atac-chipseq-downstream-analysis
CommunityEnd-to-end ATAC/ChIP downstream peak analysis.
AuthorMDhewei
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Analyzes ATAC-seq or ChIP-seq peak sets to annotate genomic context, assess quality, and compare conditions, delivering ready-to-publish results.
Core Features & Use Cases
- Annotates peaks to genomic features (promoter, exonic, intronic, intergenic, downstream) and reports nearest genes.
- Generates QC metrics and plots (peak width distribution, score distribution, TSS enrichment).
- Performs differential/overlap analyses across multiple conditions and outputs summary statistics and Venn/heatmaps.
- Suitable for MACS2/SEACR-like peak files in narrowPeak, broadPeak, or BED formats, with genome-aware annotation.
Quick Start
Run the downstream analysis by executing the Python script on your peak file and saving results to your chosen output directory.
Dependency Matrix
Required Modules
pandasnumpymatplotlibrequests
Components
scripts
💻 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: atac-chipseq-downstream-analysis Download link: https://github.com/MDhewei/bioinfor-claw/archive/main.zip#atac-chipseq-downstream-analysis Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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