Chrombpnet Tools

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

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

Available Tools

run_chrombpnet_predict (Type: RemoteTool)

Predict chromatin accessibility (ATAC/DNase) from a DNA sequence with a trained ChromBPNet model …

run_chrombpnet_predict tool specification

Tool Information:

  • Name: run_chrombpnet_predict

  • Type: RemoteTool

  • Description: Predict chromatin accessibility (ATAC/DNase) from a DNA sequence with a trained ChromBPNet model (Pampari 2025) — the bias-corrected, base-resolution successor to DeepSEA/Basset. The sequence is center-cropped/N-padded to 2,114 bp; returns predicted log total counts (coverage magnitude), total counts, and the base-resolution accessibility profile (1,000 bp). Requires a server-side cell-type-specific model_path (.h5).

Parameters:

  • model_path (string) (required) Server-accessible path to a trained ChromBPNet Keras model (.h5), cell-type-specific.

  • sequence (string) (required) DNA sequence (A/C/G/T/N); cropped/padded to 2,114 bp around its center.

  • return_profile (boolean) (optional) Include the full 1,000-bp profile array in the response (default false; summary stats always returned).

Example Usage:

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

run_chrombpnet_variant_effect (Type: RemoteTool)

Score a non-coding regulatory variant with ChromBPNet (Pampari 2025): predict accessibility for t…

run_chrombpnet_variant_effect tool specification

Tool Information:

  • Name: run_chrombpnet_variant_effect

  • Type: RemoteTool

  • Description: Score a non-coding regulatory variant with ChromBPNet (Pampari 2025): predict accessibility for the reference and alternate sequences (each 2,114 bp, variant at center) and return the count log2 fold-change (alt vs ref accessibility magnitude) and the profile Jensen-Shannon divergence (change in base-resolution accessibility shape) — the canonical ChromBPNet variant-effect scores for interpreting non-coding GWAS/eQTL variants. Requires a server-side cell-type-specific model_path (.h5).

Parameters:

  • model_path (string) (required) Server-accessible path to a trained ChromBPNet Keras model (.h5), cell-type-specific.

  • ref_sequence (string) (required) Reference DNA sequence centered on the variant (cropped/padded to 2,114 bp).

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

Example Usage:

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