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remap-database

Query ReMap 2022 ChIP-seq binding peaks via REST API and BED downloads.

298|27|Updated Feb 18, 2026
Search Tags:#bioinformatics#genomics#chip-seq#peak calling#transcription factors#regulatory elements
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill remap-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: remap-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/remap-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill remap-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, matplotlib, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill allows you to query the ReMap 2022 database to find transcription factor (TF) binding sites from ChIP-seq experiments, enabling detailed analysis of gene regulation.

Core Features & Use Cases

  • Genomic Region Overlap: Find all TF binding peaks that overlap a specific genomic region.
  • Gene-Centric Queries: Retrieve TF peaks located near a gene's transcription start site (TSS).
  • TF-Specific Peak Retrieval: Get all binding peaks for a particular TF across different cell types.
  • Biotype Filtering: Filter peaks based on their regulatory annotation (e.g., promoter, enhancer).
  • Data Download: Download peak data in BED format for offline analysis.
  • Use Case: Identify which TFs bind near a specific gene of interest to understand its regulatory network, or find all TFs binding at a GWAS locus to prioritize candidate genes.

Quick Start

Use the remap-database skill to find all TF binding peaks overlapping the genomic region chr17:7670000-7690000 in the hg38 assembly.

Frequently Asked Questions about remap-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find transcription factor ChIP-seq peaks overlapping a specific genomic region?▼

To find transcription factor ChIP-seq peaks, query the ReMap 2022 database via its REST API using genomic coordinates and assemblies like hg38 or mm10 to retrieve overlapping TF binding sites.

Can I retrieve all binding peaks for a specific transcription factor near a gene's TSS?▼

Yes, you can retrieve TF binding peaks near a gene's transcription start site or for a specific transcription factor across cell types by querying the ReMap 2022 database.

What is the best way to download ChIP-seq peak data for offline regulatory analysis?▼

The best way to download ChIP-seq peak data for offline regulatory analysis is querying the ReMap 2022 database to download peak data directly in BED file format.

Does the ReMap database query tool support filtering peaks by regulatory biotype?▼

Yes, the ReMap database query tool supports biotype filtering, allowing you to filter ChIP-seq peaks based on regulatory annotations like promoter or enhancer regions.

Do I need Python pandas and requests to query TF binding sites from ReMap?▼

Yes, you need Python packages like requests and pandas to query the ReMap 2022 database for TF binding sites, as they handle REST API data retrieval and subsequent data manipulation.

How do I identify which transcription factors bind at a GWAS locus to prioritize candidate genes?▼

To identify which transcription factors bind at a GWAS locus, query the ReMap 2022 database with the locus genomic region to find all overlapping TF binding peaks and prioritize candidate genes.

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