Remap Tools

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

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

Available Tools

ReMap_get_peaks_in_region (Type: ReMapRESTTool)

Retrieve all ChIP-seq transcriptional-regulator (TR) binding peaks from the ReMap catalog that ov…

ReMap_get_peaks_in_region tool specification

Tool Information:

  • Name: ReMap_get_peaks_in_region

  • Type: ReMapRESTTool

  • Description: Retrieve all ChIP-seq transcriptional-regulator (TR) binding peaks from the ReMap catalog that overlap a genomic interval. Give a region (chrom:start-end) and get back every overlapping peak with its genomic coordinates plus the bound TF, the cell line/tissue (biotype), the source experiment accession (GEO/ENCODE), and any treatments. This is the defining ReMap capability (region in -> all overlapping TR peaks out). Use for: enumerating which transcription factors bind a locus, finding regulatory occupancy of a promoter/enhancer interval, listing TFs near a variant. Keep regions modest (<=1 Mb) - large intervals can return tens of thousands of peaks.

Parameters:

  • operation (string) (optional) Operation selector. Must be ‘get_peaks_in_region’.

  • region (string) (required) Genomic interval as chrom:start-end (e.g. ‘chr1:1000000-1100000’). Commas in coordinates are tolerated.

  • assembly (string) (optional) Genome assembly.

  • version (string) (optional) ReMap catalog release year.

  • datatype (string) (optional) Peak datatype: ‘all’ for the non-redundant merged peak set across all TFs.

  • limit ([‘integer’, ‘null’]) (optional) Optional cap on the number of peaks returned (peak_count still reports the true total). Omit to return all overlapping peaks.

Example Usage:

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

ReMap_get_transcription_factor_binding (Type: ReMapRESTTool)

Get transcription factor binding sites from ReMap database for specific genes and cell types

ReMap_get_transcription_factor_binding tool specification

Tool Information:

  • Name: ReMap_get_transcription_factor_binding

  • Type: ReMapRESTTool

  • Description: Get transcription factor binding sites from ReMap database for specific genes and cell types

Parameters:

  • gene_name (string) (required) Gene symbol (e.g., BRCA1, TP53, MYC)

  • cell_type (string) (optional) Cell type (e.g., HepG2, K562, MCF-7)

  • limit (integer) (optional) Number of results to return

Example Usage:

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