MengQiuchen/cPeaks: v1.0.0

Overview

This is the first stable release of cPeaks, a scalable and unified pipeline for generating consensus peaks from large-scale bulk ATAC-seq and single-cell ATAC-seq datasets. This version corresponds to the codebase used in the associated manuscript.

Included functionalities

• End-to-end pipeline for processing >1700 bulk ATAC-seq and >230 scATAC-seq datasets
• Construction of consensus peak references across tissues and cell types
• Quality control and filtering modules
• Peak merging and reproducibility assessment
• Tissue-level and cell-type-level peak integration
• Utility functions for peak annotation, comparison, and downstream analysis

Main features

• Consensus peak construction using multi-sample merging and reproducibility scoring
• Scale-optimized implementation, suitable for large public datasets
• Cross-modality integration between bulk and single-cell ATAC-seq
• Reproducibility-focused design with deterministic outputs
• Fully open-source implementation in R/Python (depending on repository structure)

Repository contents

• src/ — Core pipeline code
• scripts/ — Helper scripts for batch processing
• notebooks/ — Example analyses and visualization workflows
• data/ — Example input files (if included)
• docs/ — Documentation and usage instructions
• README.md — Quick start guide

Version information

This release captures the exact version of the code used in the manuscript to ensure long-term reproducibility.
A DOI will be assigned after archiving this release on Zenodo/Figshare/Code Ocean.

Citation

If you use this release in your work, please cite it as:

Meng Q., et al. A generic reference defined by consensus peaks for scATAC-seq data analysis. GitHub repository, version v1.0.0 (2025). DOI: to be added