Borzoi), which have no public REST endpoint. Use it to find which regulatory elements lie in a locus and how strong their chromatin signals are. Coordinates are genome-build specific; default assembly is GRCh38. Reliability note: queries the SCREEN staging GraphQL endpoint (the production host is rate-limited/unavailable for the API), so it may be intermittently unstable.

Parameters:

  • chrom (string) (required) Chromosome, e.g. ‘chr8’ or ‘8’ (the ‘chr’ prefix is added automatically).

  • start (integer) (required) Region start coordinate (1-based).

  • end (integer) (required) Region end coordinate (1-based, must be greater than start).

  • assembly (string) (optional) Genome assembly: ‘GRCh38’ (human, default) or ‘mm10’ (mouse).

  • element_type ([‘string’, ‘null’]) (optional) Optional element-type hint to bias results toward a class: ‘PLS’, ‘pELS’, ‘dELS’, ‘CTCF-only’, or ‘DNase-H3K4me3’. Omit (null) to return all overlapping cCREs.

Example Usage:

query = {
    "name": "SCREEN_search_cCREs_by_region",
    "arguments": {
        "chrom": "example_value",
        "start": 10,
        "end": 10
    }
}
result = tu.run(query)