bio-workflows-hic-pipeline

Name: bio-workflows-hic-pipeline
Availability: InStock
Author: stellaromics

Automate Hi-C data analysis from raw reads to genome features.

Updated Aug 23, 2026

Search Tags:#pipelining #loops #hic #compartments #cooler #tads

Ready to run

npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-workflows-hic-pipeline

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bio-workflows-hic-pipeline
Source: https://github.com/stellaromics/fast-bioinfo/tree/main/.claude/agents/spatial-analysis/skills/bio-workflows-hic-pipeline
Command: npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-workflows-hic-pipeline

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This workflow automates the end-to-end Hi-C analysis from raw contact data to higher-order genome features, consolidating steps and guidance into a single reproducible process.

Core Features & Use Cases

End-to-end pipeline: alignment, matrix generation, ICE balancing, compartment analysis, TAD detection, loop calling, and visualization.
Compatible with cooler matrices and cooltools for downstream analysis and visualization, with example workflows and code snippets.
Use Case: process Hi-C data to identify A/B compartments, TAD boundaries, and chromatin loops across resolutions.

Quick Start

Provide Hi-C reads and a reference, then run the complete Hi-C workflow to obtain compartments, TADs, and loops.

Frequently Asked Questions about bio-workflows-hic-pipeline

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

FAQPage Schema

How do I process raw Hi-C reads to identify A/B compartments and TAD boundaries?▼

To process Hi-C reads into A/B compartments and TAD boundaries, you need an end-to-end workflow handling alignment, matrix generation, and ICE balancing. This pipeline automates those steps to generate balanced matrices and detect higher-order genome features across resolutions.

What is the best way to call chromatin loops from Hi-C contact matrices using cooler?▼

Calling chromatin loops from cooler matrices requires applying cooltools for downstream analysis and visualization. This workflow provides compatible code snippets and example workflows to automate loop calling across multiple resolutions from balanced contact matrices.

Can I use cooltools with cooler matrices for Hi-C compartment analysis across different resolutions?▼

Yes, cooltools works with cooler matrices for Hi-C compartment analysis. This workflow is compatible with both tools, enabling you to identify A/B compartments, TAD boundaries, and chromatin loops across various resolutions from the generated balanced matrices.

Do I need to perform ICE balancing before detecting TADs and loops in Hi-C data?▼

ICE balancing is required before detecting TADs and loops in Hi-C data to correct raw contact matrices. This pipeline includes the ICE balancing step as part of the end-to-end process, ensuring matrix quality before downstream compartment and TAD analysis.

How does an end-to-end Hi-C pipeline generate balanced matrices from raw contact data?▼

An end-to-end Hi-C pipeline generates balanced matrices by automating alignment, contact matrix generation, and ICE balancing from raw reads. This workflow consolidates these preprocessing steps into a single reproducible process before identifying compartments and loops.

What dependencies are needed to run a complete Hi-C workflow for compartments and loops?▼

Running a complete Hi-C workflow requires cooler and cooltools for matrix handling and downstream analysis. This pipeline includes specific version requirements and tool dependencies aligned with these frameworks for preprocessing and feature detection.