Enformer Tools

Configuration File: remote_tools/enformer_tools.json Tool Type: Remote Tools Count: 2

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

Available Tools

run_enformer_predict (Type: RemoteTool)

Predict genomic track activity (CAGE/DNase/ATAC/ChIP; 5,313 human or 1,643 mouse tracks) directly…

run_enformer_predict tool specification

Tool Information:

  • Name: run_enformer_predict

  • Type: RemoteTool

  • Description: Predict genomic track activity (CAGE/DNase/ATAC/ChIP; 5,313 human or 1,643 mouse tracks) directly from a DNA sequence using Enformer (Avsec 2021), which integrates long-range regulatory interactions. The sequence is center-cropped / N-padded to 196,608 bp. Returns the central-bin value for requested tracks, or the top-signal tracks.

Parameters:

  • sequence (string) (required) DNA sequence (A/C/G/T/N). Cropped/padded to 196,608 bp around its center.

  • organism (string) (optional) ‘human’ (5,313 tracks, default) or ‘mouse’ (1,643 tracks).

  • track_indices (array) (optional) Track indices to report (optional). If omitted, the top-signal tracks are returned.

  • top_n (integer) (optional) When track_indices is omitted, how many top tracks to return (default 20).

Example Usage:

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

run_enformer_variant_effect (Type: RemoteTool)

Score a regulatory variant with Enformer: predicts tracks for the reference and alternate sequenc…

run_enformer_variant_effect tool specification

Tool Information:

  • Name: run_enformer_variant_effect

  • Type: RemoteTool

  • Description: Score a regulatory variant with Enformer: predicts tracks for the reference and alternate sequences (each 196,608 bp, variant at center) and returns the central-bin delta (alt - ref) per track — the canonical sequence-model variant-effect-on-expression score.

Parameters:

  • ref_sequence (string) (required) Reference DNA sequence centered on the variant (cropped/padded to 196,608 bp).

  • alt_sequence (string) (required) Alternate DNA sequence (same length/centering as ref).

  • organism (string) (optional) ‘human’ (default) or ‘mouse’.

  • track_indices (array) (optional) Track indices to report (optional; default = top |delta| tracks).

  • top_n (integer) (optional) When track_indices omitted, number of top |delta| tracks to return (default 20).

Example Usage:

query = {
    "name": "run_enformer_variant_effect",
    "arguments": {
        "ref_sequence": "example_value",
        "alt_sequence": "example_value"
    }
}
result = tu.run(query)