iterative-peak-merging
CommunityConsolidate ATAC-seq peaks into a robust 501bp set
Authortony-zhelonkin
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Iterative overlap peak merging resolves the challenge of consolidating per-sample ATAC-seq peak sets into a single, consistent reference by avoiding daisy-chaining and preserving cell-type-specific peaks through a fixed-width peak framework.
Core Features & Use Cases
- Fixed-width peak construction: Generates 501bp peaks centered on summits for uniform downstream analysis.
- Tiered merging: Performs within-group then across-group merging to preserve reproducibility and capture group-specific accessibility.
- Compatibility: Designed to work with MACS2 summit files, reproducibility rules, and downstream tools in ATAC-seq pipelines (e.g., ArchR, chromVAR, DESeq2).
Quick Start
Run the createIterativeOverlapPeakSet.R script with your MACS2 summit files and metadata to generate the final merged peak set
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: iterative-peak-merging Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#iterative-peak-merging Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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