differential-tad-analysis
This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It compares Hi-C contact matrices between two conditions based on existing TAD definitions to identify significantly altered chromatin domains.
npx skills add majiayu000/claude-skill-registry --skill 20-toolbased-differential-tad-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Differential TAD Analysis with HiCExplorer ## Overview This skill identifies differentially interacting TADs between two experimental conditions using HiCExplorer. It assumes that TADs have already been called for the target condition. Steps: 1. Normalize Hi-C matrices between conditions. Modify the chromosome name in the .mcool file if not started with "chr". 2. Prepare TAD domains (BED file) of the target sample. Make sure the consistence of the chromosame names between .mcool files and BED files. Modify the chromosome name in the BED file if not consistent with the .mcool file. 3. Perform differential TAD analysis. 4. Visualize the Hi-C contact maps for the target and control conditions. 5. Visualize and interpret significant TAD changes. ## When to Use This Skill Use this skill when: - You have already called TADs for one condition. - You want to detect TADs that show significant interaction changes between two Hi-C matrices. - You are comparing chromatin architecture between experimental conditions (e.g., treated vs. control, different cell types). --- ## Inputs & Outputs ### Inputs - **File format:** Two files in .mcool, .cool, or .hic format for the target and control cond
- Overview
- When to Use This Skill
- Inputs & Outputs
- Inputs
- Outputs
- Allowed Tools
- Decision Tree
- Step 0 — Gather Required Information from the User
- Step 1: Initialize Project
- Step 2. Normalize Hi-C matrices
- Step 3. Prepare TAD domains for the target condition
- Step 4. Run differential TAD analysis
- Step 5. Visualize the Hi-C matrices
- Step 6. Overlay differential TADs
normalize/ TADs/ diff_TADs/ plots/
What does the differential-tad-analysis skill do?
This skill performs differential topologically associating domain (TAD) analysis using HiCExplorer's hicDifferentialTAD tool. It compares Hi-C contact matrices between two conditions based on existing TAD definitions to identify significantly altered chromatin domains.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 20-toolbased-differential-tad-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.